Printer Friendly

Towards a temporal framework for "inordinate fondness": reconstructing the macroevolutionary history of beetles (coleoptera).

Abstract.--Most molecular phylogenetic studies of beetles (order Coleoptera) using 18S rDNA have recovered the suborders Adephaga and Polyphaga as sister groups, together sister to the suborders Myxophaga and Archostemata, with Archostemata alone or in combination with Myxophaga as the closest relative of all other beetles. Analyses of data from other genes have recovered alternative arrangements. Estimated subordinal divergence times based on analyses of DNA sequence data and fossil calibrations range from ~ 285-266 million years ago (Ma), with most extant families estimated to have originated in the Jurassic. However, timing and patterns of ecological and taxonomic diversification remain uncertain for most beetle groups primarily due to limited gene and nucleotide sampling, missing data, and a corresponding lack of well-supported resolution. Consequently, the nature and degree to which events in earth's history (e.g., the diversification and rise of angiosperms to ecological dominance) have influenced the success of Coleoptera remains unclear. Nevertheless, the phylogeny of beetles is being revealed via molecular studies with large taxon and gene samples, presenting renewed and novel opportunities for the study of beetle macroevolution.

Key words: Evolution, molecular phylogenetics, nodal support, timetree.

INTRODUCTION

Coleoptera comprise the largest order of animals with more than 350,000 named species. They are part of the food web in nearly every nonmarine habitat, and play numerous and important ecological roles, for example as consumers, pollinators, and decomposers. Here I review our current understanding of higher-level (particularly subordinal) relationships in beetles based on DNA sequence data. I also elaborate upon a previous review of beetle molecular chronograms (timetrees) (McKenna and Farrell, 2009) by adding newly published data and discussing how phylogenetic methods have been used to reconstruct timing and patterns of ecological and taxonomic diversification in beetles.

The 16 superfamilies and 168 families of extant beetles are separated into four suborders: Adephaga (~35,000 species), Archostemata (~35 species), Myxophaga (~65 species), and Polyphaga (~315,000 species) (Lawrence and Newton, 1995; Arnett and Thomas, 2000; Arnett et al., 2002; Beutel and Leschen, 2005). Adephaga are largely predators and their earliest known fossils are from the early Triassic (Grimaldi and Engel, 2005). The abdominal sternite II of Adephaga is divided by the metacoxae. Archostemata feed on decaying wood as larvae and pollen as adults. The earliest known fossil Archostemata are from the late Permian (H6rnschemeyer, 2005). Archostemata have the labrum fused to the head capsule and roll the tips of their wings under the elytra. Myxophaga are aquatic or semiaquatic and feed on algae (Beutel and Leschen, 2005). They are not definitively known from the fossil record, but possible relatives are known from the Permian (e.g., Ponomarenko, 1969; Lawrence and Newton, 1982). Myxophaga are highly specialized for aquatic life. Adults respire via a plastron, and larvae have tracheal gills. Polyphaga exhibit diverse feeding habits, but most consume living plants or dead and decaying plant parts (Arnett and Thomas, 2000; Arnett et al., 2002). The earliest known polyphagan fossils are from the early Triassic (Grimaldi and Engel, 2005). Polyphaga have presternal cervical sclerites, and the propleura is internalized.

Relationships among the four suborders of beetles remain unsettled (e.g., see Crowson, 1960; Lawrence and Newton, 1982; Lawrence et al., 1995). However, an arrangement with Archostemata as sister to all other beetles, Myxophaga and Polyphaga as sister groups, and Adephaga as sister to Myxophaga and Polyphaga, is favored by recent morphological studies (Beutel and Haas, 2000; Beutel, 2005). Autapomorphies of Coleoptera include elytra with meso- and metathoracic locking devices, close connection of exposed sclerites, reduced abdominal sternite I, and invagination of terminal abdominal segments (Beutel and Haas, 2000). Characters supporting the monophyly of Coleoptera excluding Archostemata include the absence of the mesothoracic discriminal line and katepisternal joint (and other transformations of the thoracic sclerites), internalized or absent metathoracic trochantin, and the presence of a bending zone in the hindwing. Adult Myxophaga and Polyphaga are characterized by the rigid connection of the meso- and metathoracic ventrites, and the fusion of protrochantin and propleura (Beutel and Haas, 2000).

SUBORDINAL RELATIONSHIPS AND TIMETREES

The first study focused on reconstructing relationships in beetles using molecular data (Howland and Hewitt, 1995) sampled a 400 bp piece of cytochrome oxidase I from 37 beetle species in 15 families, with representatives from two of the four beetle suborders (Table l). The resulting neighbor joining tree was not well resolved and provided relatively little new insight into beetle phylogeny. Shull, et al. (2001) published the first comprehensive molecular phylogeny for beetles, with taxa sampled from ali four suborders. They analyzed nearly complete small subunit ribosomal RNA (18S) sequences from 48 beetle species in 19 families (taxon sampling was focused on Adephaga), and 4 neuropterid outgroups. Most of their extensive analyses recovered Adephaga and Polyphaga as sister groups, and the suborders Myxophaga and Archostemata grouped together as sister to a clade comprised of Adephaga and Polyphaga. However, in some analyses Polyphaga arose from within Hydradephaga.

Caterino, et al. (2002) reconstructed beetle phylogeny using 18S sequences from 25 beetle species in 24 families representing all four suborders. They also sampled a diverse array of 46 other insects. When Coleoptera and each of its constituent suborders were constrained to be monophyletic in a parsimony (MP) analysis, Archostemata was recovered in a position sister to the remaining beetles, Adephaga and Polyphaga were sister groups, and Myxophaga was recovered in a position sister to Adephaga and Polyphaga. Without constraints, Coleoptera were rendered paraphyletic by the inclusion of Diptera and Strepsiptera.

Caterino, et al. (2005), although focused on reconstructing relationships within Staphylinifor mia and between Staphyliniformia and Scarabaeiformia, sampled 18S sequences from 25 beetles, including representatives of ali four suborders. Analyses under Bayesian (BI) and maximum likelihood (ML) inference recovered Adephaga and Polyphaga as sister groups, and Archostemata alone or in combination with Myxophaga as the closest relative of ali other beetles. Parsimony analysis recovered Myxophaga in a position sister to Polyphaga. Vogler (2005) analyzed 18S sequences from 795 beetle taxa in 123 families. In the resulting most parsimonious tree, the single exemplar of Archostemata (Distocupes) was recovered in a position sister to the remaining beetles, Adephaga and Polyphaga were sister groups, and Myxophaga was sister to the clade comprised of Adephaga and Polyphaga.

Hughes, et al. (2006) used expressed sequence tags to generate phylogenetic markers (66 genes; matrix 28.6% complete) for 14 beetle species, which included representatives of ali four suborders. Analysis under MP, ML, and BI recovered similar phylogenetic trees. When trees were rooted with Archostemata, Myxophaga and Polyphaga were sister groups, with Adephaga as their sister group. Supertree analyses yielded generally less resolution, and favored the placement of Myxophaga within Polyphaga.

Hunt, et al. (2007) published the most extensively taxon-sampled phylogeny of beetles to date. Their study included nearly complete 18S sequences for 1,880 taxa, and sequences from mitochondrial 16S rRNA and cytochrome oxidase subunit I (COI) for nearly half of these. In the trees resulting from analysis under MP and BI, Adephaga and Polyphaga were sister groups, together sister to Myxophaga plus Archostemata. Hunt, et al. (2007) also published the first molecular timetree for beetles, based on BI analysis of a 340-taxon subset of their 1,880-taxon tree. The age of the ingroup was fixed at 285 Ma in an "all compatible" version of the resulting consensus tree, and seven fossil age constraints were used to calibrate the tree and date internal nodes under penalized likelihood (PL) in the program r8s (Sanderson, 2002, 2003). Average ages and 95% confidence intervals were reported for 13 selected clades in the resulting chronogram (1). Most families (> 100) were found to originate in the Jurassic. To investigate the role of herbivory in beetle diversification, Hunt, et al. (2007) compared species richness between clades feeding on living plants and their sister clades with hosts other than living plants. They also performed a more restrictive analysis limiting the comparison to clades feeding on angiosperms versus those with other hosts (including gymnospermous plants). Based on these analyses, they concluded that the success of beetles is "explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms." As an alternative, they proposed that the species richness of beetles is due to "high survival of lineages and sustained diversification in a variety of niches" (Hunt et al., 2007).

Wild and Maddison (2008) evaluated the phylogenetic performance of 9 nuclear genes (alpha-spectrin (AS), RNA polymerase H (RNA Pol II), topoisomerase I (TOP1), arginine kinase (AK), carbamoylphosphate synthase domain (CAD), enolase, phosphoenolpyruvate carboxykinase (PEPCK), wingless (WG), and 28S) sequenced from 31 beetles in 18 genera representing all suborders except Myxophaga (but focused on Adephaga), and 2 outgroups. Performance was evaluated by comparing the topologies obtained by analysis under BI to a "presumably known" test phylogeny in which uncertain subordinal relationships were intentionally left unresolved. Bayesian and MP analyses of the concatenated nine-gene data set recovered Archostemata and Adephaga as sister groups, together sister to Polyphaga. This was the first higher-level molecular phylogenetic study of beetles to include extensive data from nuclear protein-coding genes. Maddison, et al. (2009) used 18S and 28S DNA sequences and data from the nuclear protein-coding gene WG to reconstruct the phylogeny of Adephagan beetles. They sampled exemplars from all four suborders of beetles, including 60 species of Adephaga, 4 genera representing 2 families of Archostemata (more Archostemata than in any other study to date; Cupes capitatus, Priacma serrata, Tenomerga cinetea, and Micromalthus debilis), 3 Myxophaga, and 10 Polyphaga. Bayesian analysis of the combined data recovered Archostemata and Myxophaga as sister groups, and Adephaga and Polyphaga as sister groups.

McKenna and Farrell (2009) analyzed nearly complete 18S sequences from 955 beetle genera, including representatives of 134 beetle families. Analysis under ML inference recovered Adephaga and Polyphaga as sister groups, together sister to Myxophaga plus Archostemata. Nonparametric rate smoothing (NPRS) (Sanderson, 1997) implemented in r8s was used to generate an ultrametric tree from the ML topology. Six fossils and each of two alternative maximum constraints on the age of Holometabola (separately applied) were used to calibrate the tree and date internal nodes, resulting in the most extensively taxon-sampled molecular timetree for beetles to date. The split between Myxophaga + Archostemata and the clade comprised of the suborders Adephaga and Polyphaga was estimated to have occurred - 269 265 Ma (mean 266.8 Ma). By comparison, Hunt, et al. (2007) fixed the age of this split at 285 Ma. McKenna and Farrell (2009) estimated that the Adephaga-Polyphaga split occurred ~ 269265 Ma (mean 266.4 Ma), just slightly later than Hunt, et al. (2007), who estimated this split to have occurred ~ 277 Ma. Divergence times were not evaluated below the subordinal level in McKenna and Farrell (2009) due to the lack of well-supported resolution at lower taxonomic levels in Polyphaga and beyond. The results of Hunt, et al. (2007) and McKenna and Farrell (2009) indicate that the four living suborders of beetles diverged in the Permian, when early amniotes, conifers, and others groups of terrestrial organisms, including other insects (Labandeira and Sepkoski, 1993), were also diversifying. In a recent series of related studies, mitochondrial (mt) genomes were used to estimate the higher-level phylogeny of beetles (Sheffield et al., 2008, 2009; Song et al., 2010; Pons et al., 2010). Mitochondrial genomes have also been used to estimate the higher-level phylogeny of Neuropterida and their relationship to other holometabolous insects, including nine beetles in the suborders Adephaga and Polyphaga (Cameron et al., 2009). In addition to addressing relationships, these studies report on the effects of systematic bias contributed by base compositional heterogeneity and among-site rate variation on phylogeny reconstruction. Base compositional heterogeneity and among-site rate variation are problematic for phylogeny reconstruction because they can produce misleading estimates of topology and branch lengths and misleading bipartition posterior probabilities, and may cluster unrelated taxa based on convergent base content rather than evolutionary history (e.g., Lemmon et al., 2009; Song et al., 2010). Song, et al. (2010), with data from 24 beetles representing all 4 suborders (and 7 outgroups), included more beetles than any other of the aforementioned studies employing mt genomes. They presented numerous phylogenetic trees, e.g., some resulting from analyses designed specifically to overcome systematic bias, and others resulting from more traditional analytical methods. Their MP "reference phylogeny" based on amino acid sequences, and determined to be the least likely to violate phylogenetic assumptions, recovered Myxophaga (1 exemplar; Sphaerius) and Adephaga (3 exemplars) as sister groups, these together sister to Polyphaga (19 exemplars). Archostemata (1 exemplar; Tetraphalerus) was the sister group to all other Coleoptera. Although the monophyly of Adephaga and Polyphaga were well supported, none of the aforementioned subordinal relationships were supported by bootstrap values [greater than or equal to] 80%. Pons, et al. (2010) used mt genomes (2 newly sequenced) to reconstruct the phylogeny of beetles and to estimate nucleotide substitution rates for mitochondrial protein-coding (MPC) genes. Analysis of the nucleotide sequences of the 13 MPC's under BI recovered Polyphaga (10 exemplars) + Archostemata (1 exemplar; Tetraphalerus) as a clade, and also Adephaga (2 exemplars) + Myxophaga (2 exemplars).

Studies focused primarily on reconstructing relationships in Holometabola (e.g., Whiting et al., 1997, 2002a,b; Wheeler et al., 2001) using 18S and/or 28S DNA sequence data give some insight into subordinal relationships in beetles. For example, Whiting (2002a), used 18S sequences from 47 beetles, including representatives of all 4 suborders, and a diverse array of 100 other holometabolous insects. Parsimony analysis recovered a paraphyletic Coleoptera and Adephaga, with the single archostematan sampled (Distocupes) recovered within Myxophaga (represented by Hydroscapha and Torridincola).

Several recent molecular phylogenetic studies that focused on Holometabola or other higherlevel groups of insects indicate that Strepsiptera are closely related to beetles, if not beetles themselves (2) (Misof et al., 2007; Wiegmann et al., 2009a,b; Ishiwata et al., 2010; Longhorn et al., 2010; McKenna and Farrell, 2010). Longhorn, et al. (2010) evaluated relationships in Holometabola with a focus on the phylogenetic placement of Strepsiptera using data from 27 nuclear ribosomal proteins for 22 holometabolous insects, including 7 beetles and 2 Strepsiptera. Their taxon sample lacked representatives from the beetle suborder Archostemata and the supra-ordinal group Neuropterida (Orders Megaloptera, Neuroptera and Raphidioptera); thought to be the sister group to Coleoptera alone or to Coleoptera + Strepsiptera (Weigmann et al., 2009a,b). Analysis under BI recovered the single adephagan (Cicindela) in a position sister to Polyphaga. The single myxophagan (Sphaerius) and the two Strepsiptera were recovered in various positions in the tree depending on the nucleotide-coding scheme and method of phylogenetic inference employed (whether ML, BI, or MP). However, the most convincing placement was as sister group to Coleoptera. Regardless, Strepsiptera were recovered as close relatives of beetles under most coding schemes and analytical methods.

McKenna and Farrell (2010) used DNA sequences from 9 nuclear genes (elongation factor-1[alpha] (EF-1[alpha]), alanyl-tRNA synthetase (AATS), CAD, 6-phosphogluconate dehydrogenase (PGD), sans fille (SNF), triosephosphate isomerase (TPI), RNA Pol II, 28S, and 18S) to reconstruct the phylogeny of Holometabola with a focus on determining the phylogenetic placement of Strepsiptera. Their taxon sample was comprised of 32 exemplars representing all orders of Holometabola, including 8 beetles in as many families (and representing all 4 suborders), 2 Strepsiptera, and 2 hemimetabolous insect outgroups. Analysis under ML and BI recovered the single exemplars of Archostemata and Myxophaga together in a position sister to Adephaga, and these three suborders sister to Polyphaga + Strepsiptera. The same relationships were recovered when rDNA were excluded from ML and BI analyses, except for Strepsiptera, which were recovered in a position sister to Neuropterida and therefore outside of Coleoptera. Strepsiptera have not been included in any published analyses along with both a comprehensive sample of beetle suborders and an extensive sample of beetle families.

OTHER HIGHER-LEVEL TIMETREES

Molecular chronograms for beetles that focused on relationships at the level of series or superfamily and were calibrated with information from the geological record to produce a timetree are so far available only for the cucujiform superfamilies Chrysomeloidea (Farrell, 1998; Gomez-Zurita et al., 2007) and Curculionoidea (Farrell, 1998; McKenna et al., 2009). Farrell (1998) used MP to reconstruct the phylogeny of Phytophaga (Chrysomeloidea and Curculionoidea) from 18S sequences for 115 species, and 212 morphological characters. The resulting most parsimonious trees showed basal conifer- and cycad-feeding lineages in both superfamilies, consistent with their proposed status as ancient host associations. The age of each major constituent group, estimated from the fossil record, was used to prepare an estimated timetree for Phytophaga from the strict consensus tree. Five independent contrasts were made of sister groups where one of the groups was associated with gymnospermous plants and the other with angiosperms, all yielding a positive difference in favor of the hypothesis that feeding on angiosperms is associated with enhanced taxonomic diversity (Farrell, 1998).

Gomez-Zurita, et al. (2007) contended that available phylogenetic information and molecular clock calibrations were insufficient to conclude that the taxonomic diversity of Phytophaga can be attributed to "co-radiation with angiosperms." To revisit this subject, they obtained estimated phylogenetic trees for 167 taxa in the superfamily Chrysomeloidea (but focused on Chrysomelidae) from ML and MP analyses of data from 16S, 18S, and 28S. Penalized likelihood implemented in the program rSs was used to generate an ultrametric tree from the ML topology. Minimum age constraints were imposed based on two fossils, and the vicariant split between Palearctic and Nearctic Timarchini (Chrysomelidae). The resulting timetree was consistent with a Late Cretaceous origin for Chrysomelidae, and subsequent taxonomic diversification over the course of the Cenozoic--considerably later than proposed by Farrell (1998). Gomez-Zurita, et al. (2007) therefore argued that chrysomelid beetles radiated long after the origin of angiosperms and that their diversification was driven by repeated radiation on a pre-existing diverse resource, rather than ancient host associations.

McKenna, et al. (2009) reconstructed the evolutionary history of diversification in weevils using DNA sequence data from 6 genes (EF-1[alpha], CAD, AK, 28S, 18S, and COI) for 135 genera representing all families and subfamilies of Curculionoidea. Divergence times derived from the combined molecular and fossil data were coestimated with phylogeny using the Bayesian relaxed molecular clock method (Drummond et al., 2006) in the program BEAST (3). These analyses indicated diversification into most modern families occurred on gymnosperms in the Jurassic. Colonization of angiosperms appears to have occurred during the Early Cretaceous, with massive taxonomic diversification not beginning until the midCretaceous, when angiosperms first rose to widespread floristic dominance. The authors proposed that these and other evidence are consistent with a deep and complex history of coevolution between weevils and angiosperms (McKenna et al., 2009).

[FIGURE 1 OMITTED]

DISCUSSION AND CONCLUSIONS

Most studies of beetle molecular phylogeny with extensive taxon sampling have relied largely or solely on DNA sequences from the small subunit ribosomal RNA (18S) (e.g., Shull et al., 2001; Vogler, 2005; Hunt et al., 2007; McKenna and Farrell, 2009), and most of these studies have recovered, at least under some analytical conditions, Adephaga and Polyphaga as sister groups, and Archostemata alone or in combination with Myxophaga as the closest relative of all other beetles (Fig. 1). Despite the relative consistency of subordinal relationships recovered in these studies, they fail to recover extensive compatible and well-supported resolution below the subordinal level, particularly in the suborder Polyphaga, the most species rich of the four beetle suborders. The extensively taxon-sampled study of Hunt, et al. (2007), with data from 3 genes, is a step in the right direction. However, it too was based largely on data from 18S. Data from 16S and COI were available for slightly less than half of the taxa.

Due to limited gene and nucleotide sampling, missing data, and a corresponding lack of well-supported resolution in studies to date, existing molecular phylogenies for the order Coleoptera based largely or solely on 18S should be viewed as tentative. The recent 9-gene phylogeny of Wild and Maddison (2008) and the 6-gene phylogeny of McKenna, et al. (2009) (limited to Curculionoidea) recovered considerable well-supported resolution, and suggest that similarly large gene samples may contribute to resolving relationships in other major beetle radiations, and with sufficient taxon sampling, perhaps even across the entirety of the order Coleoptera.

On account of the current lack of strong nodal support for the interrelationships and internal relationships of most groups of beetles, it is difficult to justify detailed evaluation of the timing and causes of ecological and taxonomic diversification in most beetle groups, let alone across the entire order Coleoptera. However, methods for estimating relationships and/or node ages from molecular (and other) data have matured considerably over the approximately 15 years that have elapsed since publication of the first significant attempt at reconstructing beetle phylogeny using DNA sequence data (Howland and Hewitt, 1995). Further, recent studies of the beetle fossil record, e.g., by Oberprieler, et al. (2007) and Krell (2006), are contributing to a better understanding of timing and patterns in the appearance of major groups of beetles. Consequently, future studies that (1) obtain data from multiple molecular markers for a broad cross-section of beetles, neuropterids and Strepsiptera, (2) incorporate the latest information from the beetle fossil record, and (3) use appropriate and statistically rigorous methods for estimating beetle phylogeny and divergence times will undoubtedly contribute further and more robust insights into beetle phylogeny and macroevolution, including factors contributing to the apparent success of the order.

LITERATURE CITED

Arnett, R. H., Jr., M. C. Thomas, P. E. Skelley and J. H. Frank. 2002. American Beetles Vol. 2. CRC, Boca Raton (FL), pp. 1-867.

Arnett, R. H., Jr. and M. C. Thomas. 2000. American Beetles Volume 1. CRC, Boca Raton (FL), pp. 1-443.

Beutel, R. G. and F. Haas. 2000. Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics 16: 103-141.

Beutel, R. G. and R. A. B. Leschen. 2005. Coleoptera, Vol. 1: Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga partim). Handbook of Zoology. De Gruyter, Berlin, New York, pp. 1 567.

Beutel, R. G. 2005. Coleoptera, Vol. 1: Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga (partim), pp. 1-16 in Beutel, R. G. and R. A. B. Leschen. Handbook of Zoology, Vol. IV Arthropoda: Insecta. Part 38. DeGruyter, Berlin.

Cameron, S. L., J. Sullivan, H. Song, K. B. Miller and M. F. Whiting. 2009. A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders. Zoologica scripta 38:575-590.

Caterino, M. S., T. Hunt and A. P. Vogler. 2005. On the constitution and phylogeny of Staphyliniformia (Insecta: Coleoptera). Molecular Phylogenetics and Evolution 34: 655-672.

Caterino, M. S., V. L. Shull, P. M. Hammond and A. P. Vogler. 2002. Basal relationships of Coleoptera inferred from 18S rDNA sequences. Zoologica Scripta 31: 41-49.

Crowson, R. A. 1960. The phylogeny of Coleoptera. Annual Review of Entomology 5:111-134.

Drummond, A. J., S. Y. W. Ho, M. J. Philipps and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.

Farrell, B. D. 1998. "Inordinate fondness" explained: Why are there so many beetles? Science 281: 555-559.

Gomez-Zurita, J., T. Hunt, F. Kopliku and A. P. Vogler. 2007. Recalibrated tree of Leaf Beetles (Chrysomelidae) indicates independent diversification of angiosperms and their insect herbivores. PloS ONE 2: e360.

Grimaldi, D. and M. S. Engel. 2005. Evolution of the Insects. Cambridge University, New York (NY), pp. 357-406.

Hornschemeyer, T. 2005. Coleoptera: Archostemata. DeGruyter, Berlin, pp. 29-42.

Howland, D. E. and G. M. Hewitt. 1995. Phylogeny of Coleoptera based on mitochondrial cytochrome oxidase I sequence data. Insect Molecular Biology 4:203-215.

Hughes, J., S. J. Longhorn, A. Papadopoulou, K. Theodorides, A. de Riva, M. Mejia-Chang, P. G. Foster and A. P. Vogler. 2006. Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Molecular Biology and Evolution 23: 268-278.

Hunt, T., J. Bergsten, Z. Levkanicova, A. Papadopoulou, O. S. John, R. Wild, P. M. Hammond, D. Ahrens, M. Balke, M. S. Caterino, J. Gomez Zurita, I. Ribera, T. G. Barraclough, M. Bocakova, L. Bocak and A. P. Vogler. 2007. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318: 1913-1916.

Krell, F. 2006. Fossil record and evolution of Scarabaeoidea (Coleoptera: Polyphaga). Coleopterists Society Monograph Number 5: 120-143.

Ishiwata, K., G. Sasaki, J. Ogawa, T. Miyata and Z. Su. 2010. Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences. Molecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2010.11.001

Labandeira, C. C. and J. J. Sepkoski, Jr. 1993. Insect diversity in the fossil record. Science 261: 310-315.

Lawrence, J. F. and A. F. Newton, Jr. 1982. Evolution and classification of beetles. Annual Review of Ecology and Systematics 13:261-290.

Lawrence, J. F. and A. F. Newton, Jr. 1995. Families and Subfamilies of Coleoptera. Muzeum i Instytut Zoologii PAN, Warszawa, pp. 779-1006.

Lawrence, J. F., S. A. Slipinski and J. Pakaluk. 1995. From Latreille to Crowson: A History of the Higher-Level Classification of Beetles. Muzeum i Instytut Zoologii PAN, Warszawa, pp. 87-155.

Lemmon, A. R., J. M. Brown, K. Stanger-Hall and E. M. Lemmon. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology 58: 130-145.

Longhorn, S. J., H. W. Pohl and A. P. Vogler. 2010. Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera. Molecular Phylogenetics and Evolution 55: 846-59.

Maddison, D. R., W. Moore, M. D. Baker, T. M. Ellis, K. A. Ober, J. J. Cannone and R. R. Gutell. 2009. Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae). Zoologica Scripta 38:43-62.

McKenna, D. D. and B. D. Farrell. 2009. Beetles (Coleoptera), pp. 278-289 in Hedges, S. B. and S. Kumar. The Timetree of Life. Oxford University Press, Oxford.

McKenna, D. D. and B. D. Farrell. 2010. 9-genes reinforce the phylogeny of Holometabola and yield alternate views on the phylogenetic placement of Strepsiptera. PLoS ONE 5: e11887.

McKenna, D. D., A. S. Sequeira, A. E. Marvaldi and B. D. Farrell. 2009. Temporal lags and overlap in the diversification of weevils and flowering plant. Proceedings of the National Academy of Sciences, USA 106: 7083-7088.

Misof, B., O. Niehuis, I. Bischoff, A. Rickert, D. Erpenbeck and A. Staniczek. 2007. Towards an 18S phylogeny of hexapods: Accounting for group-specific character covariance in optimized mixed nucleotide/doublet models. Zoology 110: 409-429.

Oberprieler, R. G., A. E. Marvaldi and R. S. Anderson. 2007. Weevils, weevils, weevils everywhere. Zootaxa 1668: 491-520.

Ponomarenko, A. G. 1969. Historical development of Archostemata beetles. Trudy Paleontologicheskogo Instituta 125: 70-115.

Pons, J., I. Ribera, J. Bertranpetit and M. Balke. 2010. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Molecular Phylogenetics and Evolution 56: 796-807.

Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14: 1218-1231.

Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19: 101-109.

Sanderson, M. J. 2003. r8s; inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301-302.

Sheffield, N. C., H. Song, S. L. Cameron and M. F. Whiting. 2008. A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles. Molecular Biology and Evolution 25:2499-2509.

Sheffield, N. C., H. Song, S. L. Cameron and M. F. Whiting. 2009. Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics. Systematic Biology 58: 381-394.

Shull, V. L., A. P. Vogler, M. D. Baker, D. R. Maddison and P. M. Hammond. 2001. Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: Evidence for monophyly of aquatic families and the placement of Trachypachidae. Systematic Biology 50: 945-969.

Song, H., N. C. Sheffield, S. L. Cameron, K. B. Miller and M. F. Whiting. 2010. When the phylogenetic assumptions are violated: The effect of base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Systematic Entomology 35: 429-448.

Vogler, A. 2005. Handbook of Zoology, Vol. IV Arthropoda: Insecta, pp. 17-22 in Beutel, R. G. and R. A. B. Leschen. Part 38. Coleoptera, Vol. 1: Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga (partim). DeGruyter, Berlin.

Wheeler, W. C., M. F. Whiting, Q. D. Wheeler and J. Carpenter. 2001. Phylogeny of the extant hexapod orders. Cladistics 17: 1-89.

Whiting, M. F., J. C. Carpenter, Q. D. Wheeler and W. C. Wheeler. 1997. The Stresiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology. Systematic Biology 46: 1-68.

Whiting, M. F. 2002a. Phylogeny of the holometabolous insect orders: Molecular evidence. Zoologica Scripta 31: 3-17.

Whiting, M. F. 2002b. Phylogeny of the holometabolous insect orders based on 18S ribosomal data: when bad things happen to good data: Molecular Systematics and Evolution: Theory and Practice. R. DeSalle, G. Giribet and W. Wheeler (eds.), Birkhauser Press, pp. 69-83.

Wiegmann, B. M., J. Kim and M. D. Trautwein. 2009a. Holometabolous Insects (Holometabola), pp. 260-263 in Hedges, B. and S. Kumar. The Timetree of Life. Oxford Univ. Press, Oxford.

Wiegmann, B. M., M. D. Trautwein, J. Kim, B. K. Cassel, M. Bertone, S. L. Winterton and D. K. Yeates. 2009b. Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biology 7: 34.

Wild, A. L. and D. R. Maddison. 2008. Evaluating nuclear protein-coding genes for phylogenetic utility in the Coleoptera. Molecular Phylogenetics and Evolution 48: 877-891.

Received 24 September 2010; accepted 17 March 2011.

(1) McKenna and Farrell (2009) reported estimated divergence times for ali family-level groups in the timetree published by Hunt, et al. (2007).

(2) See McKenna and Farrell (2010) for a discussion of possible placements within or near beetles.

(3) Despite the popularity of BI in studies of beetle molecular phylogeny, Bayesian methods for co-estimating node ages and phylogeny have not yet been applied to the study of major beetle radiations outside of Curculionoidea.

DUANE D. MCKENNA (1)

Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA

(1) Email address for correspondence: dmckenna@ memphis.edu
Table 1. Studies reviewed.

 DNA sequence
Authors Taxonomic focus data used

Howland & Hewitt Coleoptera COI
 1995
Whiting et al. 1997 Holometabola 18S, 28S
Farrell1998 Chrysomeloidea, 18S
 Curculionoidea
Shull et al. 2001 Adephaga 18S
Wheeler et al. 2001 Hexapoda 18S, 28S
Whiting 2002a Holometabola 18S
Whiting 2002b Holometabola 18S
Caterino et al. 2002 Coleoptera 18S
Caterino et al. 2005 Staphyliniformia 18S
 Scarabaeiformia
Vogler 2005 Coleoptera 18S
Hughes et al. 2006 Coleoptera 66 RP genes
Gomez-Zurita et al. Chrysomeloidea 18S, 28S, 16S
 2007
Hunt et al. 2007 Coleoptera 18S, 16S, COI
Misof et al. 2007 Hexapoda 18S
Wild & Maddison Coleoptera 28S, AK, AS, CAD,
 2008 Enolase, PEPCK,
 RNA Pol II, TOPI,
 WG
Sheffield et al. 2008 Coleoptera mt genomes
Cameron et al. 2009 Neuropterida mt genomes
Maddison et al. 2009 Adephaga 18S, 28S, WG
McKenna & Farrell Coleoptera 18S
 2009
McKenna et al. 2009 Curculionoidea EF-1[alpha], AK, 28S,
 18S, 16S, COI
Sheffield et al. 2009 Coleoptera mt genomes
Wiegmann et al. Holometabola AATS, CAD, PGD,
 2009a SNF, TPI, RNA
 Pol II
Wiegmann et al. Holometabola AATS, CAD, PGD,
 2009b SNF, TPI, RNA
 Pol II
Ishiwata et al. 2010 Insecta DNA polymerase
 delta, RNA Pol II
Longhorn et al. 2010 Holometabola 27 RP genes
McKenna & Farrell Holometabola EF-l[alpha], AATS,
 2010 CAD, PGD, SNF, TPI,
 RNA Pol II, 28S,
 18S
Pons et al. 2010 Coleoptera mt genomes
Song et al. 2010 Coleoptera mt genomes

 Beetle
 suborders Strepsiptera
Authors sampled * included? Timetree?

Howland & Hewitt Ad, Po No No
 1995
Whiting et al. 1997 Ad, Ar, Po Yes No
Farrell1998 N/A N/A Yes

Shull et al. 2001 All 4 No No
Wheeler et al. 2001 Ad, Po Yes No
Whiting 2002a All 4 Yes No
Whiting 2002b Ad, My, Po Yes No
Caterino et al. 2002 All 4 Yes No
Caterino et al. 2005 All 4 No No

Vogler 2005 All 4 No No
Hughes et al. 2006 All 4 No No
Gomez-Zurita et al. N/A N/A Yes
 2007
Hunt et al. 2007 All 4 No Yes
Misof et al. 2007 Ad, Po Yes No
Wild & Maddison Ad, Ar, Po No No
 2008

Sheffield et al. 2008 All 4 No No
Cameron et al. 2009 Ad, Po No No
Maddison et al. 2009 All 4 No No
McKenna & Farrell All 4 No Yes
 2009
McKenna et al. 2009 N/A N/A Yes

Sheffield et al. 2009 Ar, Po No No
Wiegmann et al. Po Yes Yes
 2009a

Wiegmann et al. Po Yes Yes
 2009b

Ishiwata et al. 2010 Ad, Po Yes No

Longhorn et al. 2010 Ad, My, Po Yes No
McKenna & Farrell All 4 Yes No
 2010

Pons et al. 2010 All 4 No No
Song et al. 2010 All 4 No No

* Ad = Adephaga, Ar = Archostemata, My = Myxophaga, Po = Polyphaga
COPYRIGHT 2011 New York Entomological Society
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 2011 Gale, Cengage Learning. All rights reserved.

Article Details
Printer friendly Cite/link Email Feedback
Author:McKenna, Duane D.
Publication:Entomologica Americana
Article Type:Report
Geographic Code:1USA
Date:Jan 1, 2011
Words:5450
Previous Article:Fossil cross-validation of the dated ant phylogeny (hymenoptera: formicidae).
Next Article:Obituary, Lawrence Hubert Rolston.
Topics:

Terms of use | Privacy policy | Copyright © 2019 Farlex, Inc. | Feedback | For webmasters