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Natural and anthropogenic forces shape the population genetics and recent evolutionary history of eastern United States bay scallops (Argopecten irradians).

ABSTRACT Bay scallops (Argopecten irradians Lamarck) are ecologically important in U.S. Atlantic waters off northeastern states and in the Florida Gulf of Mexico, and have been intensely harvested from both of those regions for decades. However, a detailed study comparing their basic population genetic structures using more than a single type of genetic marker has not been conducted. Through such a study, key phylogeographic, taxonomic, and fisheries issues can be addressed. We used variation in allozyme loci and mitochondrial DNA restriction fragment length polymorphisms to evaluate and compare the population genetic structures of bay scallops from those two regions, to propose a new interpretation for the composition of the North Carolina bay scallop population, to resolve the taxonomic quandary of Argopecten irradians taylorae, and to evaluate the apparent and potential genetic effects of the common fishery practice of hatchery-based stock enhancement on the genetic diversity and relatedness of Atlantic bay scallop populations. Atlantic Ocean (North Carolina through New York) bay scallop populations are genetically more distant from each other than are Florida Gulf bay scallop populations, except those in Florida Bay. Each Atlantic population has a different phylogeographic history, is quasi-independent, and should be treated as a genetically unique entity. The North Carolina bay scallop population is composed of Argopecten irradians irradians individuals, but also has genetic input from Argopecten irradians concentricus. Bay scallops occurring in Florida Bay constitute a population of A. i. concentricus that has diverged from other Florida Gulf populations because it has undergone repeated contractions and expansions of varying magnitude and is nearly isolated from other bay scallop populations. For the common practice of hatchery-based stock enhancement in the Atlantic, broodstock bay scallops should be taken from the same genetic population, and all stock enhancement efforts should include comprehensive genetic monitoring programs. In some cases, improving the abundance and density of bay scallop aggregations through habitat improvement may be preferable to stock enhancement for bay scallop restoration, but in other cases genetically conscientious stock supplementation or restoration may be the only alternative.

KEY WORDS: aquaculture, Argopecten irradians, Atlantic, bay scallop, evolution, fishery, Florida, Gulf of Mexico, population genetics, stock enhancement, taxonomy

INTRODUCTION

The charismatic, environmentally, and economically important bay scallop Argopecten irradians (Lamarck) inhabits shallowwater seagrass flats and algal beds in the eastern United States. In the western North Atlantic Ocean (henceforth, Atlantic), bay scallops range in the United States from Massachusetts (Clarke 1965) through North Carolina (NC) and, below a 10[degrees] latitudinal gap extending from South Carolina to east-central Florida (Heffernan et al. 1988), occur again in southeastern Florida from West Palm Beach to Biscayne Bay (Marelli et al. 1997a) (Fig. 1). In the Gulf of Mexico (henceforth, Gulf), bay scallops range from Florida Bay (FB) northward through Florida Gulf waters and westward to the Chandeleur Islands, LA (Waller 1969). Westward of a gap along the northern Gulf, they occur again from northeastern Texas southward through Mexico (Waller 1969, Wakida-Kusunoki 2009) to Colombia (Abbott 1974).

Within its range, A. irradians has been divided into several subspecies. Argopecten irradians irradians occurs in the northeastern United States, Argopecten irradians concentricus occurs in the extreme southeastern United States and eastern Gulf, and Argopecten irradians amplicostatus occurs in the western Gulf (Waller 1969) (Fig. 1A). Since the first publication of the subspecies' ranges, and despite numerous taxonomic studies that evaluated variation in morphometrics, meristics, and multiple types of genes, the locations of sympatry between A. i. irradians and A. i. concentricus in the Atlantic, the taxonomic identity of A. irradians in NC, and the existence of a fourth subspecies (Argopecten irradians taylorae (Petuch 1987)) in and around FB have remained ambiguous. The confusion is understandable, given the considerably different results that can emerge among these character sets, even when all data are taken from the same individuals (e.g., Wilbur 1995, Wilbur & Gaffney 1997).

Population genetics analyses have been woven into these principally taxonomic studies, and also into other ecological and biological studies on bay scallops, but a thorough comparison of the population genetic structure of bay scallops in the Atlantic and Gulf basins using multiple genetic markers has not yet been conducted. Understanding the population genetic structure of bay scallops is important for conservation and restoration of populations as well as for fisheries management because destructive natural and anthropogenic phenomena, coupled with intense commercial and recreational fisheries, have greatly reduced the number of dense aggregations and overall population sizes of bay scallops in both the Atlantic and Gulf during the past few decades (Peterson & Summerson 1992, Tettelbach & Wenczel 1993, Arnold et al. 1998).

[FIGURE 1 OMITTED]

Historically, A. irradians was generally abundant but patchily distributed throughout its ranges. Its high fishery value has resulted in considerable attention toward increasing the numbers of individuals and geographic expanses of existing aggregations and regenerating lost aggregations, principally through some form of hatchery-based stock enhancement (seeding depleted wild populations or suitable unpopulated areas with aquacultured young individuals or placing aquacultured mature individuals in cages in the ocean and allowing them to spawn) (Tettelbach & Wenczel 1993, Peterson et al. 1996, Arnold et al. 2005, Tettelbach 2009, Tettelbach et al. 2010). The potential genetic impacts of both the depletions and the restorations are numerous, varied, and potentially threatening to the species' ability to survive over evolutionary time (Bert et al. 2007).

Here, we address these three conundrums. We evaluate and compare the population genetic structures of bay scallops from Atlantic and Florida Gulf waters using allozyme loci and a segment of the mitochondrial DNA (mtDNA) molecule. Collectively considering the information provided by analysis of both nuclear and mitochondrial genes often provides a more complete picture of population genetic structure and the mechanisms driving that structure (Edmands et al. 1996, Rigaa et al. 1997, Shaklee & Bentzen 1998, Busack & Lawson 2008). Together, the allozyme data and mtDNA data enabled us to provide a fresh interpretation of the taxonomic composition of bay scallops in the Atlantic area of sympatry between A. i. irradians and A. i. concentricus, and to probe the phylogeographic history of the genetic differentiation between the two subspecies. We then draw upon both data sets to resolve the taxonomic ambiguity of A. i. taylorae and deepen our understanding of its population history. Last, we discuss the potential influence of the common fishery management practice of hatchery-based stock enhancement on Atlantic bay scallop population genetic structure and speculate about its impacts on Atlantic bay scallop populations. Our results are particularly relevant because they are based on genetic data collected prior to stock enhancement efforts for Florida Gulf bay scallops, and much stock enhancement has continued in Atlantic bay scallop populations since our samples were collected. Future studies using the same loci and collecting sites could reveal the effects of the numerous, subsequent stock enhancement programs on the population genetic structures of both Florida Gulf and Atlantic bay scallops.

METHODS AND MATERIALS

Field and Laboratory

From 1995 through 1998, we obtained collections of bay scallops from 15 locations in eastern U.S. nearshore waters (Table 1, Fig. 1B). Whole wild bay scallops were collected from Atlantic locations during summers and were shipped alive to us by colleagues. Scuba divers collected adult bay scallops from 12 locations in the Florida Gulf during annual surveys. All bay scallops were dissected, and samples of adductor muscle, gills, and digestive gland were excised, wrapped, immediately frozen in liquid nitrogen, and stored at -80[degrees]C.

For allozyme electrophoresis, small pieces of the three tissue types were combined and homogenized in 0.1 M Tris-EDTA, pH 7.0: the supernatant was used as the enzyme source. Horizontal starch gel electrophoresis was conducted using standard protocols (Selander et al. 1971). Eighteen loci were resolved using 4 buffer systems and were visualized using appropriate staining procedures (Table 2). All gels were scored and checked by at least two researchers. Alleles were identified by their mobility relative to that of the most common allele, which was designated as 100: the numerical code was translated into an alpha code for statistical analysis (e.g., 100 = A).

For the mtDNA analysis, purified mtDNA extracts (see Blake and Graves (1995) for methods of extraction) were amplified using primers Patinopecten yessoensis primers 40-F and 40-R (Boulding et al. 1993) generating a 610-base pair (bp) fragment that was manually sequenced for 28 individuals (19 from Florida, 5 from NC, and 4 from Massachusetts). An internal Argopecten-specific primer was generated and used to acquire an additional ~490-bp mtDNA sequence by genome walking (vectorette PCR protocols; Sigma-Genosys, Woodlands, TX). The ~1-kb fragment was sequenced, and new primers were designed (AI99F: ATT CCC CCT CAA CAA ART CA and AI912R: ACA AAC TGC CCG TCG CTC TC), and amplification yielded an 833-bp fragment, which we used during the RFLP analysis. Analysis by a BLAST search indicates the fragment to include portions of the 12s ribosomal subunit, transfer RNAs for glutamine and valine, and the NADH 1 coding regions. The PCR amplification conditions to yield this fragment were as follows: 40 cycles, each of 30 sec at 94[degrees]C, 30 sec at 53[degrees]C, and 1 min at 72[degrees]C. Reactions were performed in 100-[micro]L volumes of 1x PCR buffer containing 1.5 mM Mg[Cl.sub.2], 0.2 [micro]M each primer, 800 mM dNTP, and 2.5 U Taq polymerase.

Each PCR product (10 [micro]L) was digested with a battery of 9 enzymes: Alu I, Ban II, Bgl II, BsiHKA I, HinF I, Rsa I, ScrF I, Tsp 509 I, and [Taq.sup.[alpha] I (5 U enzyme, 20-[micro]L total volume) according to the manufacturer's specifications (New England BioLabs, Beverly, MA). The digests were incubated for 3 h and stopped with 5 [micro]L of loading dye (20% Ficol 400, 0.1 M Na EDTA, pH 8), 1% sodium dodecyl sulfate, 0.25% bromophenol blue). Entire digests were loaded onto 20-cm, 2%, low-melting point agarose gels and electrophoresed for 3-4 h at 90-100 V. Fragment patterns were visualized by ethidium bromide staining and were photographed under UV light. Fragment sizes were determined from migration distances relative to known standards.

Statistical Analysis

Many statistical analyses of Atlantic samples were performed at both the collection level and the subpopulation level. The three NC collections were combined to form that subpopulation; the single New Jersey (NJ) and New York (NY) collections also served as those subpopulations. Sample designations for collection-level analyses include both the location and year of collection (e.g., NC97); designations for subpopulation-level analyses include only the location abbreviation (e.g., NC). For brevity, we refer to all subpopulations and populations by their location names. Sample sizes differed between the two genetic techniques used, and they are given in Table 1.

Allozyme Locus Analysis

Our Florida Gulf allozyme and mtDNA data were drawn from a complementary study (Bert et al. in prep.). In that study, the multiple annual collections were combined to form subpopulation samples from each of 12 locations. Based on common genetic characteristics, the subpopulations were grouped into 4 populations which, except for FB, were composed of bay scallops from several locations (Fig. 1B). Here, we synthesized the allele frequency data and related statistics, including genetic distances, at the population level. Unless otherwise noted, we obtained population-level values by averaging the subpopulation values presented in Bert et al. (in prep.), which compensated for the sometimes highly unequal sample sizes among subpopulations. For the mtDNA data, we merged haplotypes from all locations used in Bert et al. (in prep) into population-level haplotype frequencies.

We used BIOSYS-1 (Swofford & Selander 1981) to calculate allele and genotype frequencies. For each Atlantic collection, we compared observed genotype frequencies of each locus with Hardy-Weinberg (H-W) expected genotype frequencies using Fisher's exact test and determined heterozygote deficiency or excess using the D statistic (Selander 1970). To describe deviations from H-W genotype frequency expectations for each Florida Gulf population, we provide the proportion of the appropriate Florida Gulf subpopulations that did not conform to H-W expectations in Bert et al. (in prep). We tested for significant differences in proportion of loci deviating from H-W equilibrium among Atlantic subpopulations and Florida Gulf populations separately and between those 2 groups using the RXC G-test followed by the simultaneous test procedure (STP) for frequencies (BIOMstat, version 3; http://www.ExeterSoftware. com; Sokal & Rohlf (1995)). We used GENEPOP (version 3.2a; Raymond & Rousset (1995)) to calculate the following genetic variability statistics: average (direct-count) heterozygosity per locus ([[bar.H].sub.o]), percentage of polymorphic loci at the [P.sub.95] and the [P.sub.99] levels (frequency of rarest allele was 0.05 or 0.01, respectively), and mean number of alleles per locus ([[bar.n].sub.a]).

We searched for patterns of significance in allele frequency differences at each polymorphic locus ([P.sub.95] level) among North Carolina collections, Atlantic subpopulations, and Florida Gulf populations independently and among Atlantic subpopulations and Florida Gulf populations together using RxC G-tests to establish the significance followed by pairwise RxC G-tests to locate the sources of the differences. To eliminate cells with 0 frequencies, we combined rare alleles so that no cell had a frequency of 0. Then, using the exact probability test, we tested allele frequencies collectively over all loci for homogeneity between all pairwise combinations of Atlantic subpopulations and Florida populations. In each set of analyses, we compensated for multiple testing of the null hypothesis of homogenous allele frequencies by adjusting the significant probability values accordingly using the sequential Bonferroni method (Rice 1989).

We examined geographic relationships by first calculating pairwise Nei's genetic distances (Nei's D; Nei (1972)) and pairwise [[THETA].sub.ST] (Wright's [F.sub.ST] analogue; Weir & Cockerham (1984)) values over all loci, following Slatkin (1993; in GENEPOP), for all pairwise combinations of Atlantic collections and of Atlantic subpopulations and Florida populations. Values for Atlantic/ Florida Gulf comparisons were obtained by averaging Atlantic collection/Florida subpopulation values. We analyzed spatial variation of the pairwise Nei's D and [[THETA].sub.ST] genetic distance values by calculating the means of various combinations of pairwise values and testing those means for significant differences using the Kruskal-Wallis test or Wilcoxon's 2-sample test followed by the Ryan-Einot-Gabriel-Welsch multiple range test. If needed, we transfomaed [[THETA].sub.ST] values using log n + 1. This approach capitalizes on the idea that the nonrandom distribution of small genetic differences is more convincing than a single tablewide [F.sub.ST] or [G.sub.ST] value calculated for an entire data set (Palumbi 2003), and also allows for exploration of the connectivity of collections and subpopulations separated by varying geographic distances while avoiding the unreliability of single pairwise [F.sub.ST] values (Hellberg 2006). Relational patterns can be detected in high-dispersal species (e.g.. those with pelagic larvae) using this approach (Palumbi 2003). For bay scallops, establishing connections within and between ocean basins can, by inference, reveal underlying successful larval dispersal patterns.

We also used the pairwise Nei's D values calculated for Atlantic (presented herein) and Florida subpopulations (from Bert et al. in prep) to generate unweighted pair group method of analysis (UPGMA) and neighbor-joining (N-J) phenograms (UPGMA Tree software,(Jin & Ferguson 1990)). To estimate statistical confidence in the phenograms, we calculated standard errors for the nodes in the UPGMA phenogram (Nei et al. (1985), as implemented in UPGMA Tree) and bootstrap probability values for the nodes in the N-J phenogram (1,000 replicates DISPAN; Ota (1993)).

mtDNA Analysis

We calculated haplotype frequencies using REAP (version 4, McElroy et al. (1992)). We used both Monte Carlo simulation (in REAP) and the RxC G-test followed by the STP to search for significant differences in haplotype frequencies among Atlantic collections and subpopulations. For the RxC G-tests, haplotypes other than the common haplotype were combined. For each Atlantic collection and subpopulation, we calculated haplotype diversity (h) and nucleotide diversity ([pi]) (Nei 1987), and calculated pairwise [pi] for subpopulations (REAP). For Florida Gulf population-level h and [pi], we averaged the collection-level values reported in Bert et al. (in prep.); for population-level pairwise [pi] values, we averaged the subpopulation-level values presented in that report. The h and [pi] values of Atlantic collections and Florida Gulf populations were tested for significant outliers within each group using Dixon's test; the means of the Atlantic and Florida Gulf values for those statistics (omitting FB) were compared using Wilcoxon's 2-sample test (Sokal & Rohlf 1995).

We investigated genetic relationships between pairs of Atlantic subpopulations, Florida populations, and Atlantic-Florida combinations by testing the significance of Cockerham's (1969, 1973) pairwise genetic distances ([[PHI].sub.ST]; exact test, Arlequin, version 2.0; Schneider et al. (2000)) and of pairwise nucleotide divergences (d; Nei (1987)) (REAP). We used the sequential Bonferroni test (Rice 1989) to correct for multiple tests of the null hypothesis that no significant differences existed.

To search for genetic population structure, we analyzed isolation by distance by regressing the geographic distances of all pairwise combinations of Atlantic subpopulations and the subpopulations composing the Florida Gulf populations (Bert et al. in prep.) against the pairwise [[PHI].sub.ST] values (Slatkin 1993). We estimated geographic distances by following the major contours of the coastline using the ruler tool in Google Earth. We tested groupings of pairwise [[PHI].sub.ST] values for significant differences within and between Atlantic subpopulations and Florida Gulf populations, as we did for the allozyme pairwise genetic distance measures; and, using the pairwise [[PHI].sub.ST] values, we generated an N-J tree (PHYLIP version 3.5c; distributed by J. Felsenstein, Department of Genetics, University of Washington, Seattle, WA). We also conducted AMOVA analyses (Arlequin) using all pairwise [[PHI].sub.ST] values; and, exclusively, Atlantic values and Florida Gulf values.

To explore mtDNA haplotype variation in depth, we first used the pairwise d values to produce a minimum spanning network (MSN; Arlequin), and visualized the haplotype relationships using the VGJ graph-drawing tool in http://www.eng. auburn.edu/department/csse/research/research_groups/research/ graph_drawing/vgj.html. Using the TCS program (Clement et al. 2000), we checked for parsimony probabilities indicative of the number of mutational steps between haplotypes that we can accept in the MSN to generate the step 1 groupings for a nested clade phylogeographic analysis (NCPA; Templeton (1998)). To perform the TCS, we changed our 0/1-coded haplotype data to an A/T code (D. Posada, Universidad de Vigo, Spain; pers. comm.). We used the GeoDis program (Posada et al. 2000) to test for significant geographic associations among haplotypes and applied the NCPA to the clades with significant associations. We also performed sequence mismatch analyses (Slatkin & Hudson 1991, Rogers & Harpending 1992, Templeton 1998) (Arlequin; 1,000 bootstrap replicates) on, separately, all samples, Atlantic samples, and Gulf samples, as well as on each level-3 NCPA clade. The NCPA provides information useful for inferring past phylogeographic events, and the mismatch analysis performed on clades provides insight into the contribution of lineages through time to current phylogeographic patterns. To assist with interpretations further, we produced separate MSNs for Atlantic and Florida Gulf haplotypes and used those, together with information gained from the NCPA and mismatch analyses and other accessory statistics, including Tajima's (1989) D and Fu's (1997) Fs, to generate an interpretation of the full MSN different from that produced solely by the NCPA.

RESULTS

Allozyme Electrophoresis Analysis

Genetic Diversity

We consider genetic diversity to be composed of 2 types of genetic variability: the number of alleles present (genetic variation) and the frequencies of those alleles (genetic composition). Genetic diversity measures for the 18 loci are presented in Table 3. Although no loci differed significantly in allele frequencies among Atlantic subpopulations, NJ had unusual allele frequencies at several loci, notably LAP.

Patterns of rare-allele (frequency, <0.1) occurrence revealed relationships and provided information for inferring the recent history of the subpopulations. At 7 of the 10 highly polymorphic loci, a total of 8 rare alleles were shared only by NY and NC. In contrast, only 1 rare allele was shared by NJ and NC, and no rare alleles were shared by NJ and NY. Sixteen NC individuals (16% of the sample) and 3 NY individuals (5% of the sample) possessed rare alleles otherwise found only in Florida Gulf populations (NC: AAT-1*C, D; EST*B, F; LAP*B, G; MDH-1*C; MPI*E; OPDH*E; NY: AAT-2*B, MDH-2*C, SOD*B). Four NC individuals carried 2 alleles; 2 of the individuals were homozygotes, 1 was a heterozygote for 2 EST alleles, and 1 was heterozygous for a rare allele at 2 loci. The probabilities that any of these individuals would exist in our NC sample ranged from 0.0004-0.0009. Two of the NY individuals were also homozygores; their probabilities of existence in that sample were each also 0.0004. In contrast, NJ was depleted of rare alleles at multiple loci (AAT-1, AAT-2, DPEP, GPI, OPDH, LAP) and had no private rare alleles in common with Florida Gulf populations.

Genotype frequencies at the DPEP, EST, and MPI loci did not conform to H-W expectations in nearly all samples, particularly in the subpopulations that composed the Florida Gulf populations (Table 3). All significant deviations from H-W expectations but one (NJ, at GPI) were the result of heterozygore deficits. The incidence of nonconformity did not differ significantly among either Atlantic or Florida Gulf subpopulations, or between subpopulations from the 2 ocean basins. NY's relatively high proportion (39%) of deviating loci was the result of the high incidence of rare-allele homozygotes (at 10 of 13 polymorphic loci) that had low probabilities of existing (one-half to one-hundredth of their actual frequencies; data not shown); this also was the major contributor to the relatively low dc[H.sub.o] value and high [[bar.n].sub.a] value for NY (Table 3). The relatively low dc[H.sub.o] value and [[bar.n].sub.a] value for NJ were attributable to higher frequencies of common-allele homozygotes at multiple loci.

Most measures of genetic variability were related to sample size in the NC collections, but measures of genetic variability and H-W conformation were inversely related to heterozygosity. NC97 had the highest values for both levels of polymorphism, [[bar.n].sub.a], and number of loci deviating from H-W expectations, but the lowest value for dc[H.sub.o], whereas [NC.sub.B]98 and [NC.sub.C]98 had lower values for the 4 former measures but higher values for heterozygosity. This relationship may be associated with the origins of the bay scallops that formed the aggregations we sampled rather than the consequence of the absence of rare alleles in the 1998 collections resulting from their smaller sample sizes. At the highly polymorphic GPI and LAP loci, rare alleles are replete in the 1998 collections.

All measures of heterozygosity and polymorphism in Florida Gulf populations, including FB, were comparable with Atlantic values. Values for FB were also usually the highest among the Florida populations, despite the absence of rare alleles at nearly every locus and a comparatively very small sample size (Table 3). FB differed from other Florida Gulf populations in that allele frequencies at highly polymorphic loci (AAP-1, AAP-2, DPEP, PGM, OPDH) were more equivalently distributed and, at loci with low levels of polymorphism (AAT-2, GP, HDH), the rare alleles were present at higher frequencies.

Population Genetic Relationships

The only significant difference in single-locus allele frequencies among Atlantic collections or subpopulations was at LAP: NC97 allele frequencies differed significantly from those of both NC 1998 collections (P < 0,001 for both). Allele frequencies in Florida Gulf populations differed significantly at 5 loci (AA P-2, LAP: P < 0.0001; DPEP, OPDH: P < 0.005, AAP-1 : P < 0.01). The difference among Florida Gulf populations was principally the result of uniqueness of Panhandle (PN). More than twice as many pairwise RxC G-tests were significant in pairs with PN as a pair member compared with all other pairs (Table 4A).

Although Atlantic subpopulations and Florida Gulf populations shared most or all alleles at all loci, 6 loci differed significantly in allele frequencies between bay scallops from the 2 ocean basins (AAP-1, GPL LAP, PGM: P < 0.0001: OPDH: P < 0.001; AAP-2: P < 0.005). Nearly twice as many NY/Florida Gulf pairs and NC/Florida Gulf pairs differed significantly in allele frequencies at individual loci than did N J/Florida Gulf pairs (Table 4B), principally because NJ was lacking in rare alleles.

All Atlantic subpopulation pairs differed significantly from each other in overall genetic composition (Table 4C), as did all Florida pairs except the Core (CO)-Southwest Florida (SF) comparison, which was marginally nonsignificant. NY was the most differentiated among the Atlantic subpopulations. Of the Florida populations, the pivotal core was more closely related to SF than to PN, and the uniqueness of FB was reconfirmed. All comparisons between Atlantic subpopulations and Florida Gulf populations were highly significant.

Pairwise Nei's D and [[THETA].sub.ST] values for Atlantic collections were very low for NC collection pairs (Table 5A). Indeed, although [[THETA].sub.ST] values are usually higher than Nei's D values, all pairwise [[THETA].sub.ST] values for NC collection pairs were 0. In our grouping analyses of pairwise Nei's D and [[THETA].sub.ST], the mean genetic distance between NC collections was significantly smaller than the means of those collections paired with NJ97 or NY98 (Table 6A). Genetic distances between collection pairs from different Atlantic locations varied among the collections (Table 5A). The [[THETA].sub.ST] values for NJ98/[NC.sub.C]98 and NJ98/NY97 were notably higher than the values for all other collection pairs and were as high as the values between NC and FB (Table 5B).

Other than pairs with FB, pairwise genetic distances for Atlantic bay scallop subpopulations were, significantly, 2-9 times higher than the means for the very low and statistically homogeneous Florida Gulf bay scallop populations (Tables 5B and 6B; [D.sub.1, [[THETA].sub.ST1]. The Atlantic subpopulation most genetically distant from the Florida populations was NJ; NJ/Florida Gulf genetic distances were generally 20-33% greater than were NY/ Florida Gulf genetic distances (Table 5B), and the means of some N J/Florida Gulf pairs were significantly higher than the means of some NY/Florida Gulf pairs (Table 6B; [D.sub.1], [[THETA].sub.ST1]).

The means with Atlantic subpopulations and FB as pair members were among the most differentiated of all pairwise combinations (Tables 5B and 6B; [D.sub.1], [[THETA].sub.ST1], in part because FB is enriched in rare alleles specific to Florida subpopulations (i.e., AAP-2*D, DPEP*B, GP*C,D, HDH*D, OPDH*B; Table 3). Interestingly, the genetic distances of FB paired with other Florida Gulf populations was equivalent to the genetic distances of NC paired with those populations (Table 5B), and the mean genetic distances of FB or NC paired with other Florida Gulf populations were approximately 25-50% smaller than the mean distances between other Atlantic/Florida Gulf pairs (Table 6B: [D.sub.1], [[THETA].sub.ST1]). However, FB and NC were not closely related; their genetic distances from each other were equivalent to those of either one paired with other Florida Gulf populations (Table 5B).

Grouping the genetically similar PN, CO, and SF populations into a single peninsular Florida (FLA) population provided additional insight into intra- and interbasin relationships (Table 6B: [D.sub.2], [[THETA].sub.ST2]). The very low mean genetic distances between the population pairs forming FLA emphasizes their genetic similarity compared with the far more distant Atlantic subpopulations. The high mean genetic distances between NJ and FLA are the result of the unique absence of rare Florida Gulf alleles in NJ.

In both allozyme cluster phenograms (Fig. 2, A, B), A. i. irradians and A. i. concentricus were clearly separated, NC grouped with A. i. irradians and FB with A. i. concentricus, and some or all CO subpopulations grouped together. The Florida Gulf populations advocated by Bert et al. (in prep) were fully maintained in the UPGMA phenogram; the N-J phenogram may more reflect source-sink genetic relationships in that metapopulation. FB has unique positions in both phenograms--the most basal of the Florida subpopulations in the UPGMA phenogram and the most highly derived in the N-J phenogram. Those placements further emphasize the genetic distance of FB from the rest of the Florida Gulf.

mtDNA RFLP Analysis

Genetic Diversity

We found 53 haplotypes (H) in the 534 bay scallops that we examined. The estimated restriction fragment sizes characterizing those haplotypes are in Table 7, and their frequencies are in Table 8, as are h and [pi] values. Except for NY, which had codominant haplotypes (H2, H3), the common haplotype in Atlantic collections was H2. Haplotype 11 clearly predominated in Florida Gulf populations and, except for one other, was the only haplotype in the FB sample. Haplotype frequencies did not differ significantly among groups within either ocean basin.

Although they were elevated, the h value for NY97 and the [pi] value for NJ98 did not differ significantly from the corresponding values for other Atlantic collections, but both h and [pi] for FB were significantly lower (P < 0.05 and 0.01, respectively) than the mean values for the collections forming other Florida Gulf populations. Discounting FB, the mean [pi] value for Atlantic subpopulations was significantly lower than the mean for Florida Gulf populations (P < 0.01) and, compared with the average molluscan [pi] value (0.85 (Bazin et al. 2006)), Atlantic subpopulation values were much lower and Florida Gulf population values much higher. Pairwise values for all Atlantic pairs were equivalent, as were those for all Florida Gulf pairs except those with FB as a member (Table 9). The near fixation of the common Florida Gulf haplotype in FB decreased all within-Gulf, and increased all Atlantic-Gulf, pairwise [pi] values that included that sample. The mean [pi] values for populations paired with FB were significantly lower than the means of pairs with other Gulf collections (P = 0.0003).

The [[PHI].sub.ST] values for Atlantic subpopulation pairs were significantly higher than those for Florida Gulf population pairs (P < 0.0001); and the NY/NC pair differed significantly at the tablewide level (Table 9). Within the Florida Gulf, the genetic distance between FB and other populations was 2-3 times greater than the distance between the other populations. Genetic distances between all pairs of Atlantic subpopulations paired with Florida Gulf populations were comparatively quite large. Nucleotide divergences between Atlantic subpopulations were small (NC/NJ = 0.0001, NC/NY = 0.0020, NJ/NY = 0.0007), but both pairs with NY were highly significant, tablewide (P < 0.001: data not shown). All pairwise d values for Florida Gulf populations were 0, except those with FB (range, 0.0009-0.0016). All d values for Atlantic/Florida Gulf pairs were highly significant (range, 0.0092-0.0215). Pairs with FB as a member were highest because FB lacked Atlantic haplotypes.

[FIGURE 2 OMITTED]

Population Genetic Relationships

Isolation by distance explained a significant component of the pairwise genetic distances between Atlantic subpopulations and Gulf populations (y = 0.0008x - 0.11; r = 0.84, P < 0.001), and both the grouping analysis of mean pairwise genetic distances (Table 6, [[PHI].sub.ST]) and the NJ dendrogram (Fig. 2C) illustrate the magnitude of the difference between Atlantic and Florida Gulf mtDNA RFLPs, as well as the greater genetic distance between Atlantic subpopulations compared with the distance between Florida Gulf populations.

For the AMOVA analysis involving all pairwise [[PHI].sub.ST] values, we partitioned the data into Atlantic and Gulf groups. That grouping explained 58% (P < 0.0001) of the variation in haplotype diversity. Variation among individuals within populations explained nearly all remaining differentiation (41%: P < 0.0001). Variation among populations within groups was significant (P = 0.03), but explained only 1% of the population genetic structure. The data were not partitioned for the within-ocean basin AMOVA analyses. Among Atlantic subpopulations, a small but significant amount (5%; P = 0.01) of the genetic structuring was explained by variation among the subpopulations. Among Florida Gulf populations, virtually all variation was explained by differences among individuals within populations; the populations were not genetically structured (P = 0.45).

The TCS program revealed that level 1 clades (C) that included up to 2 mutations between haplotypes could be generated. Only 1 haplotype (H27) exceeded this limit. The MSN was composed of 3 level 3 clades (C3-1, C3-2, C3-3; Fig. 3A), each containing 2 level 2 clades. Within C3-1, C2-1 included principally Atlantic haplotypes, whereas C2-2 contained only Florida Gulf haplotypes except for H15, which also occurred in North Carolina (2 individuals). Both level 2 clades in C3-2 were a mixture of Gulf and Atlantic haplotypes from widely scattered locations. Within C3-3, C2-5 had, by far, the most Gulf haplotypes; nearly all were 1 or 2 steps removed from the very common H11, which was also found in 3 NC individuals. C2-6, a small clade with only NC haplotypes, was derived from H13, a member of C2-5. Thus, C3-3 was essentially a Florida Gulf clade with a few haplotypes found also or exclusively in North Carolina.

Clades at all levels were significant in the NCPA (Fig. 3A, Table 10). Independently significant level 1 clades were exclusive to C3-1. The inferred demographic event for both C2-1 and its constituent C1-2 was contiguous range expansion. Within C2-1, the significance of H2, the most common Atlantic haplotype within C1-2, and of C l-l, which contained principally Atlantic haplotypes (Fig. 3A, Table 8), indicated that C2-1 originated in the Atlantic. C2-4, the only significant component of C3-2, and for which contiguous range expansion was also inferred, was composed of haplotypes from widely ranging locations (Fig. 3A, Table 8). Because no haplotypes in that clade were shared between the Gulf and Atlantic, it seems more likely that some other process, perhaps dispersal within regions and fragmentation between regions, shaped C2-4. C2-5 was significant, due principally to the significance of nested clades 1-10 and 1-14 (Table 10). The phylogeographic processes inferred for C2-5 were restricted gene flow and dispersal, some of which was long distance. Long-distance dispersal to NC is evidenced by C1-14, but limited gene flow is not consistent with the previous analyses of Florida Gulf mtDNA population genetic structure, which supported panmixia for all populations, perhaps other than FB. Alternatively, the C2-5 "starburst" haplotype array may have been generated by another phylogeographic process: demographic expansion (Slatkin & Hudson 1991, Fu 1997). Demographic expansion may also be the process operating in C2-2, a clade deemed to be inconclusive in the NCPA and with a less diverse but similar structure to C2-5.

Overall, the NCPA supports the idea of recent, contiguous range expansion in Atlantic bay scallops and both limited dispersal (with population expansion) in the Gulf, and occasional long-distance dispersal from Florida Gulf populations into NC. The significant higher level clades 3-1 and 3-3 illustrate that long-distance dispersal and colonization were the past processes that shaped present-day bay scallop phylogeographic structure. At the highest clade level (4-1) and most distant past (Templeton 1998), allopatric fragmentation between the Gulf and Atlantic clades generated the genetically differentiated subspecies existing today.

Multiple lines of evidence from MSNs generated separately for Atlantic and Florida Gulf haplotypes (Fig. 3B, C) and from the studywide, regional, and level 3 clade mismatch frequency profiles (Fig. 4A, B) and accompanying and accessory mismatch statistics (Table 11) indicate that Atlantic subpopulations are older and demographically more static than Florida Gulf populations, which are younger and collectively have experienced recent large population expansions, as follows. First, the Atlantic haplotype MSN (Fig. 3B) bears the intricacy and geographic expanse of an ancient lineage in which haplotypes have gone extinct, and multiple stepwise mutations within distinct lineages have generated sublineages with haplotypes related to each other by sequential mutations (Bargelloni et al. 2005, Grant 2005, Teske et al. 2005). In sharp contrast, the highly abundant H11 and numerous closely related, rare haplotypes in the Florida Gulf lineage (Fig. 3C) are characteristic of a recent lineage marked by a rapid demographic expansion (Bowen & Grant 1997, Grant & Bowen 1998, Avise 2000; Teske et al. 2005). Second, the mean numbers of haplotype differences and the T values of Atlantic groups are generally greater than those of Florida Gulf groups (Table 11), and the Atlantic values are generally hierarchical (clade level 2 < clade level 3 < Atlantic). Haplotype differences accumulate through time; higher numbers of differences characterize older populations, and T values are related to the mean numbers of haplotype differences between groups (Bargelloni et al. 2005). Third, the multimodal mismatch distributions (Fig. 4A) for the Atlantic groups imply that Atlantic bay scallops have undergone several population demographic and spatial contractions and expansions and/or selective sweeps through a longer time period in the past (Rogers et al. 1996), whereas Florida Gulf bay scallops have the steep, unimodal mismatch distribution indicative of a dramatic population expansion in the recent past (Rogers & Harpending 1992). Moreover, the y-axis scales for the Atlantic and C3-2 demographic and spatial expansion profiles are much lower compared with the Florida Gulf and C3-3 profiles, showing that expansions in the Atlantic have been less dramatic than the Florida Gulf expansion (Schneider & Excoffier 1999). Fourth, the high modal number of nucleotide differences of clade C3-2 shows that it is ancient (Fauvelot et al. 2003) and has undergone a previous population expansion and decline (Fig. 4B); that clade now contains haplotypes that persisted through that demographic event. Florida Gulf C3-3 has the sharply declining mismatch profile (Fig. 4B) and numerous, closely related haplotypes associated with a recent expansion (Slatkin & Hudson 1991, Rogers & Harpending 1992). Fifth, positive Tajima's D values (Table 11) indicate that C3-2 and its component C2-4 may have undergone an overall reduction in population size ((Harpending et al. 1993, Schneider & Excoffier 1999), whereas all Florida Gulf clades have highly negative (all P < 0.001) Tajima's D values, indicative of substantial demographic expansion following a bottleneck or selective sweep (Rand 1996). Sixth, and last and unique to the Atlantic--the declining hierarchical M values of Atlantic groups (infinite for level 2 clades, intermediate for level 3 clades, small for Atlantic; Table 11) indicate that short-term gene flow is much higher than long-term gene flow as geographic expanse increases.

Despite their many differences, Atlantic and Gulf bay scallops have one feature in common. All values for both [[theta].sub.0] (demographic expansion) and e (spatial expansion), and for their confidence intervals, were very small. The reductions in effective population size experienced by both groups have been severe, near-extinction events; aggregations have recolonized or regenerated from very few founders (Grant 2005).

Three features of the NCPA analyses and mismatch statistics generated values that were difficult to reconcile with the predominant Atlantic and Florida Gulf patterns. First, the existence of the older, principally Atlantic, C2-1 together with the starburst Florida Gulf C2-2 in C3-1 generated infinite [[THETA].sub.1] and M values, and the appearance of recent demographic and spatial expansions in the C3-1 mismatch distribution (Fig. 4B). Separate mismatch frequency distributions for those clades (not shown) were strikingly different. Second, the much greater number of Florida Gulf haplotypes compared with the number of Atlantic haplotypes biased some of the Gulf and Atlantic group mismatch statistics such that they resembled those of the Florida Gulf alone. Third, because Florida Gulf subpopulations individually expand, contract, and go extinct (Bert et al. in prep), the demographic expansion model C2-2, C2-5, and C3-3 [PHI] and HR (for C2-5 and C3-3) statistics did not show the demographic expansion demonstrated by the Florida Gulf and C3-3 mismatch distributions (Fig. 4).

The separate MSNs for Atlantic and Florida Gulf haplotypes, considered together with the results of the NCPA and mismatch analyses, the knowledge that older haplotypes tend to have broader distributions and to be present in higher frequencies, and the knowledge that older lineages tend to be complex (Castelloe & Templeton 1994, Excoffier and Smouse 1994, Pruett et al. 2005), prompted us to formulate an alternative interpretation for the bay scallop MSN. We considered the lineage that includes all shared Gulf Atlantic haplotypes, all intermediate haplotypes linking those haplotypes in Figures 3A-C, and all branches in which Atlantic and Florida Gulf haplotypes are interspersed as representing the ancestral lineage (Fig. 3D). This interpretation clearly illustrates the proliferation of Florida Gulf haplotypes belonging to or derived from core haplotypes with widespread distributions. It also suggests that NC haplotypes H12, H14, and H17 were derived from the ancestral Florida Gulf H11 lineage.

[FIGURE 3 OMITTED]

DISCUSSION

Population Genetic Structure

Atlantic and Florida Gulf bay scallops have very different population genetic structures, both within and between ocean basins. These differences reflect the diverse array of demographic and ecological events that have affected these subpopulations and populations, as well as the numerous, substantial anthropogenic activities that, over time, impinged principally on Atlantic subpopulations prior to the time of our sampling. The individuality of these influences on each Atlantic subpopulation warrants close examination. We present our deductions about NY and NJ in this section, and about NC in Taxonomic Puzzles.

New York

NY bay scallops comprise a relatively sequestered subpopulation located in an area with a low probability of gene flow from more southerly subpopulations. Thus, not surprisingly, our NY sample emerged as the most genetically distant among Atlantic subpopulations in the pairwise tests of overall allozyme allele frequencies and of mtDNA nucleotide divergences. NY also had low allozyme heterozygosity and [P.sub.95] values coupled with high frequencies of common alleles at nearly all loci, high [P.sub.99] values resulting from a high incidence of rare-allele homozygotes, a high mean number of alleles over all loci, a high frequency of loci deviating from H-W equilibrium, the lowest mean pairwise difference between haplotypes, and high mtDNA haplotype diversity resulting from codominant haplotypes, one of which is otherwise rare in Atlantic subpopulations. Together, these features indicate that the Peconic Bay aggregation from which we obtained our NY98 collection experienced a recent genetic bottleneck or colonization from a few founders (Grant 2005), and an infusion of new genotypes from genetically differentiated individuals within the recent past. Two NY individuals were homozygous for rare Florida Gulf alleles, and NY shared some rare alleles with NC, but shared none with NJ. A commonality of rare alleles indicates gene flow (Slatkin 1985, Saavedra et al. 1993), suggesting that our hypothesized infusion of bay scallops into the Peconic Bay aggregation came directly or indirectly from NC or the Florida Gulf, and that gene flow between NY and NJ bay scallops is very rare, at least within the time frame of our study.

Multiple factors could have contributed to the high incidence of rare homozygotes, limited genetic diversity, predominance of NY haplotypes in a single small clade (C2-1), and codominance of mtDNA haplotypes H2 and H3 seen in the NY bay scallops. First, all NY bay scallop aggregations inhabit territory formerly covered by the Laurentide glacier up to about 20,000 y ago (Balco & Schaefer 2006). Remnants reflecting the genetic diversity of the colonizing (presumably) larvae, which likely constituted a relatively small subset of the total Atlantic larval pool, could still remain. Post-Pleistocene founding populations often have limited or altered genetic diversity compared with comparatively older, established populations (e.g., Dillon & Manzi 1992). Second, many NY aggregations, including that inhabiting Peconic Bay, have been particularly besieged by sometimes multiyear blooms of the "brown tide" alga Aureococcus anophagefferens and, to a lesser degree, by outbreaks of shell-boring parasites, and starfish and crab predators, all of which can cause repeated reductions or local extirpations (Tettelbach & Wenczel 1993). Repeated demographic flushes and crashes can change population genetic diversity significantly (e.g., Haag et al. 2005). Third, because the time of recovery to high density levels can be protracted in bay scallops (Peterson & Summerson 1992, Tettelbach 2009), the Peconic Bay aggregation has been intermittently supplemented since 1985--until 2004 (S. Tettelbach, Long Island University: pers. comm.)--with bay scallops principally from an aquaculture-based aggregation in Maine and from the wild aggregation in Massachusetts (Tettelbach & Wenczel 1993). At least occasionally, these enhancements were successful: seeded scallops contributed an estimated one quarter of the Peconic Bay scallop set in 1989 (Krause 1992). Supplementing with bay scallops from either of these sources could have affected the genetic diversity of NY bay scallops. Unless generally large numbers of broodstock are used and care is taken to maintain the genetic diversity of the recipient population, supplementation with aquacultured broods can significantly alter the genetic diversity of the admixed (hatchery component + wild component) population, particularly if aquaculture-based supplementation is successful and repeated (Bert et al. 2007). Although the Massachusetts aggregation has been stable for decades (S. Tettelbach, pers. comm.), it is at the northern limit of the bay scallop range (Waller 1969), and it, too, is post-Pleistocene in age-both reasons that may contribute to limited or altered genetic diversity compared with aggregations farther south (e.g., Hellberg et al. 2001).

[FIGURE 4 OMITTED]

At least some of the unusual features of our NY sample likely are not sampling artifacts or temporary conditions. The fact that Krause (1992) could distinguish hatchery bay scallops from wild bay scallops using allozyme loci indicates that the hatchery scallops were significantly genetically differentiated from the native aggregation. A bay scallop sample (CR) obtained from a hatchery and used for mtDNA RFLP analysis by Blake and Graves (1995) also had codominant haplotypes, suggesting that the codominance of H2 and H3 we observed resulted from supplementation with hatchery bay scallops.

New Jersey

At multiple loci, our NJ sample was depleted in rare allozyme alleles otherwise present in our NC and/or NY samples: and NJ was underrepresented in Florida Gulf alleles compared with NC and NY. NJ had a high incidence of homozygous genotypes for common Atlantic alleles (data not shown), and uniquely different allele frequencies at some loci. The comparatively low sample size of NJ could have contributed to the low number of alleles, but other measures of heterozygosity and polymorphism were not well correlated with overall Atlantic collection sample sizes, and NJ's high mtDNA nucleotide diversity suggests that the sample sizes adequately represented that subpopulation. Together, NJ's genetic attributes signal a genetic bottleneck in the NJ aggregation in the recent past, and no subsequent input of Florida Gulf genes.

NJ bay scallops were harvested intensely from the 1950s to late 1960s (Campanella et al. 2007), which depleted the subpopulation. Since then, sufficient bay scallops to support a fishery have been present only infrequently (Bologna et al. 2001, Campanella et al. 2007). NJ bay scallops may be a small, self-seeding population (Bologna et al. 2001), or the Little Egg Harbor colony may have originated principally from a small group of immigrants swept in as larvae or transplanted at some life stage from another location. The location of the aggregation--close to the mouth of an ocean-to-bay inlet supports the former interpretation. Pairwise allozyme relationships, water current patterns, coastal geography, and the inferred time of settlement (fall) (Bologna et al. 2001) suggest that NC was a source of that NJ aggregation. In contrast to the summer spawning peak of NY, NC bay scallops have a fall spawning peak (Bologna et al. 2001). Differences in the inferred origins of NJ bay scallop aggregations (Bologna et al. 2001, Campanella et al. 2007, this study) may be the result of actual disparities in source subpopulations over time. Although we view NC as a likely source of immigrants into N J, larvae may also occasionally be swept in from NY or other areas that harbor aggregations temporarily (e.g., Maryland waters, where small aggregations have recently been seen in the seaward areas of bays; S. Tettelbach, pets. comm.). Regardless of the source, the overall paucity of genetic variation in the NJ subpopulation indicates that it was parented by few individuals and is isolated.

Florida Gulf

The allozyme and mtDNA RFLP analyses yielded radically different images of the genetic relationships among Florida Gulf populations. The allozyme analysis confirmed the hierarchical structure of the Florida Gulf metapopulation first proposed by Arnold et al. (1998) and confirmed by Bert et al. (in prep). Here, at the population level, significant differences in allele frequencies at multiple loci, overall differences in allele frequencies, and the structure of the UPGMA phenogram confirmed the validity of the 4 populations and supported the closer relationship of CO and SF than of other population pairs. The occurrence of many significant allele frequency differences among conspecific populations can be the result, in part, of large sample sizes (Gold et al. 2001); but in this case, differences in recruitment sources and patterns and in population dynamics (Bert et al. in prep) are also contributing factors. PN is principally differentiated from the CO-SF population complex because of its apparently independent recruitment in some years (Bert et al. in prep). The relationship of FB to this metapopulation structure is even more peripheral (see A. i. taylorae, discussed later).

Bay scallop mtDNA diversity, homogeneous throughout the Florida Gulf except for FB, reflects phylogenetic history rather than current population genetic structure. Collectively, the NCPA, MSN, and mismatch analyses support a large, regional, demographic expansion that occurred recently in the past. This sudden expansion and the NCPA conclusion of limited gene flow seem to be reflecting permanent attributes of the Florida Gulf bay scallop core--periphery metapopulation structure (Bert et al. in prep.). The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth (Rogers et al. 1996). The stable, CO population is likely the principal source of bay scallops for both SF, which has subpopulations that go extinct intermittently, and, to a lesser degree, PN, which in some years is genetically indistinguishable from CO and other years is quite distinct (Bert et al. in prep.). This permanent expansion mode could facilitate the retention of mutations in rapidly evolving genes such as mtDNA (Saavedra & Pena 2005).

The presence of the ancestral lineage in Atlantic bay scallops and the cool-water ancestry of Argopecten (Waller 1969) support the concept that the genus evolved in cool waters. The predominance of H11 could have resulted from a selective sweep of an alternative mtDNA haplotype better adapted to function in the warmer Gulf waters. ATP production by mtDNA is temperature sensitive in marine molluscs because, in high water temperatures, oxygen becomes limited, mitochondria become hypoxic, and anaerobiosis affects ATP production (Sokolova & Portner 2003). Oxygen is important for functioning of both the 12S RNA gene, which assists in assembling amino acids to build proteins used in oxidative phosphorylation, and the ND-1 gene, which provides instructions for making a component of an enzyme complex essential in the oxidative phosphorylation process (Portner et al. 1999, Abele et al. 2002). Positive selection drives mtDNA evolution in animals (Bazin et al. 2006), and a selected haplotype tends to become the major haplotype (Mousset et al. 2004). A contribution of mtDNA HI I to greater efficiency of ATP production in warm water could have facilitated that proliferation of that haplotype in Florida Gulf bay scallops.

The abundance of H11, generation and persistence of low-frequency mutations derived from that haplotype, and far greater mtDNA [[PHI].sub.T] values (nearly an order of magnitude) compared with the allozyme [[THETA].sub.ST] values signal a selective sweep and recovery from a population crash sufficiently in the past to allow 1-step mutations to flourish (Saavedra & Pena 2005). The H15 haplotype cluster (Fig. 3A) may also be such a selective sweep/mutational proliferation in an earlier stage of progress. Collectively, the MSN structure and mismatch statistics reflect all of the processes affecting Florida Gulf bay scallop population genetic structure severe, sporadic population declines or local extinctions and rapid recovery to variable, sometimes high, numbers of individuals: selective sweeps, possibly for metabolic processes in which specific mtDNA haplotypes are beneficial; generation of numerous, closely related haplotypes resulting from relaxed selection during population explosions (Rand 1996, Lessios et al. 2001, Bargelloni et al. 2005); and a coreperiphery metapopulation structure perpetually in nonequilibrium (Slatkin 1977).

Atlantic-Florida Gulf Comparison

Although allozymes differentiate Atlantic subpopulations and Florida Gulf populations only by allele frequencies, mtDNA differentiation is quite distinct. Although Atlantic and Florida Gulf bay scallops could be distinguished by allozymes, we found no fixed allozyme allele frequency differences between the 2 groups, measures of genetic variability were similar, and both groups exhibited a north-to-south trend in increasing heterozygosity. In contrast, mtDNA differentiation between the groups appeared as isolation by distance, widely separated lineages in the cluster and AMOVA analyses, and highly differentiated haplotype frequencies, lineage structures, and demographic histories. Only 4% of the Florida Gulf individuals possessed haplotypes in the Atlantic clades (C3-1 and C3-2), and only NC individuals possessed Florida Gulf haplotypes. In recently diverged taxa, greater differentiation in mtDNA than in nuclear genes is not uncommon because mtDNA effective population sizes are much lower (in the case of hermaphroditic species, half) (Grant & Bowen 1998, Fauvelot et al. 2003).

The two sets of populations also differ greatly in population genetic structure. Atlantic subpopulations are more genetically independent than Florida Gulf populations (except FB). Atlantic lineages are much older and more complex than Florida Gulf lineages. Atlantic subpopulations exhibit considerable evidence of ancient, repeated population declines to low levels and recoveries to moderate levels (Rogers & Harpending 1992, Rogers et al. 1996), whereas Florida Gulf populations exhibit evidence of a single, large, recent population expansion.

Many features of the Atlantic subpopulations contribute to the relatively large interpopulation genetic distances: (l) repeated population depletions resulting from natural and anthropogenic causes and subsequent expansions from sometimes few individuals (Chakraborty & Nei 1977, Gruenthal & Burton 2008), (2) substantial geographic distances devoid of bay scallops except for infrequent ephemeral populations (Bricelj & Krause 1992, Heffernan et al. 1988, Bologna et al. 2001), (3) occurrences limited to bays and sounds with limited water exchange between subpopulations and between them and the open ocean (Peterson & Summerson 1992, Marelli et al. 1997a), (4) probable sweepstakes recruitment (Hedgecock 1994, Li & Hedgecock 1998), and (5) generations of supplementation with bay scallops from other locations (Bert et al. 2007). In contrast, the Florida Gulf CO population resides in nearshore, open-ocean waters: thus, larval transport from that population to the peripheral populations is more likely than it is between Atlantic subpopulations. The critical shallow-water seagrass habitat is distributed more continuously in Florida Gulf waters than in Atlantic waters; geographically large intervals devoid of sea-grasses are not common. Last, no hatchery-based stock enhancement of Florida Gulf bay scallop aggregations preceded our sampling. Thus, Atlantic subpopulations have experienced many generations of genetic bottlenecking, genetic drift, stochastic genetic changes, and extinction of local genomes not experienced by Florida Gulf bay scallops at the population level. Atlantic bay scallops do not exhibit a metapopulation structure but, rather, comprise a set of nearly independent populations.

Taxonomic Puzzles

North Carolina Bay Scallops

The NC population has genetic characteristics indicating that it contains principally A. i. irradians genes, but also possesses A. i. concentricus genes at low frequencies. NC allozyme allele frequencies do not differ significantly from those of other Atlantic populations, and Atlantic allozyme pairwise genetic distances with NC as a pair member are about half the values for NJ/NY pairs. The NC population differs from Florida Gulf populations in a manner similar to that of other Atlantic populations in the number and magnitude of significant allele frequency differences at specific allozyme loci, in overall allele frequencies, and in its positions in all allozyme and mtDNA RFLP cluster analyses. However, compared with other Atlantic populations, NC's allozyme-locus pairwise genetic distances from Florida Gulf populations are significantly (33-50%) smaller, significantly more rare alleles are uniquely shared with Florida populations (P < 0.01, RxC and pairwise G-tests), and highly unlikely rare-allele combinations for Florida Gulf alleles (homozygotes, 2 alleles appearing in 1 individual) occur. Moreover, 15% of the NC individuals possessed Florida Gulf haplotypes H11 or H15, or derivatives of those haplotypes (vs. 0% for NJ and NY). Shared haplotypes from different, high-level clades indicate recent or ongoing secondary contact (Excoffier & Smouse 1994, Carlin et al. 2003). The presence of multiple NC haplotypes derived from the H11 lineage, some sequentially, indicates that H 11 has existed in the NC population for considerable time. Intermittent gene flow between Florida Gulf bay scallops and the NC population must have a long history.

We propose that the NC population subspecies affiliation has long been dubious because both A. i. irradians and A. i. concentricus genes contribute to that population, perhaps in different proportions over time: and because, in scallops, morphological data vary in ways that might not reflect taxonomic affiliation (Heipel et al. 1998). Based on morphology, Clarke (1965) first differentiated northern A. i. irradians and southern A. i. concentricus, assigned the NC population to A. i. concentricus, and noted that Maryland/Virginia waters (probably Chesapeake Bay: Fig. 1A) had an overlap population where both subspecies were found. Soon thereafter, Waller (1969) gave the range of A. i. irradians as Massachusetts to NJ and of A. i. concentricus as NJ to Louisiana, and he cited Clarke (1965) as identifying the bays of both NJ and Maryland as locations of overlap zones. Thus, in early morphologically based taxonomic work, NC bay scallops were deemed to be A. i. concentricus. Wilbur (1995, Wilbur & Gaffney 1997), the first researcher to apply a scientifically controlled approach to bay scallop morphologically based taxonomic classification, reared bay scallops from Massachusetts, NC, and the Florida Gulf in a common garden experiment and performed a detailed morphological analysis on the [F.sub.1] progeny along with wild bay scallops from those 3 locations plus Texas. In a principal components analysis (PCA) of [F.sub.1]-progeny morphometrics and meristics, the Atlantic samples grouped together; however, in a PCA of the wild bay scallop data, NC (then still considered to be A. i. concentricus) and Texas individuals (A. i. amplicostatus) overlapped.

In sharp contrast, we maintain that genetics studies have always shown that NC bay scallops are principally A. i. irradians. However, only very recently has that taxonomic association been recognized, and no genetics study has yet recognized the inclusion of A. i. concentricus genes in that population. Despite genetic evidence to the contrary presented in their papers, multiple researchers held to the identification of NC bay scallops as A. i. concentricus for a number of years. Blake and Graves' (1995) whole-molecule mtDNA RFLP analysis showed that bay scallops from NC more closely resembled A. i. irradians from Massachusetts than A. i. concentricus from the Florida Gulf. In separate cluster analyses, one based on the RFLPs of 2 mtDNA gene fragments (Wilbur 1995) and the other on allozyme loci (Marelli et al. 1997b), NC samples grouped with other Atlantic samples of A. i. irradians on branches clearly and sometimes significantly (Wilbur 1995) separated from the Florida Gulf A. i. concentricus branch. In another analysis of RFLP variation in 2 mtDNA gene fragments (Bologna et al. 2001), nucleotide divergences between NC and Florida Gulf samples were nearly 3-10 times greater than those between NC and other Atlantic samples. Only very recently, Hemond and Wilbur (2011) recognized NC bay scallops as A. i. irradians, based on allele frequency differences at several microsatellite DNA (msDNA) loci.

Close examination of the results presented in past studies also supports our finding that A. i. concentricus genes are present in the NC population. In the cluster phenograms presented by both Wilbur and Gaffney (1997) and Marelli et al. (1997b), the NC sample was included in the A. i. irradians branch but was notably more basal, as it is in our UPGMA phenogram. This position could be expected if that sample contained some A. i. concentricus genes, and Wilbur and Gaffney's (1997) PCA showed a few individuals nested within the Florida Gulf A. i. concentricus group. In Campanella et al.'s (2007) analysis of 8 msDNA loci for Atlantic samples only, all alleles were shared between NY and NJ samples, but the NC sample had unique alleles at 3 loci, leading them to conclude that NJ was the point of contact between northern A. i. irradians and NC A. i. concentricus. However, without including Floridian A. i. concentricus, the greater genetic distance of NC bay scallops from the more closely related northern populations could not be put into its proper perspective. The unique alleles in their NC sample could have been A. i. concentricus alleles embedded in the essentially A. i. irradians population.

The A. i. concentricus genetic input in NC bay scallops could be the product of a former predominance of A. i. concentricus in NC during a warm climatic period and hybridization between the 2 subspecies when A. i. irradians invaded, possibly during a Pleistocene cool period. When closely related species hybridize, nuclear genes may show little indication of interbreeding, but haplotypes characteristic of one species can occur in comparatively high frequencies in the other species because mtDNA does not undergo recombination with each generation. The occurrence of root haplotypes H11 and H15 in NC, and the complexity of NC haplotype relationships in clades C1-14 and C2-6 combined, and their derivation from H11, support this idea. The A. i. concentricus genetic input must have occurred long enough in the past for haplotypes to evolve from H13.

The presence of a few individuals homozygous for rare Florida Gulf allozyme alleles and the existence of common Florida Gulf haplotypes also argue for occasional contemporary dispersal of individuals with Florida Gulfgenomes into the NC population. The probability that those homozygotes would exist in NC A. i. irradians is remarkably low. The broad distributional gap in the Atlantic between east central Florida and southern NC disrupts gene flow from the most likely source of Florida bay scallop alleles in NC the small A. i. concentricus aggregation inhabiting southeastern Florida. But proximity of the Gulf Stream to both coasts may facilitate larval transport from southeastern Florida to NC, particularly when hurricanes travel northward along the Atlantic coast: or boat traffic (e.g., via bilge discharge) may occasionally transport larvae. Hurricane frequency is highest during the late-summer/fall spawning season (http://www.nhc.noaa.gov), and coastal Atlantic hurricanes have been common in some years (e.g., 1972, 1997, 2004; http:// www.nhc.noaa.gov.pastall.shtml) just prior to bay scallop population flushes at some locations in the following years (e.g., 1973 to 1974, 1998, 2004 to 2005: see Bologna et al. (2001) and Campanella et al. (2007)). In addition, Pleistocene fluctuations in sea level have, at times, made the Florida peninsula a less formidable barrier to gene flow between the Gulf of Mexico and Atlantic Ocean (Healy 1975).

Some, but not all, of the samples analyzed in this study were included in Hemond and Wilbur's (2011) msDNA study. It would be interesting to match their NC msDNA genotypes with our genotype/haplotype combinations to investigate further the context of A. i. concentricus genes in the NC population.

Argopecten irradians taylorae

FB is uniquely distinct among Florida bay scallop populations. Although its allozyme diversity was not low compared with other Florida Gulf populations, its mtDNA diversity certainly was. Despite its far smaller sample size, FB had the highest values for all measures of allozyme genetic variability except average number of alleles per locus. In nuclear genes, drift-induced changes in allele frequencies can increase heterozygosity in bottlenecked populations (Leberg 1992, Brookes et al. 1997, Planes & Fauvelot 2002). In sharp contrast, FB was nearly fixed for the most common mtDNA RFLP in Florida Gulf bay scallops, resulting in significantly lower measures of mtDNA genetic diversity compared with other Florida Gulf populations. These extremes affected all pairwise comparisons with FB as a pair member.

Including Atlantic bay scallops in our analyses eliminated the possibility that the FB population is related to A. i. irradians. FB was highly differentiated from all Atlantic samples, including NC. In both allozyme and mtDNA cluster phenograms, FB clearly grouped with Florida Gulf A. i. concentricus collections: and FB was enriched in rare Florida Gulf allozyme alleles as well as in the common Florida Gulf mtDNA haplotype.

The type of contrast in genetic diversity we observed between allozyme loci and mtDNA can result from a brief, severe population bottleneck (Birky 1991, Snowbank & Krajewski 1995, Grant & Bowen 1998). The only indication of a recent genetic bottleneck in the FB allozyme data was a low [[bar.n].sub.a], but the striking contrast between the low mtDNA diversity of our sample (the common Florida Gulf haplotype found in 20 of 21 individuals) and the highly diverse sample analyzed by Blake and Graves (1995) (17 haplotypes found in 34 individuals), clearly demonstrates that a population collapse and regeneration must have occurred sometime between the collection of Blake and Graves" (1995) sample in 1993 and the collection of our sample in 1998. Population expansions and collapses, which can eliminate mtDNA lineages (Carlin et al. 2003) and rare haplotypes (Matocq et al. 2000), have repeatedly occurred in this population at least since 1980 (T. M. Bert and J. M. Stevely, University of Florida Cooperative Extension Service, pers. obs.). The FB population principally inhabits nearly isolated lagoons with restricted water exchange with the open ocean and intermittent extreme phytoplankton blooms (Butler et al. 1995, Phlips et al. 1999, Stevely et al. 2010) that can kill bay scallops. Thus, population crashes of varying magnitude are highly likely. Over time, they have rendered the FB population as genetically differentiated from other Florida Gulf populations as is NC. Nevertheless, our genetic analyses show that the FB population is highly differentiated A. i. concentricus, confirming the opinion of Blake and Graves (1995) and Marelli et al. (1997a) that A. i. taylorae is not a valid subspecies.

Atlantic Bay Scallop Fisheries Management

The large genetic distances between Atlantic populations compared with Florida populations may be, in part, the consequence of both long-term overfishing and repeated bay scallop stock enhancement in the Atlantic. Both heavy harvesting (Allendorf et al. 2008) and stock enhancement (Bert et al. 2007) can perturb genetic population subdivision, increase genetic distances between populations, and cause evolutionarily important genetic damage that not only affects the population's long-term survivability negatively, but also decreases fishery yield. Because all population genetics studies on Atlantic bay scallops have been done after years of problematic fisheries management and of stock enhancement, the natural degree of population connectivity can never be known. Today, we see relatively independent populations that flourish infrequently. Differences in their genetic diversity, population dynamics, degree of geographic and genetic isolation, and ecological history justify their independent management. Although some small amount of gene exchange may occur between bay scallops from separate Atlantic coastal bay systems, reliance on gene flow between populations to supplement depleted stocks is not a viable management option.

Atlantic bay scallop populations have been heavily fished for decades (Bologna et al. 2001). Local fisheries have been allowed to harvest local aggregations heavily, even when densities were low (Peterson & Summerson 1992); and harvest seasons may be timed to maximize yield of muscle per scallop (e.g., Geiger et al. 2006) or to satisfy other economic interests, regardless of spawning season. Bay scallops typically undergo natural interannual fluctuations in population abundance (Rhodes 1991). The abundance of all Atlantic populations is further affected by unpredictable brown and red (Karenia brevis) tides (Tettelbach & Wenczel 1991, Peterson & Summerson 1992, Campanella et al. 2007), which can deplete or destroy aggregations or whole populations and, less frequently, by population explosions of parasites or predators (Tettelbach & Wenczel 1993), which weaken and deplete local aggregations. In the past, affected aggregations refurbished themselves sooner or later, so a liberal harvesting strategy seemed reasonable. However, within the past few decades, loss of critical seagrass habitat (Thayer & Stuart 1974, Pohle et al. 1991) has also contributed to declines in numbers of bay scallops in all areas where they have been traditionally harvested (Tettelbach et al. 1990, Peterson & Summerson 1992, Bologna et al. 2001), and recovery of populations to harvestable densities now can take years (Peterson & Summerson 1992) or decades (Bologna et al. 2001, Tettelbach 2009) because local recruitment is limited when bay scallop density is low (Peterson & Summerson 1992, Arnold et al. 1998), and reliable recruitment from elsewhere is unlikely (this study). Therefore, fisheries managers have turned to various types of stock enhancement to bolster or regenerate Atlantic bay scallop aggregations (Peterson & Summerson 1992, Arnold et al. 1998, Goldberg et al. 2000, Tettelbach et al. 2010; see also Blake and Graves (1995) and Marko and Barr (2007)).

Thus far, stock enhancement efforts of Atlantic bay scallop aggregations have met with varying degrees of success (Arnold 2008). Intensive, multiyear efforts seem to be the most successful (Tettelbach et al. 2010). The high value of bay scallops as a seafood item ensures that efforts to rebuild stocks to harvestable levels will continue, principally through hatchery-based stock enhancement. In early stock enhancement efforts, the number of individuals in and sources of the broodstock, the effective number of spawners contributing to each brood, and the number of broods and of released (seeded) individuals in each brood were typically not published and may not have been recorded. Nor was the genetic diversity of the broodstock or broods estimated before or after release of the broods. Only two assessments of the hatchery contribution to an enhanced stock have been done (Krause 1992, Seyoum et al. 2003, Wilbur et al. 2005). Hatchery-based stock enhancement can alter genetic diversity, decrease fitness, and reduce effective population size, principally through reduction of allelic variability and change in allele frequencies of both the recipient population and the admixed population if the broodstock or released broods are genetically differentiated from the recipient population (Bert et al. 2007). Damage can occur in many direct and indirect ways, even if care is taken to obtain broodstock that is representative of the genetic diversity in the recipient population and to release broods that should not alter the genetic diversity of the recipient population or admixed population after enhancement. The risk of genetic damage to enhanced populations is particularly high when the wild individual-to-hatchery individual ratio is low or the enhancement is repeated (Laikre et al. 2010). The genetic diversity of repeatedly enhanced populations can differ from that of unenhanced populations as much as that of different species (Bert & Tringali 2001).

Two important steps toward minimizing the probability of inadvertent genetic damage to bay scallop populations are to ensure that harvest levels do not impede the population's reproductive potential and to ensure that stock enhancement efforts include a genetic monitoring program. Several models for such a program exist (e.g., Gold 2004, Bert et al. 2007); one has been applied to Florida Gulf bay scallop restoration (Wilbur et al. 2005). However, hatchery-based stock enhancement has limited potential to remedy the problems that chronic overfishing causes. It is, by far, cheaper, easier, and evolutionarily safer to manage fisheries sustainably (e.g., Jackson et al. 2001).

ACKNOWLEDGMENTS

We are grateful to all FWC staff involved with this project for assisting with the collection of Florida samples; to S. Tettelbach, P. Murphy, and P. Bologna for providing Atlantic samples; to S. Stephenson for providing the maps for Figure 1; to T. Jones and S. Campbell for assisting with the genetic analysis' and to S. Tettelbach for reviewing the manuscript. Financial support was provided by NOAA grant NA76FK0426, project FWC 2234, and the state of Florida. The view expressed herein are those of the authors and do not necessarily reflect the views of NOAA or any of its subagencies.

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Tettelbach, S. T. & P. Wenczel. 1993. Reseeding efforts and the status of bay scallop Argopecten irradians (Lamarck, 1819) populations in New York following the occurrence of "brown tide" algal blooms. J. Shellfish Res. 122:423-431.

Thayer, G. W. & H. H. Stuart. 1974. The bay scallop makes its bed of seagrass. Mat. Fish. Rev. 36:27-30.

Wakida-Kusunoki, A. 2009. The bay scallop, Argopecten irradians amplicostatus, in northeastern Mexico. Mat'. Fish. Rev. 71:17-19.

Waller, T. R. 1969. The evolution of the Argopecten gibbus stock (Mollusca: Bivalvia), with special emphasis on the tertiary and quaternary species of North America. J. Paleontol. 43:1-125.

Weir, B. S. & C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evohaion 38:1358-1370.

Wilbur, A. E. 1995. Population genetics of the bay scallop, Argopecten irradians (Lamarck): an analysis of geographic variation and the consequences of self-fertilization. PhD diss., University of Delaware. 128 pp.

Wilbur, A. E. & P. M. Gaffney. 1997. A genetic basis for geographic variation in shell morphology in the bay scallop, Argopecten irradians. Mar. Biol. 128:97-105.

Wilbur, A. E., S. Seyoum, T. M. Bert & W. S. Arnold. 2005. A genetic assessment of bay scallop (Argopecten irradians) restoration efforts in Florida's Gulf of Mexico coastal waters (USA). Conserv. Genet. 6:111-122.

THERESA M. BERT, * WILLIAM S. ARNOLD, ([dagger]) ANNE L. MCMILLEN-JACKSON, AMI E. WILBUR ([double dagger]) AND CHARLES CRAWFORD

Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, 100 Eighth Avenue Southeast, St. Petersburg, Florida 33701

* Corresponding author. E-mail: theresa.bert@myfwc.com

([dagger]) Current address. National Marine Fisheries Service, 203 13th Avenue South, St. Petersburg, FL 33701

([double dagger]) Current address: Department of Biology and Marine Biology and the Center for Marine Science, University of North Carolina-Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409

DOI: 10.2983/035.030.0302
TABLE 1.
Numbers of individuals and collecting locations for a study
of population genetic structure and genetic relationships
of eastern U.S. bay scallops.

                                                 Collecting Years

Group                                             E           R

Atlantic Ocean subpopulation/
    collection
  North Carolina (NC)
    Bogue Sound/Core Sound                      1997        1997
      area (NC97)
    Bogue Sound (NCB98)                         1998        1998
    Core Sound (NCc98)                          1998        1998
  New Jersey, Little Egg Harbor                 1998        1998
    (NJ98)
  New York, Peconic Bay, eastern                1997        1997
  Long Island Sound (NY97)
Florida Gulf of Mexico population/component subpopulations
  Panhandle (PN)
    Saint Andrew Bay (SA)                     1995-1998     1998
    Crooked Island Sound (CI)                 1995-1996      --
    Saint Joseph Bay (SJ)                     1995-1998   1995-1998
  Core (CO)
    Steinhatchee (ST)                         1995-1998   1995-1998
    Cedar Key (CK)                              1997         --
    Homosassa Bay (HO)                        1995-1998   1995-1998
    Hernando County (HE)                      1997-1998      --
    Anclote Estuary (AN)                      1996-1998     1998
  Southwest Florida (SF)
    Tampa Bay (TB)                              1997        1997
    Sarasota Bay (SS)                           1998        1998
    Pine Island Sound (PI)                    1995-1998   1995-1998
    Florida Bay (FB)                            1998        1998
Total

                                                  Total

Group                                           E      R

Atlantic Ocean subpopulation/
    collection
  North Carolina (NC)
    Bogue Sound/Core Sound                       55    24
      area (NC97)
    Bogue Sound (NCB98)                          25    22
    Core Sound (NCc98)                           20    27
  New Jersey, Little Egg Harbor                  20    15
    (NJ98)
  New York, Peconic Bay, eastern                 65    20
  Long Island Sound (NY97)
Florida Gulf of Mexico population/component subpopulation
  Panhandle (PN)
    Saint Andrew Bay (SA)                       129    25
    Crooked Island Sound (CI)                    64   --
    Saint Joseph Bay (SJ)                       154    69
  Core (CO)
    Steinhatchee (ST)                           174    69
    Cedar Key (CK)                               53   --
    Homosassa Bay (HO)                          180    87
    Hernando County (HE)                         41   --
    Anclote Estuary (AN)                        113    41
  Southwest Florida (SF)
    Tampa Bay (TB)                               57    23
    Sarasota Bay (SS)                            35    24
    Pine Island Sound (PI)                      149    66
    Florida Bay (FB)                             35    21
Total                                         1,335   534

Subpopulation and population abbreviations in parentheses. E, samples
used for allozyme electrophoresis; R, samples used for restriction
fragment length polymorphism analysis of mitochondrial DNA; --, no
sample. Collection locations shown in Figure 1.

TABLE 2.
Proteins used to investigate population genetic structure of
Argopecten irradians.

                                                       Enzyme
Abbreviation   Protein                                No. (EC)

AAP            Alanyl aminopeptidase                  3.4.1.-
AAT            Aspartate aminotransferase             2.6.1.1
dPEP           Nonspecific aminopeptidase             3.4.1.-
EST            Esterase                               3.1.-.-
GP             General proteins                          NA
GPI            Glucose-6-phosphate dehydrogenase      5.3.1.9
HDH            Hexanol dehydrogenase                  1.1.1.71
IDH            Isocitrate dehydrogenase               1.1.1.42
LAP            [alpha]-amino acyl peptide hydrolase   3.4.1.-
MDH            Malate dehydrogenase                   1.1.1.37
MPI            Mannose 6-phosphate isomerase          5.3.1.8
PGD            6-phosphogluconate dehydrogenase       1.1.1.44
PGM            Phosphoglucomutase                     5.4.2.2
OPDH           D-octopine dehydrogenase               1.5.1.11
SOD            Superoxide dismutase                   1.15.1.1

                                                      No. of Loci
Abbreviation   Protein                                 Resolved

AAP            Alanyl aminopeptidase                       2
AAT            Aspartate aminotransferase                  2
dPEP           Nonspecific aminopeptidase                  1
EST            Esterase                                    1
GP             General proteins                            l
GPI            Glucose-6-phosphate dehydrogenase           1
HDH            Hexanol dehydrogenase                       1
IDH            Isocitrate dehydrogenase                    1
LAP            [alpha]-amino acyl peptide hydrolase        1
MDH            Malate dehydrogenase                        2
MPI            Mannose 6-phosphate isomerase               1
PGD            6-phosphogluconate dehydrogenase            1
PGM            Phosphoglucomutase                          1
OPDH           D-octopine dehydrogenase                    1
SOD            Superoxide dismutase                        1

Abbreviation   Protein                                Buffer System

AAP            Alanyl aminopeptidase                       PC
AAT            Aspartate aminotransferase                  PC
dPEP           Nonspecific aminopeptidase                  TCI
EST            Esterase                                   TCII
GP             General proteins                           LiOH
GPI            Glucose-6-phosphate dehydrogenase          LiOH
HDH            Hexanol dehydrogenase                       TCI
IDH            Isocitrate dehydrogenase                   TCII
LAP            [alpha]-amino acyl peptide hydrolase       LiOH
MDH            Malate dehydrogenase                       TCII
MPI            Mannose 6-phosphate isomerase              TCII
PGD            6-phosphogluconate dehydrogenase            PC
PGM            Phosphoglucomutase                          PC
OPDH           D-octopine dehydrogenase                    TCI
SOD            Superoxide dismutase                       TCII

                                                      Reference
Abbreviation   Protein                                for Stain

AAP            Alanyl aminopeptidase                      A
AAT            Aspartate aminotransferase                 E
dPEP           Nonspecific aminopeptidase                 G
EST            Esterase                                   E
GP             General proteins                           F
GPI            Glucose-6-phosphate dehydrogenase          G
HDH            Hexanol dehydrogenase                      C
IDH            Isocitrate dehydrogenase                   F
LAP            [alpha]-amino acyl peptide hydrolase       D
MDH            Malate dehydrogenase                       G
MPI            Mannose 6-phosphate isomerase              A
PGD            6-phosphogluconate dehydrogenase           G
PGM            Phosphoglucomutase                         G
OPDH           D-octopine dehydrogenase                   B
SOD            Superoxide dismutase                       D

Buffer systems are as follows. LiOH: electrode, 0.03 M lithium
hydroxide, 0.19 M boric acid, pH 8.1; gel, 0.05 M Tris, 0.008 M
citric acid, pH 8.4, PC: electrode, 0.214 M potassium phosphate,
0.027 M citric acid, pH 6.7, gel, 0.0061 M potassium phosphate,
0.0012 M citric acid, pH 7.0; TCI: electrode, 0.30 M borate, pH
8.2; gel. 0.076 M Tris, 0.005 M citric acid, pH 8.7, TCII:
electrode, 0.687 M Tris, 0.157 M citric acid, pH 8.0: gel, 0.023
M Tris, 0.005 M citric acid, pH 8.0.

References: A, Bricelj and Krause (1992): B, Dando et al. (1981);
C, Dillon and Davis (1980): D, Koehn et al. (1988); E. Murphy et
al. (1990); F, Selander et al. (1971); G, Shaw and Prasad (1970).

NA, not applicable.

TABLE 3.
Allozyme locus allelic frequencies and measures of genetic
variability for bay scallops.

                          Atlantic Ocean Collection/y
                               or Subpopulation

Allozyme                 NC         NC           NC
Diversity                97     [98.sub.B]   [98.sub.C]

Locus/alleles (Number of individuals)

AAP-1
  A                      0.53   ND           ND
  B                      --     ND           ND
  C                      0.04   ND           ND
  D                      0.10   ND           ND
  E                      0.12   ND           ND
  F                      0.21   ND           ND
  (N)                   55
AAP-2                    *
  A                      0.78   ND           ND
  B                      0.10   ND           ND
  C                      0.12   ND           ND
  D                      --     ND           ND
  E                      --     ND           ND
  (N)                   24
AAT-1
  A                      0.90    1.00         0.92
  B                      0.06    --           --
  C                      0.01    --           0.06
  D                      0.03    --           0.02
  (N)                   36      23           25
AAT-2
  A                      0.99    1.00         1.00
  B                      --      --           --
  C                      0.01    --           --
  (N)                   45      25           25
DPEP                     *
  A                      0.65    0.74         0.70
  B                      --      --           --
  C                      0.04    --           0.08
  D                      0.29    0.22         0.20
  E                      0.02    0.04         0.02
  F                      --      --           --
  (N)                   50      25           25
EST                      *
  A                      0.62    0.63         0.50
  B                      0.03    --           --
  C                      0.26    0.24         0.31
  D                      0.06    0.13         0.17
  E                      0.01    --           0.02
  F                      0.02    --           --
  (N)                   46      23           24
GP
  A                      1.00    1.00         1.00
  B                      --      --           --
  C                      --      --           --
  D                      --      --           --
  (N)                   45      22           25
GPI
  A                      0.44    0.36         0.34
  B                     --       0.02        --
  C                      0.22    0.26         0.26
  D                      0.30    0.34         0.34
  E                      0.03    0.02         0.04
  F                      0.01    --           0.02
  G                      --      --           --
  (N)                   55      25           25
HDH
  A                      1.00    1.00         1.00
  B                      --      --           --
  C                      --      --           --
  D                      --      --           --
  (N)                   44      19           21
IDH
  A                      1.00    1.00         1.00
  B                      --      --           --
  C                      --      --           --
  (N)                   46      22           24
LAP                                           *
  A                      0.31    0.08         0.24
  B                      --      --           0.02
  C                      0.36    0.26         0.22
  D                      0.32    0.28         0.20
  E                      0.01    0.12         0.24
  F                      --      0.24         0.08
  G                      --      0.02         --
  (N)                   53      25           25
MDH-1
  A                      1.00    0.98         1.00
  B                      --      --           --
  C                      --      0.02         --
  D                      --      --           --
  (N)                   55      25           25
MDH-2
  A                      1.00    1.00         1.00
  B                      --      --           --
  C                      --      --           --
  D                      --      --           --
  (N)                   51      25           25
MPI                      *
  A                      0.87    0.98         0.98
  B                      0.01    --           --
  C                      0.09    0.02         --
  D                      0.01    --           0.02
  E                      0.02    --           --
  F                      --      --           --
  (N)                   54      25           25
PGD
  A                      0.99    0.94         1.00
  B                      0.01    0.06         --
  C                      --      --           --
  D                      --      --           --
  (N)                   44      25           25
PGM
  A                      0.20    0.34         0.30
  B                      0.21    0.21         0.26
  C                      0.07    0.06         0.06
  D                      0.09    0.04         0.06
  E                      0.18    0.08         0.04
  F                      0.22    0.23         0.28
  G                      0.02    0.04         --
  H                      0.01    --           --
  (N)                   55      24           25
OPDH
  A                      0.82    0.90         0.94
  B                      --      --           --
  C                      0.14    0.06         0.06
  D                      0.02   --            --
  E                      --      0.02         --
  F                      --      0.02         --
  G                      0.02    --           --
  H                      --      --           --
  I                      --      --           --
  (N)                   55      25           25
SOD
  A                      1.00    1.00         1.00
  B                      --      --           --
  C                      --      --           --
  (N)                   55      24           25
Dev. H-W expectations
  No.                    4       0            1
  %                     33       0           13
Genetic variability
  dc[H.sub.o]            0.20    0.23         0.27
  [P.sub.95]            56      44           50
  [[P.sub.99]           67      56           56
  [[bar.n].sub.a]        3.2     2.5          2.6

                        Atlantic Ocean Collection/y
                          or Subpopulation

Allozyme                  NC      NJ      NY
Diversity                 SP      98      97

Locus/alleles (Number of individuals)

AAP-1
  A                       0.53    0.63    0.49
  B                       --      --      --
  C                       0.04    0.02    0.05
  D                       0.10    0.13    0.15
  E                       0.12    0.10    0.19
  F                       0.21    0.12    0.12
  (N)                    55      20      65
AAP-2                     *               *
  A                       0.78    0.81    0.88
  B                       0.10    0.03    0.08
  C                       0.12    0.16    0.04
  D                       --      --      --
  E                       --      --      --
  (N)                    24      19      25
AAT-1
  A                       0.94    1.00    0.98
  B                       0.02    --      0.02
  C                       0.02    --      --
  D                       0.02    --      --
  (N)                    84      18      48
AAT-2                                     *
  A                       0.99    1.00    0.97
  B                       --      --      0.02
  C                       0.01    --      0.01
  (N)                    95      19      63
DPEP                      *       *       *
  A                       0.69    0.47    0.78
  B                       --      --      --
  C                       0.04    0.06    0.09
  D                       0.24    0.47    0.10
  E                       0.03   --       0.03
  F                       --      --      --
  (N)                   100      17      60
EST                       *
  A                       0.59    0.65    0.58
  B                       0.02   --      --
  C                       0.27    0.17    0.39
  D                       0.10    0.10    0.02
  E                       0.01    0.08    0.01
  F                       0.01   --      --
  (N)                    93      20      58
GP
  A                       1.00    1.00    1.00
  B                       --       --      --
  C                       --       --      --
  D                       --       --      --
  (N)                    92       8      59
GPI
  A                       0.40    0.48    0.35
  B                       0.01    --      --
  C                       0.24    0.12    0.08
  D                       0.32    0.40    0.52
  E                       0.03     --     0.04
  F                      <0.01     --     0.01
  G                       --       --      --
  (N)                   105      20      65
HDH
  A                       1.00    1.00    1.00
  B                       --       --      --
  C                       --       --      --
  D                       --       --      --
  (N)                    84      16      47
IDH
  A                       1.00   ND       1.00
  B                       --     ND       --
  C                       --     ND       --
  (N)                    92              53
LAP                               *       *
  A                       0.24    0.05    0.36
  B                       0.01    --      --
  C                       0.30    0.75    0.41
  D                       0.28    0.15    0.16
  E                       0.09    0.05    0.05
  F                       0.07    --      0.02
  G                       0.01    --      --
  (N)                   103      10      65
MDH-1
  A                       0.99    1.00    1.00
  B                       --      --      --
  C                       0.01    --      --
  D                       --      --      --
  (N)                   105      20      65
MDH-2
  A                       1.00    1.00    0.99
  B                       --      --      --
  C                       --      --      0.01
  D                       --      --      --
  (N)                   101      20      63
MPI                       *               *
  A                       0.92    0.90    0.95
  B                       0.01    0.05    --
  C                       0.05    0.02    0.01
  D                       0.01    0.03    0.04
  E                       0.01    --      --
  F                       --      --      --
  (N)                   104      20      64
PGD
  A                       0.98    0.95    0.98
  B                       0.02    0.05    0.02
  C                       --      --      --
  D                       --      --      --
  (N)                    94      20      55
PGM
  A                       0.25    0.10    0.04
  B                       0.22    0.30    0.40
  C                       0.07    0.15    0.08
  D                       0.07    --      0.14
  E                       0.12    0.10    0.12
  F                       0.24    0.23    0.16
  G                       0.02    0.10    0.06
  H                       0.01    0.02    --
  (N)                   104      20      55
OPDH                                      *
  A                       0.88    0.90    0.91
  B
  C                       0.08    0.08    0.05
  D                       0.01     --     0.02
  E                       0.01     --     --
  F                       0.01    0.02    0.01
  G                       0.01            0.01
  H                       --       --      --
  I                       --       --      --
  (N)                   105      20      65
SOD                                       *
  A                       1.00    1.00    0.97
  B                       --      --      0.02
  C                       --      --      0.01
  (N)                   104      20      64
Dev. H-W expectations
  No.                     4       2       6
  %                      31      20      43
Genetic variability
  dc[H.sub.o]             0.23    0.18    0.18
  [P.sub.95]             56      56      44
  [[P.sub.99]            61      56      72
  [[bar.n].sub.a]         3.6     2.6     3.2

                            Florida Gulf of Mexico Population

Allozyme
Diversity                  PN         CO         SF       FB

Locus/alleles (Number of individuals)

AAP-1                       0/3      2/5          0/3
  A                         0.48       0.41       0.45    0.33
  B                         0.01       --         0.04    --
  C                         0.03       0.02       0.04    --
  D                         0.29       0.28       0.24    0.32
  E                         0.10       0.18       0.15    0.30
  F                         0.10       0.11       0.10    0.05
  (N)                     318        544        221      30
AAP-2                       3/3        4/5        1/3
  A                         0.91       0.79       0.80    0.62
  B                         0.01       0.04       0.10    --
  C                         0.06       0.16       0.12    0.21
  D                         0.01       0.03       0.03    0.17
  E                         --         0.01       --      --
  (N)                     235        425        161      29
AAT-1                       0/3        1/5        1/3
  A                         0.99       0.99       0.98    1.00
  B                        <0.01       0.01       0.01    --
  C                         0.01      <0.01       0.01    --
  D                         --         --        <0.01    --
  (N)                     303        508        219      33
AAT-2                     0/3          0/5        1/3     --
  A                         0.98      >0.99       0.98    0.97
  B                         0.02      <0.01       0.01    --
  C                        <0.01      <0.01       0.01    0.03
  (N)                     335        526        234      35
DPEP                        3/3        4/5        3/3
  A                         0.59       0.63       0.58    0.46
  B                         0.01       0.01       --      0.01
  C                         0.07       0.04       0.02    0.17
  D                         0.24       0.24       0.28    0.27
  E                         0.09       0.08       0.12    0.09
  F                         0.01       --         --      --
  (N)                     303        456        233       5
EST                         3/3        4/5        2/3
  A                         0.51       0.57       0.51    0.54
  B                         0.06       0.04       0.03    0.03
  C                         0.37       0.31       0.37    0.31
  D                         0.05       0.05       0.07    0.07
  E                         0.01       0.05       0.04    0.04
  F                         0.01       0.01       --      0.01
  (N)                     336        494        221      35
GP                          0/3        0/5        1/3
  A                        >0.99      >0.99      >0.99    0.96
  B                        <0.01      <0.01      --       --
  C                         --         --        <0.01    0.02
  D                         --         --        <0.01    0.02
  (N)                     322        514        216      31
GPI                         0/3        0/5        0/3
  A                         0.59       0.61       0.57    0.70
  B                         --         --         --      --
  C                         0.04       0.05       0.05    0.07
  D                         0.37       0.33       0.36    0.23
  E                         --         0.01       0.01    --
  F                         0.01       0.01       0.01    --
  G                         --         --         0.01    --
  (N)                     247        561        241      35
HDH                         1/3        2/5        1/3
  A                         0.99       0.99       0.99    0.98
  B                         0.01       0.01       0.01    --
  C                        <0.01      <0.01      <0.01    --
  D                        <0.01      <0.01      --       0.02
  (N)                     287        308        197      34
IDH                         0/3        0/5        0/3     --
  A                        >0.99      >0.99       0.99    1.00
  B                        <0.01      <0.01      <0.01    --
  C                        <0.01      <0.01       0.01    --
  (N)                     293        428        183      22
LAP                         2/3        2/5        3/3
  A                         0.44       0.47       0.40    0.19
  B                         0.01       --         0.01    --
  C                         0.28       0.19       0.20    0.08
  D                         0.19       0.29       0.21    0.48
  E                         0.08       0.04       0.11    0.25
  F                         0.01       --         0.10    --
  G                        --          0.01       --      --
  (N)                     332        394        222      24
MDH-1                       0/3        0/5        0/3
  A                        >0.99       0.99       0.99    0.99
  B                        <0.01       --         --      --
  C                        <0.01      <0.01               0.01
  D                         --         0.01      <0.01   --
  (N)                     349        558        240      35
MDH-2                       0/3        0/5        0/3     0.01
  A                        >0.99      >0.99       0.99    1.00
  B                        <0.01      <0.01       --
  C                        --         <0.01       0.01    --
  D                        <0.01      --          --      --
  (N)                     340        542        231      30
MPI                         3/3        5/5        3/3
  A                         0.85       0.87       0.85    0.84
  B                         0.04       0.02       0.02    0.03
  C                         0.06       0.04       0.06    0.01
  D                         0.06       0.06       0.05    0.06
  E                         0.02       0.02       0.03    0.06
  F                         --         --         0.01    --
  (N)                     326        550        227      35
PGD                         1/3        1/5        0/3
  A                         0.97       0.95       0.96    0.92
  B                         0.01       0.03       0.03    0.03
  C                         0.01       0.01       0.01   --
  D                         0.01       0.01      <0.01    0.05
  (N)                     246        523        224      30
PGM                         3/3        3/5        1/3
  A                         0.47       0.43       0.48    0.42
  B                         0.01       --         0.01    0.01
  C                         0.03       0.04       0.05    --
  D                         0.25       0.20       0.21    0.13
  E                         0.15       0.17       0.17    0.17
  F                         0.05       0.09       0.03    0.17
  G                         0.02       0.05       0.04    0.06
  H                         0.02       0.02       0.01    0.04
  (N)                     341        543        231      35
OPDH                        1/3       15          0/3
  A                         0.82       0.80       0.73    0.74
  B                        <0.01      <0.01      <0.01    0.04
  C                         0.10       0.13       0.22    0.10
  D                         0.02       0.02       0.01    --
  E                        <0.01       0.01       0.01    --
  F                         0.05       0.02       0.02    0.06
  G                        <0.01       0.01       0.01    0.06
  H                         0.01       0.01      <0.01    --
  I                        --         <0.01      --
  (N)                     349        550        241      35
SOD                         0/3        0/5        0/3
  A                         1.00       1.00      >0.99    1.00
  B                         --         --        <0.01    --
  C                         --
  (N)                     348        551        241      35
Dev. H-W expectations
  No.                      20/54      28/90      17/54    2
  %                        37         31         31      14
Genetic variability
  dc[H.sub.o]               0.19       0.21       0.21    0.25
  [P.sub.95]               50         50         50      56
  [[P.sub.99]              63         61         74      78
  [[bar.n].sub.a]           3.5        3.4        3.5     3.2

Allozyme abbreviations are defined in Table 2. Collections,
subpopulations (SP), and populations are defined in Table 1 and
shown in Figure 1. Fractions above allelic frequencies for
Florida Gulf populations are the proportions of the population's
component subpopulations (Fig. 1) deviating from Hardy-Weinberg
(H-W) genotype equilibrium expectations. Dev. H-W expectations,
number of loci and percent of all polymorphic loci deviating
significantly from H-W expectations: ND, no data: * , individual
locus deviated significantly (P [less than or equal to] 0.05)
from H-W expectations after correction for multiple tests at that
locus: de [[bar.H].sub.o] direct count heterozygosity:
[P.sub.95], [P.sub.99], percentage of loci polymorphic when
frequency of most common allele is, respectively. [less than or
equal to] 0.95 or [less than or equal to] 0.99: [[bar.n].sub.a],
average number of alleles per locus: --, frequencies of 0.00.

TABLE 4.
Significance values for pairwise tests for genetic homogeneity of
bay scallop allozyme allelic frequencies at polymorphic loci. (A)
Paired Florida Gulf of Mexico populations.

                              Locus

Pop. 1          Pop. 2        AAP-1          AAP-2

PN                CO        P < 0.01#     P < 0.0001#
PN                SF            NS        P < 0.0001#
PN                FB        P < 0.01#     P < 0.0001#
CO                SF            NS            NS
CO                FB            NS            NS
SF                FB          P<0.05          NS

(B) Atlantic subpopulations paired with Florida populations.

                              Locus
Atlantic        Florida
Subpop.        Gulf Pop.      AAP-1          AAP-2

NC                PN        P < 0.005#        NS
NC                CO        P < 0.005#        NS
NC                SF       P < 0.0001#        NS
NC                FB        P < 0.001#        NS
NJ                PN            NS            NS
NJ                CO            NS            NS
NJ                SF        P < 0.001#        NS
NJ                FB         P < 0.05         NS
NY                PN         P < 0.05         NS
NY                CO            NS            NS
NY                SF       P << 0.0001#       NS
NY                FB         P < 0.05       P<0.05

(C) All pairwise combinations of Atlantic subpopulations and
Florida Gulf populations, all loci.

                           Atlantic Subpop.

Group             NC            NJ            NY

Atlantic
subpop.

NC                --
NJ              0.037#          --

Florida pop.

PN                ***          ***            ***
CO                ***          ***            ***
SF                ***          ***            ***
FB                ***          ***            ***

                                Locus

Pop. 1            DPEP           LAP          OPDH

PN                 NS        P < 0.0001#    P ~ 0.05
PN             P < 0.005#    P < 0.001#    P < 0.001#
PN                 NS        P < 0.0001#       NS
CO              P ~ 0.05     P < 0.0001#    P < 0.05
CO              P < 0.025    P < 0.0001#       NS
SF             P < 0.005#      P<0.01#         NS

(B) Atlantic subpopulations paired with Florida populations.

                                        Locus
Atlantic
Subpop.            GPI           LAP           PGM          OPDH

NC             P < 0.0001#   P < 0.005#    P < 0.0001#       NS
NC             P < 0.0001#   P < 0.0001#   P < 0.0001#       NS
NC             P < 0.0001#    P < 0.025    P < 0.0001#     P<0.01
NC             P ~ 0.005#     P < 0.05         NS            NS
NJ                 NS         P < 0.05     P < 0.005#        NS
NJ                 NS        P < 0.005#     P < 0.01#        NS
NJ                 NS         P < 0.01#    P < 0.001#        NS
NJ                 NS        P < 0.005#     P < 0.05#        NS
NY             P < 0.005#        NS        P < 0.0001#    P ~ 0.05
NY             P < 0.001#    P < 0.001#    P < 0.001#     P <0.05
NY             P ~ 0.005#    P < 0.001#    P < 0.0001#   P < 0.001#
NY             P ~ 0.005#    P < 0.0001#   P < 0.0001#    P = 0.05

(C) All pairwise combinations of Atlantic subpopulations and
Florida Gulf populations, all loci.

                             Florida Pop.

Group           Panhandle       Core        Southern

Atlantic
subpop.

NC
NJ

Florida pop.

PN                 --
CO               0.002#          --
SF                 ***          0.057          --
FB                 ***           ***           ***

*** Cell significance of P [less than or equal to] 0.001 and
tablewide significance of P [less than or equal to] 0.05, after
correction for multiple tests of the null hypothesis.
Subpopulations (Subpop.) and populations (Pop.) defined in Table
l, shown in Figure 1; loci defined in Table 2. Bold print: (A)
and (B), significant after sequential Bonferroni adjustment for
multiple tests of the null hypothesis of no cell significance;
(C) cell significance only.

NS, not significant.

Note: Bold print: (A) and (B), significant after sequential
Bonferroni adjustment for multiple tests of the null hypothesis
of no cell significance; (C) cell significance only is indicated
with #.

TABLE 5.
Matrices of bay scallop allozyme--allele pairwise genetic distances
(X[10.sup.3]).

(A) Atlantic collections.

Collection         NC97   [NC.sub.B]98   [NC.sub.C]98   NJ98   NY97

NC97               --      0              0             22     24
NCB98               5     --              0             24     26
NCc98               l      3             --             42     18
NJ98               10     17             16             --     48
NY97                9     17              6             18

[[THETA].sub.]ST], above bars; Nei's D, below bars.

(B) Atlantic subpopulations (Subpop.) and Florida populations (Pop.).

                                   Atlantic subpop.

Group                   NC              NJ              NY

Atlantic subpop.

NC                      --              29              24
NJ                      10              --              48
NY                       9              18              --

Florida pop.

PN                 15 [+ or -] 3   32 [+ or -] 2   22 [+ or -] 1
CO                 14 [+ or -] 4   36 [+ or -] 6   24 [+ or -] 4
SF                 16 [+ or -] 3   35 [+ or -] 7   27 [+ or -] 4
FB                      22              42              42

                             Florida pop.

Group                Panhandle          Core

Atlantic subpop.

NC                 40 [+ or -] 4   36 [+ or -] 9
NJ                 81 [+ or -] 8   86 [+ or -] 13
NY                 60 [+ or -] 3   64 [+ or -] 9

Florida pop.

PN                      --          9 [+ or -] 4
CO                  4 [+ or -] 2         --
SF                  4 [+ or -] 2    2 [+ or -]  1
FB                 17 [+ or -] 2   11 [+ or -] 2

                              Florida pop.

Group                 Southern           FB

Atlantic subpop.

NC                 38 [+ or -] 8          48
NJ                 79 [+ or -] 17         91
NY                 69 [+ or -] 12        101

Florida pop.

PN                  9 [+ or -] 5    44 [+ or -] 1
CO                  8 [+ or -] 5    26 [+ or -] 7
SF                       --         30 [+ or -] 4
FB                 14 [+ or -] 2         --

(B) Atlantic subpopulations (Subpop.) and Florida populations (Pop.).

                                   Atlantic subpop.

Group                   NC              NJ              NY

Atlantic subpop.

NC                      --              29              24
NJ                      10              --              48
NY                       9              18              --

Florida pop.

PN                 15 [+ or -] 3   32 [+ or -] 2   22 [+ or -] 1
CO                 14 [+ or -] 4   36 [+ or -] 6   24 [+ or -] 4
SF                 16 [+ or -] 3   35 [+ or -] 7   27 [+ or -] 4
FB                      22              42              42

                             Florida pop.

Group                Panhandle          Core

Atlantic subpop.

NC                 40 [+ or -] 4   36 [+ or -] 9
NJ                 81 [+ or -] 8   86 [+ or -] 13
NY                 60 [+ or -] 3   64 [+ or -] 9

Florida pop.

PN                      --          9 [+ or -] 4
CO                  4 [+ or -] 2         --
SF                  4 [+ or -] 2    2 [+ or -]  1
FB                 17 [+ or -] 2   11 [+ or -] 2

                              Florida pop.

Group                 Southern           FB

Atlantic subpop.

NC                 38 [+ or -] 8          48
NJ                 79 [+ or -] 17         91
NY                 69 [+ or -] 12        101

Florida pop.

PN                  9 [+ or -] 5    44 [+ or -] 1
CO                  8 [+ or -] 5    26 [+ or -] 7
SF                       --         30 [+ or -] 4
FB                 14 [+ or -] 2         --

[[THETA].sub.ST], above bars; Nei's D, below bars.

Groups shown in Figure 1. See text for method of calculating values
presented as mean [+ or -] SD.

TABLE 6.
Significant statistical groupings of average pairwise genetic
distances (X [10.sup.3]) between bay scallop subpopulations and
populations.

Category Data            Statistic           Means and statistically
set: pairs                                      similar groupings
used, n values

A. Between
Atlantic
subpopulations

Allozyme loci;    Nei's D                     NC/NC         NC/NY
  all pairs:                                    3            11
  n = 3

                                           (NJ/NY = 18)

                  [[THETA].sub.ST]            NC/NC         NC/NY
                                                0            23

                                           (NJ/NY = 48)
B. Between
Atlantic and
Florida Gulf
bay scallops

Allozyme loci;    Nei's D, *                  CO/CO         PN/PN
  Atlantic                                      1             2
  subpopulations
  and Florida                                 FB/CO      NC-NY/NC-NY
  populations,                                  11           12
  all pairwise                                NY/PN         NY/CO
  combinations:                                 22           24
  CO/CO, n = 10;
  PN/CO, CO /FS,
  n = 15; PN
  /FS, n = 9;
  CO/FB, NC/CO,
  NJ/CO, NY/CO,
  n = 5; all
  others,
  n = 3

                  [[THETA].sub.ST1.sup.*]     CO/CO         PN/PN
                                                2             4

                                              FB/CO         FB/SF
                                                26           30
                                              NY/PN         NY/CO
                                                59           65

                  Nei's [D.sub.2]            FLA/FLA       FB/FLA
                                                3            12

                  [[THETA].sub.ST2]          FLA/FLA       FB/FLA
                                                7            32

mtDNA; Atlantic   [[PHI].sub.ST]             FLA/FLA       FLA/FB
  subpopulations                                1             2
  and Florida
  populations;
  FLA /FLA, n =
  28; FLA/ FB,
  n = 8,
  FLA /NC-NY,
  n = 24; NC-NY/
  NC-NY, FB/
  NC-NY, n = 3

Category Data            Statistic           Means and statistically
set: pairs                                      similar groupings
used, n values

A. Between
Atlantic
subpopulations

Allozyme loci;    Nei's D                     NC/NJ
  all pairs:                                   14
  n = 3

                  [[THETA].sub.ST]            NC/NJ
                                               29

B. Between
Atlantic and
Florida Gulf
bay scallops

Allozyme loci;    Nei's D, *                  PN/CO        CO/SF
  Atlantic                                      4            4
  subpopulations
  and Florida                                 FB/SF        NC/CO
  populations,                                 14            14
  all pairwise                                NY/SF        NJ/PN
  combinations:                                27            32
  CO/CO, n = 10;
  PN/CO, CO /FS,
  n = 15; PN
  /FS, n = 9;
  CO/FB, NC/CO,
  NJ/CO, NY/CO,
  n = 5; all
  others,
  n = 3

                  [[THETA].sub.ST1.sup.*]     SF/CO        PN/CO
                                                8            9

                                           NC-NY/NC-NY     NC/CO
                                               34            35
                                              NY/SF        NJ/PN
                                               69            79

                  Nei's [D.sub.2]          NC-NY/NC-NY     NC/FLA
                                               13            15

                  [[THETA].sub.ST2]          NC/ FLA    NC-NY/ NC-NY
                                               38            45

mtDNA; Atlantic   [[PHI].sub.ST]           NC-NY/NC-NY   FLA/NC-NY
  subpopulations                                8            53
  and Florida
  populations;
  FLA /FLA, n =
  28; FLA/ FB,
  n = 8,
  FLA /NC-NY,
  n = 24; NC-NY/
  NC-NY, FB/
  NC-NY, n = 3

Category Data            Statistic         Means and statistically
set: pairs                                      similar groupings
used, n values

A. Between
Atlantic
subpopulations

Allozyme loci;    Nei's D
  all pairs:
  n = 3

                  [[THETA].sub.ST]

B. Between
Atlantic and
Florida Gulf
bay scallops

Allozyme loci;    Nei's D, *                PN /SF       SF/SF
  Atlantic                                     4           6
  subpopulations
  and Florida                                NC/PN       NC/SF
  populations,                                15          16
  all pairwise                               NJ/SF     NC-NY/FB
  combinations:                               35          35
  CO/CO, n = 10;
  PN/CO, CO /FS,
  n = 15; PN
  /FS, n = 9;
  CO/FB, NC/CO,
  NJ/CO, NY/CO,
  n = 5; all
  others,
  n = 3

                  [[THETA].sub.ST1.sup.*]    PN/SF       SF/SF
                                              10          11

                                             NC/SF       NC/PN
                                              38          40
                                             NJ/SF     NC-NY/ FB
                                              79          81

                  Nei's [D.sub.2]           NY/FLA      NJ/FLA
                                              24          35

                  [[THETA].sub.ST2]         NY/FLA     NC-NY/FB
                                              64          81

mtDNA; Atlantic   [[PHI].sub.ST]           FB/NC-NY
  subpopulations                              63
  and Florida
  populations;
  FLA /FLA, n =
  28; FLA/ FB,
  n = 8,
  FLA /NC-NY,
  n = 24; NC-NY/
  NC-NY, FB/
  NC-NY, n = 3

Category Data            Statistic          Means and statistically
set: pairs                                     similar groupings
used, n values

A. Between
Atlantic
subpopulations

Allozyme loci;    Nei's D
  all pairs:
  n = 3
                  [[THETA].sub.ST]

B. Between
Atlantic and
Florida Gulf
bay scallops

Allozyme loci;    Nei's D, *
  Atlantic
  subpopulations
  and Florida                                   FB/PN
  populations,                                  17
  all pairwise                                  NJ/CO
  combinations:                                 36
  CO/CO, n = 10;
  PN/CO, CO /FS,
  n = 15; PN
  /FS, n = 9;
  CO/FB,  NC/CO,
  NJ/CO, NY/CO,
  n = 5; all
  others,
  n = 3

                  [[THETA].sub.ST1.sup.*]

                                                FB/PN
                                                44
                                                NJ/CO
                                                86

                  Nei's [D.sub.2]               NC-NY/FB
                                                35

                  [[THETA].sub.ST2]             NJ/FLA
                                                82

mtDNA; Atlantic   [[PHI].sub.ST]
  subpopulations
  and Florida
  populations;
  FLA /FLA, n =
  28; FLA/ FB,
  n = 8,
  FLA /NC-NY,
  n = 24; NC-NY/
  NC-NY, FB/
  NC-NY, n = 3

Category Data            Statistic
set: pairs                                 Probability level
used, n values

A. Between
Atlantic
subpopulations

Allozyme loci;    Nei's D                  P < 0.05
  all pairs:
  n = 3
                  [[THETA].sub.ST]         P < 0.001

B. Between
Atlantic and
Florida Gulf
bay scallops

Allozyme loci;    Nei's D, *               P [less than or
  Atlantic                                 equal to] 0.0001
  subpopulations
  and Florida
  populations,
  all pairwise
  combinations:
  CO/CO, n = 10;
  PN/CO, CO /FS,
  n = 15; PN
  /FS, n = 9;
  CO/FB, NC/CO,
  NJ/CO, NY/CO,
  n = 5; all
  others,
  n = 3

                  [[THETA].sub.ST1.sup.*]  P [less than or
                                           equal to] 0.0001

                  Nei's [D.sub.2]          P < 0.0001

                  [[THETA].sub.ST2]        P < 0.0001

mtDNA; Atlantic   [[PHI].sub.ST]           P < 0.0001
  subpopulations
  and Florida
  populations;
  FLA /FLA, n =
  28; FLA/ FB,
  n = 8,
  FLA /NC-NY,
  n = 24; NC-NY/
  NC-NY, FB/
  NC-NY, n = 3

Nei's D, [[THETA].sub.ST], and [[PHI].sub.ST] (all defined in
Methods) mean values x[10.sup.3]. Atlantic subpopulation means are
averages of appropriate pairwise distance values in Table 5A.
Florida Gulf means were obtained from Bert et al. (in prep.).
Except for Nei's D * and OST * are all are underlined.
Subpopulations, where only the single lowest and 3 highest groupings
underlined, statistically homogeneous groupings and populations are
defined in Table 1 and are shown in Figure 1.

TABLE 7.
Bay scallop mitochondria) DNA nucleotide base-pair
fragment sizes for the 12s/ND1 fragment.

Enzyme     Identifier   Pattern

ScrF I         A        488 145 200
               B        488 345
               C        488 145 100 100
               D        310 178 200 145
               E        406 200 145 82

Tsp509 I       A        413 264 156
               B        264 241 172 156
               C        314 264 156 99
               D        413 200 156 64
               E        833

Alu I          A        682 72 51 28#
               B        625 72 57 51 28#
               C        392 290 72 51 28#
               D        692 123 28#
               E        710 72 51
               F        504 178 72 51 28#

Rsa I          A        437 228 112 56 52#
               B        665 112 56
               C        437 228 168
               D        437 176 112 56 52#
               E        273 228 164 112 56

HinF I         A        544 281 8#
               B        544 194 87 8#
               C        833
               D        474 281 70 8#
               E        454 194 90 87 8#

BsiHKA I       A        621 212
               B        833
               C        621 192 20#

BGL II         A        418 415
               B        833
               C        415 298 120

Ban II         A        481 323 29#
               B        833
               C        510 323

Taq I          A        598 235
               B        833
               C        598 225 10#
               D        375 235 223

Underlined estimates were inferred from discrepancies between the
uncut PCR product and the sum of the visualized fragments.

Note: Estimates indicated with # are inferred from discrepancies
between the uncut PCR product and the sum of the visualized
fragments.

TABLE 8.
RFLP haplotype frequencies and diversity measures for the bay scallop
mtDNA 12s/NDI segment.

                       Atlantic Ocean Collection/y or Subpopulation

                     [NC.sub.1]   [NC.sub.2]   NC      NJ      NY
Hap.
No.    Designation       98           98        SP      98      97

       n             22           27           49      20      15

       h              0.49         0.58         0.54    0.56    0.76

       [pi]           0.58         0.68         0.62    0.92    0.54

1      AAAEAAAAA      --           --           --      1       1
2      BABABAAAA     17           16           33      13       4
3      BAAABAAAA      1            1            2       --      6
4      BADABAAAA      --           --           --      --      1
5      BAAACAAAA      --           --           --      --      2
6      BABABBAAA      --           --           --      --      1
7      AAAECAAAA      --           --           --      3       --
8      AAAEBAAAA      --           --           --      1       --
9      BABACAAAA      --           2            2       1       --
10     BAAEAAAAA      --           --           --      1       --
II     AAAAAAAAA      1            2            3       --      --
12     BABABAABA      1            --           1       --      --
13     AAAAAAABA      1            1            2       --      --
14     AAAEAAABA      --           1            1       --      --
15     BABAAAAAA      1            1            2       --      --
16     BABEAAAAA      --           1            1       --      --
17     AABABAABA      --           2            2       --      --
18     AAFAAAAAA      --           --           --      --      --
19     AAAAABAAA      --           --           --      --      --
20     AAAAAAAAC      --           --           --      --      --
21     AAAABAAAA      --           --           --      --      --
22     AADAAAAAB      --           --           --      --      --
23     AADADAAAA      --           --           --      --      --
24     AAABAAAAC      --           --           --      --      --
25     AAAAAAACA      --           --           --      --      --
26     BABBAAAAD      --           --           --      --      --
27     ABDAEAAAA      --           --           --      --      --
28     AADAAAAAA      --           --           --      --      --
29     AAAACAAAA      --           --           --      --      --
30     AAAAAABAA      --           --           --      --      --
31     AAABAAAAA      --           --           --      --      --
32     AAAADAAAA      --           --           --      --      --
33     AACAAAAAA      --           --           --      --      --
34     BAFABAAAA      --           --           --      --      --
35     BAAAAAAAA      --           --           --      --      --
36     AABAAAAAA      --           --           --      --      --
37     AAAAAAAAB      --           --           --      --      --
38     AAEAAAAAA      --           --           --      --      --
39     AAAAABAAC      --           --           --      --      --
40     AACAABAAA      --           --           --      --      --
41     ABAAAAAAA      --           --           --      --      --
42     BABAAACAA      --           --           --      --      --
43     AEAAAAAAB      --           --           --      --      --
44     AAFBAAAAA      --           --           --      --      --
45     BABAACAAA      --           --           --      --      --
46     AADAABAAA      --           --           --      --      --
47     DADAAAAAA      --           --           --      --      --
48     ACAAAAAAA      --           --           --      --      --
49     ADAAAAAAA      --           --           --      --      --
50     BBBAAAAAA      --           --           --      --      --
51     BABAABAAA      --           --           --      --      --
52     BABABAAAC      --           --           --      --      --
53     CAAAAAAAA      --           --           --      --      --

                              Florida Gulf of Mexico Population

Hap.
No.    Designation       PN             CO             SF         FB

       n              94            198            113            21
                     (14-25)       (14-31)        (12-25)

       h              0.52           0.50           0.54         0.09
                     (0.360         (0.36-0        (0.36-0

       [pi]           1.21           1.17           1.23         0.28
                     (0.90-1.39)    (0.85-1.34)    (0.90-1.42)
1      AAAEAAAAA      1              1             --            --
2      BABABAAAA      2              5              4            --
3      BAAABAAAA      --             1              1            --
4      BADABAAAA      --            --             --            --
5      BAAACAAAA      --            --             --            --
6      BABABBAAA      --            --              1            --
7      AAAECAAAA      --            --             --            --
8      AAAEBAAAA      --            --             --            --
9      BABACAAAA      --            --             --            --
10     BAAEAAAAA      --            --             --            --
II     AAAAAAAAA     67            139             76            20
12     BABABAABA      --            --             --            --
13     AAAAAAABA      --             5              1            --
14     AAAEAAABA      --            --                           --
15     BABAAAAAA      3              3              4            --
16     BABEAAAAA      --            --             --            --
17     AABABAABA      --            --             --            --
18     AAFAAAAAA      1              2              1            1
19     AAAAABAAA      4              4              6            --
20     AAAAAAAAC      --             1              2            --
21     AAAABAAAA      2              1              5            --
22     AADAAAAAB      --             1              1            --
23     AADADAAAA      --            --              1            --
24     AAABAAAAC      --            --              1            --
25     AAAAAAACA      --            --              1            --
26     BABBAAAAD      --            --              1            --
27     ABDAEAAAA      --            --              1            --
28     AADAAAAAA      2              1              1            --
29     AAAACAAAA      1              1              1            --
30     AAAAAABAA      --            --              1            --
31     AAABAAAAA      1              3              1            --
32     AAAADAAAA                    --              1            --
33     AACAAAAAA      2              3              1            --
34     BAFABAAAA      --             1             --            --
35     BAAAAAAAA      --             1             --            --
36     AABAAAAAA      1              1             --            --
37     AAAAAAAAB      3              8             --            --
38     AAEAAAAAA      --             2             --            --
39     AAAAABAAC      1              1             --            --
40     AACAABAAA      --             1             --            --
41     ABAAAAAAA      1              1             --            --
42     BABAAACAA      --             1             --            --
43     AEAAAAAAB      --             1             --            --
44     AAFBAAAAA      --             1             --            --
45     BABAACAAA      --             1             --            --
46     AADAABAAA      --             1             --            --
47     DADAAAAAA      --             1             --            --
48     ACAAAAAAA      1              2             --            --
49     ADAAAAAAA      --             1             --            --
50     BBBAAAAAA      --             1             --            --
51     BABAABAAA      --             1             --            --
52     BABABAAAC      --             1             --            --
53     CAAAAAAAA      1             --             --            --

Numbers in parentheses are the ranges of values for collections
composing Florida populations (Bert et al. in prep.). Composite
haplotypes correspond to restriction endonuclease fragment
patterns in Table 7. Collection, subpopulation (SP), and
population abbreviations are defined in Table 1; locations are
shown in Figure 1.

Hap. no., haplotype number; n, number of individuals; h,
haplotype diversity (SD range, 0.05-0.1); [pi], nucleotide
diversity (x [10.sup.3]); h, [pi] in bold print are values
significantly higher or lower than others.

Note: [pi] indicated with # are values significantly higher or
lower than others.

TABLE 9.
Bay scallop pairwise nucleotide diversities (a) and genetic
distances (([[PHI].sub.ST]) (both x [10.sup.3]) based on RFLP
analyses of mtDNA 12S/ND1 segment.

               Atlantic
           Subpopulation     Florida Population

Group   NC     NJ     NY     PN   CO   SF   FB

Atlantic subpopulation

NC       --      8      8    22   22   22   26
NJ        6     --      8    23   23   22   27
NY       13#     5     --    20   20   19   24

Florida population

PN      576#   507#   553#   --   12   12    1
CO      579#   518#   547#    3   --   12    1
SF      571#   457#   496#    4    3   --    1
FB      635#   578#   666#   20   11   23   --

[pi], above bars; [[PHI].sub.ST], below bars.

Abbreviations are defined in Table 1; locations are shown in
Figure 1.

Bold print represents OST values significant after correction for
multiple tests.

Note: OST values significant after correction for multiple tests is
indicated with #.

TABLE 10.
Significant bay scallop Glades as determined by nested Glade
phylogeographic analysis performed on mtDNA restriction fragment
length patterns.

Sig.            Chain of Inference              P Value [inference
Clade         Significant Components                direction)

1-2     1-2- 11b - 12 - No
          Hap                                [D.sub.C] [[less than
                                               or equal to]] 0.03;
                                               [D.sub.N] [[less than
                                               or equal to]] 0.04
          I-T [D.sub.N]                      [s] 0.03

1-3     1-2 - 11-17 - No
          Hap 15                             [D.sub.N] [[greater than
                                               or equal to]] 0.02

2-1     1-2-11ac - 12 - No
          2-1                                  0.01
          1-1 (Haps. 3, 4, 34)               [D.sub.C] [[greater than
                                               or equal to] 0.04,
                                               [D.sub.N] [[greater
                                               than or equal to]] 0.06
          I-T Dc                               [s] 0.05

2-4     1-2 - 11a-12 - No
          1-7 (Haps. 7, 29)                  [D.sub.C] [[less than
                                               or equal to]] 0.02;
                                               [D.sub.N] [[less than
                                               or equal to]] 0.02

2--5    1-2a - 3c - 5 - 6 - 7 - Yes
          1-10 (Haps. 11, 30, 31, 32, 36,    [D.sub.C] [[less than
          41, 48, 53, 21, 25, 37, 38)          or equal to]] 0.04,
                                               [D.sub.N] [[less than
                                               or equal to]] 0.04
          1-14 (Haps. 13, 14)                [D.sub.C] [[greater
                                               than or equal to]]
                                               <0.00; [D.sub.N]
                                               [[greater than or equal
                                               to]] <0.00

3-1     1-2a - 3a -5-6 - 13-14 - Yes
          3-1                                <0.00
          2-1                                [D.sub.C] [[less than
                                               or equal to]] <0.00;
                                               D.sub.N] [[less than
                                               or equal to]] <0.00
          2-2                                [D.sub.C] [[less than
                                               or equal to]] <0.00;
                                               [D.sub.N] [[less than
                                               or equal to]] <0.00
          I-T [D.sub.C]                      [[less than or equal
                                               to]] 0.01
          I-T [D.sub.N]                      [[greater than or equal
                                               to]] 0.00

3-3     1-2a, B - 3abc - 5-6 - 13-14 - Yes
          3-3                                <0.00
          2-5                                [D.sub.C] [[less than
                                               or equal to]] <0.00;
                                               [D.sub.N] [[less than
                                               or equal to]] <0.00
          2-6 (Haps. 12, 17)                 [D.sub.C] [[less than
                                               or equal to]] <0.00;
                                               [D.sub.N] [[greater
                                               than or equal to]]
                                               <0.00
          I-T [D.sub.C]                      [[greater than or equal
                                               to]] 0.05
          I-T [D.sub.N]                      [[less than or equal
                                               to]] <0.00

4-1     1-2b - 3b - 5-15-16 - Yes
          4-1                                <0.00
          3-1                                [D.sub.C] [[greater
                                               than or equal to]] O.00
                                               [D.sub.N] [[greater
                                               than or equal to]]
                                               <0-00
          3-2                                [D.sub.C] [[greater
                                               than or equal to]]
                                               <0.01; [D.sub.N]
                                               [[greater than or equal
                                               to]] <0.00
          3-3                                [D.sub.C] [[less than
                                               or equal to]] <0.00;
                                               [D.sub.N] [[less than
                                               or equal to]] <p.00
          I-T [D.sub.C]                      [[greater than or equal
                                               to]] 0.05
          I-T [D.sub.N]                      [[greater than or equal
                                               to]] <0.00

Sig.            Chain of Inference             Inferred Demographic
Clade         Significant Components                   Event

1-2     1-2- 11b - 12 - No
          Hap                                Contiguous range
                                                 expansion
          I-T [D.sub.N]

1-3     1-2 - 11-17 - No
          Hap 15                             Inconclusive

2-1     1-2-11ac - 12 - No
          2-1                                Contiguous range
          1-1 (Haps. 3, 4, 34)                 expansion
          I-T Dc

2-4     1-2 - 11a-12 - No
          1-7 (Haps. 7, 29)                  Contiguous range
                                               expansion

2--5    1-2a - 3c - 5 - 6 - 7 - Yes
          1-10 (Haps. 11, 30, 31, 32, 36,    Restricted gene flow and
          41, 48, 53, 21, 25, 37, 38)          dispersal with some
                                               long-distance dispersal
          1-14 (Haps. 13, 14)

3-1     1-2a - 3a -5-6 - 13-14 - Yes
          3-1                                Long-distance
          2-1                                  colonization
          2-2
          I-T [D.sub.C]
          I-T [D.sub.N]

3-3     1-2a, B - 3abc - 5-6 - 13-14 - Yes
          3-3                                Long-distance
          2-5                                  colonization
          2-6 (Haps. 12, 17)
          I-T [D.sub.C]
          I-T [D.sub.N]

4-1     1-2b - 3b - 5-15-16 - Yes
          4-1                                Allopatric fragmentation
          3-1
          3-2
          3-3
          I-T [D.sub.C]
          I-T [D.sub.N]

Haplotypes [Hap(s.)] and their distributions defined in Table 8,
significant (Sig.) Blades are shown in Figure 3A.

TABLE 11.
Mismatch and related statistics relative to the expansion model
for bay scallop mtDNA haplotype groupings shown in Figure 3A.

                                      Group or Clade
Model or                            (geographic region)
Indicator
Statistic                                  Gulf

  Mean no.                         0.9
    hap. difs.
  Variance                         1.4
Demographic
  expansion
  SSD                              0.32
  P value                          0.00
  [[THETA].sub.1]                  0.0 (0.0-0.0)
  [[THETA].sub.1]               4289 (4296-4296) ([dagger])
  T (= 2 [tau] X [mu])             0.0 (0.0-0.0)
Spatial expansion
  SSD                              0.00
  P                                0.90
  [THETA] ([N.sub.em] x [mu])      0.4 (0.0-1.0)
  T                                1.3 (0.2-3.7)
  Migration                        1.1 (0.1-[infinity])
  (M = 2[N.sub.m])
                                   0.09
HR
Tajima's D
  Value                           -2.10
  P                                0.001
Fu's Fs
  Value                          -28.5
  P                                0.000

                                      Group or Clade
Model or                            (geographic region)
Indicator
Statistic                               2-2 (Gulf)

  Mean no.                       0.7
    hap. difs.
  Variance                       0.7
Demographic
  expansion
  SSD                            0.00
  P value                        0.92
  [[THETA].sub.1]                0.0 (0.0-0.3)
  [[THETA].sub.1]               42.2 (1.3-[infinity])
  T (= 2 [tau] X [mu])           0.7 (0.2-1.7)
Spatial expansion
  SSD                            0.00
  P                              0.95
  [THETA] ([N.sub.em] x [mu])    0.1 (0.0-0.2)
  T                              0.6 (0.3-1.7)
  Migration                     [infinity] (1.3-[infinity])
  (M = 2[N.sub.m])
                                 0.08
HR
Tajima's D
  Value                         -2.02
  P                              0.008
Fu's Fs
  Value                         -3.7
  P                              0.000

                                       Group or Clade
Model or                             (geographic region)
Indicator
Statistic                                2-5 * (Gulf)

  Mean no.                        0.6
    hap. difs.
  Variance                        0.7
Demographic
  expansion
  SSD                             0.00
  P value                         0.90
  [[THETA].sub.1]                 0.6 (0.0-0.0) ([dagger])
  [[THETA].sub.1]                 1.5 (4.9-[infinity])([double
                                  dagger])
  T (= 2 [tau] X [mu])            0.1 (0.0-1.4)
Spatial expansion
  SSD                             0.00
  P                               0.85
  [THETA] ([N.sub.em] x [mu])     0.1 (0.0-0.1)
  T                               0.8 (0.7-2.3)
  Migration                       2.1 (0.2-[infinity])
  (M = 2[N.sub.m])
                                  0.15
HR
Tajima's D
  Value                          -2.14
  P                               0.001
Fu's Fs
  Value                         -33.8
  P                               0.000

                                   Group or Clade
Model or                         (geographic region)
Indicator
Statistic                            3-3 * (Gulf)

  Mean no.                        0.6
    hap. difs.
  Variance                        0.9
Demographic
  expansion
  SSD                             0.00
  P value                         0.93
  [[THETA].sub.1]                 0.2 (0.0-0.3)
  [[THETA].sub.1]                 0.7 (0.0-[infinity])
  T (= 2 [tau] X [mu])            1.3 (0.0-3.3)
Spatial expansion
  SSD                             0.00
  P                               0.96
  [THETA] ([N.sub.em] x [mu])     0.1 (0.0-0.1)
  T                               0.8 (0.1-2.2)
  Migration                       1.9 (0.3-[infinity])
  (M = 2[N.sub.m])
                                  0.14
HR
Tajima's D
  Value                          -2.13
  P                               0.000
Fu's Fs
  Value                         -34 x 1038
  P                               0.000

                                     Group or Clade
Model or                           (geographic region)
Indicator
Statistic                                  Atl

  Mean no.                       1.9
    hap. difs.
  Variance                       3.8
Demographic
  expansion
  SSD                            0.02
  P value                        0.53
  [[THETA].sub.1]                0.0 (0.0-1.0)
  [[THETA].sub.1]                2.1 (0.5-[infinity])
  T (= 2 [tau] X [mu])           5.1 (0.6-91.1)
Spatial expansion
  SSD                           <0.01
  P                              0.85
  [THETA] ([N.sub.em] x [mu])    0.7 (0.0-1.3)
  T                              2.8 (0.8-6.9)
  Migration                      1.2 (0.3-[infinity])
  (M = 2[N.sub.m])
                                 0.07
HR
Tajima's D
  Value                         -0.10
  P                              0.50
Fu's Fs
  Value                         -7.7
  P                              0.002

                                      Group or Clade
Model or                            (geographic region)
Indicator
Statistic                               2-1 * (Atl)

  Mean no.                       0.4
    hap. difs.
  Variance                       0.4
Demographic
  expansion
  SSD                            0.00
  P value                        0.47
  [[THETA].sub.1]                0.0 (0.0-0.0)
  [[THETA].sub.1]                0.5 (0.0-[infinity])
  T (= 2 [tau] X [mu])           3.0 (0.4-3.5)
Spatial expansion
  SSD                            0.00
  P                              0.55
  [THETA] ([N.sub.em] x [mu])    0.0 (0.0-0.3)
  T                              0.4 (0.2-0.7)
  Migration                     [infinity] (0.9-[infinity])
  (M = 2[N.sub.m])
                                 0.20
HR
Tajima's D
  Value                         -1.36
  P                              0.07
Fu's Fs
  Value                         -3.6
  P                              0.15

                                      Group or Clade
Model or                            (geographic region)
Indicator
Statistic                                2-3 (Atl)

  Mean no.                       1.3
    hap. difs.
  Variance                       0.8
Demographic
  expansion
  SSD                            0.01
  P value                        0.56
  [[THETA].sub.1]                0.0 (0.0-0.0)
  [[THETA].sub.1]               [infinity]) (4.1-[infinity])
  T (= 2 [tau] X [mu])           1.5 (0.3-3.0)
Spatial expansion
  SSD                            0.02
  P                              0.52
  [THETA] ([N.sub.em] x [mu])    0.0 (0.0-1.0)
  T                              1.5 (0.3-2.8)
  Migration                     [infinity] (1.8-[infinity])
  (M = 2[N.sub.m])
                                 0.11
HR
Tajima's D
  Value                         -0.73
  P                              0.29
Fu's Fs
  Value                         -2.2
  P                              0.015

                                       Group or Clade
Model or                             (geographic region)
Indicator
Statistic                                2-3* (Atl)

  Mean no.                       1.4
    hap. difs.
  Variance                       1.0
Demographic
  expansion
  SSD                            0.00
  P value                        0.62
  [[THETA].sub.1]                0.0 (0.0-0.4)
  [[THETA].sub.1]               [infinity]) (11.1-[infinity])
  T (= 2 [tau] X [mu])           1.6 (0.5-2.8)
Spatial expansion
  SSD                           <0.01
  P                              0.68
  [THETA] ([N.sub.em] x [mu])    0.0 (0.0-1.0)
  T                              1.6 (0.6-2.9)
  Migration                      [infinity] (2.8-[infinity])
  (M = 2[N.sub.m])
                                 0.09
HR
Tajima's D
  Value                          1.32
  P                              0.91
Fu's Fs
  Value                          0.0
  P                              0.47

                                   Group or Clade
Model or                         (geographic region)
Indicator
Statistic                             3-2 (Atl)

  Mean no.                       2.5
    hap. difs.
  Variance                       2.3
Demographic
  expansion
  SSD                            0.00
  P value                        0.94
  [[THETA].sub.1]                0.0 (0.0-1.1)
  [[THETA].sub.1]               29.5 (8.4-[infinity])

  T (= 2 [tau] X [mu])           2.8 (1.2-3.8)
Spatial expansion
  SSD                           <0.01
  P                              0.89
  [THETA] ([N.sub.em] x [mu])    0.0 (0.0-1.7)
  T                              2.7 (1.2-3.9)
  Migration                     37.5 (12.0-[infinity])
  (M = 2[N.sub.m])
                                 0.03
HR
Tajima's D
  Value                          1.53
  P                              0.93
Fu's Fs
  Value                         -2.6
  P                              0.08

                                         Group or Clade
Model or                               (geographic region)
Indicator
Statistic                                  Gulf & Atl

  Mean no.                        1.5
    hap. difs.
  Variance                        2.2
Demographic
  expansion
  SSD                             0.49
  P value                         0.00
  [[THETA].sub.1]                 0.0 (0.0-0.1)
  [[THETA].sub.1]               [infinity] ([infinity][infinity])
  T (= 2 [tau] X [mu])            0.0 (0.0-0.2)
Spatial expansion
  SSD                             0.01
  P                               0.77
  [THETA] ([N.sub.em] x [mu])     0.2 (0.0-1.0)
  T                               2.2 (0.5-4.4)
  Migration                       2.1 (0.4-[infinity])
  (M = 2[N.sub.m])
                                  0.07
HR
Tajima's D
  Value                          -1.72
  P                               0.008
Fu's Fs
  Value                         -28.1
  P                               0.000
                                      Group or Clade
                                    (geographic region)
Model or
Indicator                                  3-1 *
Statistic                               (Gulf & All)

  Mean no.                       0.8
    hap. difs.
  Variance                       0.7
Demographic
  expansion
  SSD                            0.00
  P value                        0.91
  [[THETA].sub.1]                0.0 (0.0-0.1)
  [[THETA].sub.1]               [infinity] (24.6-[infinity])
  T (= 2 [tau] X [mu])           0.8 (0.5-1.2)
Spatial expansion
  SSD                            0.00
  P                              0.61
  [THETA] ([N.sub.em] x [mu])    0.0 (0.0-0.5)
  T                              0.8 (0.3-1.1)
  Migration                     [infinity] (3.2-[infinity])
  (M = 2[N.sub.m])
                                 0.07
HR
Tajima's D
  Value                         -1.70
  P                              0.020
Fu's Fs
  Value                         -8.6
  P                              0.000

* Clade significant in nested clade phylogenetic analysis.

([dagger]) Bounds reflect low mean value of 0.01 compared with
reported estimated value.

([double dagger]) Mean value exceeded reported estimated value;
bounds reflect mean value.

Clade 2-6 was not included because it is a 2-step clade
restricted to North Carolina. As recommended by Schneider and
Excoffier (1999), confidence intervals (in parentheses) for
mismatch statistics are for alpha = 0.10 because the mismatch
test is very conservative. Mismatch statistic values greater than
99,000 are reported as [infinity].

Gulf, Florida Gulf of Mexico bay scallops; Ad, Atlantic Ocean bay
scallops; both are defined in Table 1 and shown in Figure 1. no.
hap. difs., number of haplotype differences; SSD, sum of squared
deviations; P, significance level; 0, 2[N.sub.ef] mu], the
estimated expansion parameter; [[theta].sub.0] and
[[theta].sub.1] respectively, estimated preexpansion and
postexpansion population size; T, 2 [tau] X [mu], time in
generations since 2 populations last exchanged migrants (Rogers &
Harpending 1992), which is a relative estimate of time since
expansion event; M, 2[N.sub.ef]m, the scaled migration rate
([N.sub.m], effective number of migrants); HR, Harpending's
raggedness index (Harpending 1994). Tajima's D and Fu's Fs are
described in Methods.
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Author:Bert, Theresa M.; Arnold, William S.; McMillen-Jackson, Anne L.; Wilbur, Ami E.; Crawford, Charles
Publication:Journal of Shellfish Research
Article Type:Report
Geographic Code:1USA
Date:Dec 1, 2011
Words:23228
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