New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi)

We provide 15 new primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes in an attempt to resolve relationships of this diverse group of freshwater fishes with extensive taxonomic sampling. Sequences from this region have the following desirable characteristics for phylogenetic analyses, some of which are lacking from the more commonly used cyt b and 12S/16S rRNA genes: they are (1) easy to align, (2) relatively long (ca. 3.4 kb), and (3) contain more phylogenetically informative variation at 1st and 2nd codon positions. Moreover, the ND4/ND5 gene region is easy to amplify and sequence when employing the protocol suggested herein.     

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.     

Mexican native trouts: a review of their history and current systematic and conservation status

While biologists have been aware of theexistence of native Mexican trouts for over acentury, they have received little study. Thefew early studies that did much more thanmention their existence began in the 1930s andcontinued into the early 1960s, focusingprimarily on distributional surveys andtaxonomic analyses. Starting in the 1980s theBaja California rainbow trout became thesubject of more detailed studies, but verylittle remains known of mainland trouts of theSierra Madre Occidental. We review earlierstudies and report on our own collections andobservations made between 1975 and 2000. Wepresent newly discovered historical evidencethat leads us to conclude that a lostcutthroat trout, a lineage not previously knownfrom Mexico, was collected more than a centuryago from headwaters of the Río Conchos (amajor tributary of the Rio Grande (= RíoBravo)), a basin not previously considered toharbor a native trout. We review the lastcentury of regional natural resource managementand discuss our own observations of trouthabitats. Impacts of logging, road building andovergrazing are widespread and expanding. Manystreams suffer from heavy erosion, siltationand contamination, and though long-termhydrologic data are generally not available,there is evidence of decreased discharge inmany streams. These problems appear related toregion-wide land management practices as wellas recent regional drought. Trout cultureoperations using exotic rainbow trout haverapidly proliferated throughout the region,threatening genetic introgression and/orcompetition with native forms and predation onthem. Knowledge of distribution, abundance,relationships and taxonomy, not to mentionecology and population biology, of nativetrouts of the Sierra Madre Occidental remainsinadequate. Vast areas of most mainlanddrainages are still unexplored by fishcollectors, and even rudimentary informationregarding basic biology, ecology and populationstructure of stocks remains lacking.Concentrated exploration, research andmanagement of this long overlooked andundervalued resource are all urgently needed.The history of natural resources exploitationthat placed so many native trouts of thewestern United States on threatened andendangered species lists is repeating itself inthe Sierra Madre Occidental. Without concertedaction and development of region-widesocio-economic solutions for current, largelynon-sustainable resource management practices,native Mexican trout gene pools will soon be ingrave danger of extinction.     

Systematics of the subgenus Oligocephalus (Teleostei: Percidae: Etheostoma) with complete subgeneric sampling of the genus Etheostoma

The genus Etheostoma is the most diverse clade of freshwater fishes in North America. While studies have been performed with complete sampling of a single subgenus, none have included representatives of all remaining subgenera. The subgenus Oligocephalus is the largest, consisting of 25-27 species in four species groups, and its monophyly has never been clearly demonstrated. The monophyly of this subgenus and its constituent groups was tested using parsimony and Bayesian analyses of ND2 (mtDNA) and the first intron of S7 (nDNA) with complete species sampling from Oligocephalus and complete subgeneric sampling from Etheostoma. Although the subgenus Oligocephalus was not recovered as a monophyletic group in any analyses, monophyletic E. whipplei, Southwestern Darter, and E. spectabile (in part) species groups were recovered in all analyses. All analyses agree that E. okaloosae and both subspecies of E. hopkinsi are not closely related to other members of the subgenus Oligocephalus. E. exile is, however, presenting the strongest evidence yet that recognition of the subgenus Boleichthys is unwarranted.     

Phylogeny,genetic diversity and phylogeography of the genus Codoma (Teleostei,Cyprinidae)

This study represents a thorough analysis of Codoma, a monotypic genus endemic to north‐western Mexico. A previous morphological analysis of the species concluded that there exists several morphological groups in Codoma ornata, suggesting diversity in Codoma could be underestimated. No studies have examined the genetic diversity in Codoma ornata to test this hypothesis and identify independent lineages. We present a phylogeographic analysis using one mitochondrial and two nuclear genes, and specimens from across nine major drainages in both the Chihuahuan Desert and the Sierra Madre Occidental of western Mexico. All genes and analyses recovered populations of Codoma in a well‐supported clade and sister to Tampichthys, and this clade sister to Cyprinella. Analyses of both mitochondrial and nuclear genes indicated Codoma is not monotypic and recover more diversity in the genus than currently recognized. The four (mitochondrial) and five (nuclear) genetically distinct lineages are consistent with those groups outlined in the prior morphological study of the genus. Composition and distribution of these major lineages is also consistent with prior biogeographic hypothesis for other fishes in the region, supporting an ancestral Rio Grande system extending south towards central Mexico. Fragmentation of this paleosystem was followed by allopatric speciation in the Chihuahuan Desert. These results suggest a scenario of long‐term isolation in four major regions (upper Conchos, lower Conchos, Nazas, upper Mezquital). Resolution of the diversity and biogeography of these lineages has many implications for various biological disciplines, especially for evolutionary and conservation studies.     

Regressive progression,progressive regression or neither? Phylogeny and evolution of the Percopsiformes (Teleostei,Paracanthopterygii)

Dillman, C.B., Bergstrom, D.E., Noltie, D.B., Holtsford, T.P. & Mayden, R.L. (2010). Regressive progression, progressive regression or neither? Phylogeny and evolution of the Percopsiformes (Teleostei, Paracanthopterygii). —Zoologica Scripta, 40, 45–60. Cave animals have fascinated scientists for centuries, and clades consisting primarily of cave‐adapted species are even more intriguing. The percopsiforms are an enigmatic group of fishes comprised of nine species in seven genera, with four species in three genera exhibiting characteristic troglomorphic features, such as a lack of pigmentation and eyes. Nucleotide characters presented here provide the first test of monophyly for both the Percopsiformes and Amblyopsidae with this character type and taxonomic completeness. Characters of ND2 support a monophyletic Percopsiformes and Amblyopsidae and further document phylogeographic subdivision in two stygobitic genera, Amblyopsis and Typhlichthys, in Amblyopsidae. Age estimates from time‐calibrated branch lengths utilizing two independent intra‐lineage fossils indicate that the ancestor to amblyopsids is Eocene in age, and that phylogeographic subdivision in both Amblyopsis and Typhlichthys occurred primarily in the Miocene. Interestingly, ancestral character state reconstruction for the amblyopsids strongly supports the re‐evolution of eyes and body pigment. While certainly unconventional, but supported with this character set, the hypothesis provides continued challenge to Dollo’s Law.