Analysis of the Ictalurus pricei complex (Teleostei: Ictaluridae) in Northwest Mexico based on mitochondrial DNA.
We examined mitochondrial cytochrome oxidase subunit I (COI) in Yaqui catfish from the Yaqui River (n = 1) and the Fuerte River (n = 1) and the Sinaloa catfish from the Culiacan (n = 2) and San Lorenzo (n = 1) basins (Fig. 1; Table 1). The tissues that we used were fin clips preserved in [greater than or equal to] 95% ethanol at the time of capture. We fixed the remainder of each specimen in 10% formalin and later transferred it to 70% ethanol for deposition as vouchers in the Native Fish Collection of the Departamento de Investigaciones Cientificas y Tecnologicas de la Universidad de Sonora.
We extracted genomic DNA with the QIAamp DNA Mini Kit from QIAGEN (Venlo, Netherlands). We amplified the COI gene by using polymerase chain reaction (PCR) primers tRNATyrF and tRNASerR (Waldbieser et al., 2003). We performed the amplification with 10 pmol of each primer and approximately 200 ng of genomic DNA in a total volume of 12.5 [micro]l using PuReTaq Ready-to-Go PCR beads (GE Healthcare, Little Chalfont, United Kingdom). The PCR beads contain 2.25 units of puReTaq DNA polymerase, 100 [micro]M of each dNTP in 10 mM Tris-HCl (pH 9.0), 50 mM KCl, and 1.5 mM Mg[Cl.sub.2] when used in a total volume of 25 pl. Amplification employed the following conditions: 94[degrees]C for 5 min followed by 34 cycles of 94[degrees]C for 50 s, 55[degrees]C for 50 s, and 72[degrees]C for 3 min, and finally one cycle of 7 min at 72[degrees]C. The PCR products were sent to Macrogen, Inc. (Seoul, Korea) for purification and bidirectional sequencing with the primers used in the PCR reactions.
We edited the COI sequences to a size of 651 bp and deposited them in GenBank. For the phylogenetic analysis, the ingroup included one haplotype from the mitochondrially rather homogeneous species (McClure-Baker et al., 2010) wolf catfish (Ictalurus lupus; GenBank accession number JN026911), and three from channel catfish (Ictalurus punctatus; NC003489, JF292358, JF292388). We used two haplotypes from blue catfish (Ictalurus furcatus; EU752098, JF292374) as the outgroup (Lundberg, 1992). We translated the sequences using the online software Expasy Translate (http://web.expasy.org/translate/); alignment with BLASTP (Altschul et al., 1990) conformed to a fish mitochondrial COI gene frame.
We assessed phylogenetic relationships with neighborjoining, maximum parsimony, and maximum likelihood (ML). We set neighbor-joining analyses using Kimura's twoparameter model. For maximum parsimony we used PAUP* (Swofford, 2002) in a heuristic search with tree bisection reconnection branch swapping. We estimated nodal support by nonparametric bootstrapping with 1,000 pseudoreplicates and 10 random addition sequences. We used ModelTest 3.6 to choose the most appropriate substitution model (Posada and Crandall, 1998) and incorporated this model (Generalised time-reversible[GTR] + G + I) in the maximum likelihood heuristic search provided by PAUP*. We input the resulting maximum likelihood tree and the initial tree search settings into PHYML (Guindon and Gascuel, 2003) for a bootstrap analysis (1,000 pseudoreplicates) of nodal support.
Sequence divergence among the three Sinaloa catfish haplotypes ranged from 0.1% to 0.9% (mean = 0.6%) and that between the two Yaqui catfish haplotypes was 0.9%. Mean divergence between the two groups of haplotypes was 1.3%. In contrast, these five sequences averaged 2.8% divergent from I. lupus (range = 2.6-3.1%) and 6.3% from I. punctatus (range = 6.6-7.7%).
The maximum parsimony analysis produced three equally parsimonious trees (not shown) that were consistent with the maximum likelihood tree (Fig. 2). With both approaches, I. lupus was resolved as sister to a clade comprising the Sinaloa and Yaqui catfishes. We found no consistent support for reciprocal monophyly between the Yaqui and Sinaloa catfishes, but this possibility was not rejected by the analysis. With maximum likelihood, the two forms appeared reciprocally monophyletic in the optimal tree and the monophyly of the Sinaloa catfish received bootstrap support (81%); there was also bootstrap support (77%) for the monophyly of I. pricei. In contrast, maximum parsimony supported monophyly for the Yaqui catfish (98% bootstrap support), but did not resolve relationships of the three Sinaloa catfish haplotypes. This lack of consistency likely is a result of the short (651-bp) sequence examined. A full understanding of the I. pricei complex will require additional sequence information, including nuclear genes, and more thorough sampling of Ictalurus from Mexico. Nonetheless, this analysis provides the first phylogenetic support for recognition of the I. pricei complex and the first evidence of a possible sister relationship with I. lupus, a species endemic to the Rio Grande and drainages of northeastern Mexico.
We thank S. Sanchez-Gonzales, J. E. Brooks, and N. Smith for field assistance. Comments of J. Lundberg and one anonymous reviewer improved the manuscript. M. Castarieda-Rivera was supported by a fellowship from Consejo Nacional de Ciencia y Tecnologia. This work was funded by Consejo Nacional de Ciencia y Tecnologia. Permit for collection issued by Secretaria de Agricultura, Ganaderia, Desarrollo Rural, Pesca y Alimentacion, Permiso de Pesca de Fomento DGO-PA.03947.250406.1606.
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Submitted 13 January 2014.
Acceptance recommended by Associate Editor, Robert J. Edwards, 27 July 2014.
Melissa Castaneda-Rivera, Jose M. Grijalva-Chon, Luis E. Gutierrez-Millan, Gorgonio ruiz-campos, and Alejandro Varela- Romero *
Departamento de Investigaciones Cientificas y Tecnologicas de la Universidad de Sonora, P.O. Box 1819, Hermosillo, Sonora 83000, Mexico (MCR, JMGC, LEGM, AVR)
Universidad Autonoma de Baja California, Facultad de Ciencias, Ensenada, Baja California 22860, Mexico (GRC)
* Correspondent: email@example.com
Table 1--Collection localities, GenBank accession numbers for the cytochrome oxidase subunit 1 sequences, and catalog numbers for voucher specimens of Ictalurus from northwestern Mexico. Locality numbers as in Fig. 1. Species Locality Haplotype/ Catalog accession number (a) number Ictalurus sp. 1. El Rodeo Creek Haplotype 1 USON 01115 upstream of KJ019216 El Rodeo Haplotype 2 KJ019217 Ictalurus sp. 2. San Lorenzo Haplotype 3 USON 01120 River N of El KJ019218 Igualamo Ictalurus 3. Batopilas River, KF536995 USON 01050 pricei 15 km E of Batopilas Ictalurus 4. Tutuaca River, KF536996 USON 01183 pricei 5 km downstream of El Nogal Ranch Species Lat/long Ictalurus sp. 24[degrees]54.677'N, 106[degrees]46.941'W Ictalurus sp. 24[degrees]41.983'N, 106[degrees]33.233'W Ictalurus 27[degrees]05.923'N, pricei 107[degrees]40.773'W Ictalurus 28[degrees]34.733'N, pricei 108[degrees]23.140'W (a) USON = Native Fish Collection of the Departamento de Investigaciones Cientificas y Tecnologicas de la Universidad de Sonora.
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|Author:||Castaneda-Rivera, Melissa; Grijalva-Chon, Jose M.; Gutierrez-Millan, Luis E.; Ruiz-Campos, Gorgonio;|
|Date:||Sep 1, 2014|
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