Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications.

BACKGROUND: The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species. METHODS AND RESULTS: The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759 bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica. CONCLUSION: The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.

The complete mitochondrial genome of the Mexican blind brotula Typhlias pearsei (Ophidiiformes: Dinematichthydae): an endemic and troglomorphic cavefish from the Yucatán Peninsula karst aquifer.

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group.

The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternoninfernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics.

Ophisternoninfernale is one of the 200+ troglobitic fish species worldwide, and one of the two cave-dwelling fishes endemic to the karstic aquifer of the Yucatán Peninsula, Mexico. Because of its elusive nature and the relative inaccessibility of its habitat, there is virtually no genetic information on this enigmatic fish. Herein we report the complete mitochondrial genome of O.infernale, which overall exhibits a configuration comparable to that of other synbranchiforms as well as of more distantly related teleosts. The KA/KS ratio indicates that most mtDNA PCGs in synbranchiforms have evolved under strong purifying selection, preventing major structural and functional protein changes. The few instances of PCGs under positive selection might be related to adaptation to decreased oxygen availability. Phylogenetic analysis of mtDNA comparative data from synbranchiforms and closely related taxa (including the indostomid Indostomusparadoxus) corroborate the notion that indostomids are more closely related to synbranchiforms than to gasterosteoids, but without rendering the former paraphyletic. Our phylogenetic results also suggest that New World species of Ophisternon might be more closely related to Synbranchus than to the remaining Ophisternon species. This novel phylogenetic hypothesis, however, should be further tested in the context of a comprehensive systematic study of the group.

Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history.

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity. Goodea (Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history of Goodea from across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub-group II of the Northeast haplogroup. All this suggests a recent colonization of Goodea atripinnis throughout some of the biogeographic regions currently inhabited by this species.