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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.

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Background: Marine species constitute commercially important resources, and knowledge about mechanisms that shape phylogeographic patterns and genetic structure provides valuable information for conservation. The dolphinfish, Coryphaena hippurus, is one of the most important species caught in the Tropical Eastern Pacific (TEP). However, the lack of consensus about the existence of genetically differentiated populations in the area has hindered the adoption of management strategies to ensure its viability. Methods: We assessed genetic variation and phylogeographic structure using two mitochondrial genes and 14 nuclear DNA microsatellite loci. Population genetic tools were used to characterize the spatial distribution of genetic variation of C. hippurus in the TEP, evaluate the extent of connectivity between dolphinfish populations, infer potential barriers to gene flow, and test for signals of contemporary and historical demographic expansions. Results: Mitochondrial DNA sequences showed genetic homogeneity across locations in the TEP, as well as a strong signal of population expansion dated to the late Pleistocene. In contrast, nuclear microsatellite markers resolved four genetically distinct groups with a remarked genetic differentiation between the most distant locations, at the northern and southern boundaries of the species' range. High mean genetic diversity was found at all localities (Hs = 0.66-0.81). Notwithstanding, positive F IS and low effective population size (Ne = 77.9-496.4) were also recorded. Conclusions: The distribution of genetic variation could be related to expansion-contraction cycles following seasonal temperature changes at transitional areas, promoting population subdivisions. However, we cannot rule out the effect of oceanographic dynamics to the observed patterns. Although this marine species remains highly abundant despite commercial exploitation, the low Ne values are of conservation concern and must be considered in fishery management plans.

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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.

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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.

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We report for the first time a highly divergent lineage in the Caribbean Sea for the bull shark (Carcharhinus leucas) based on the analysis of 51 mitochondrial DNA genomes of individuals collected in the western North Atlantic. When comparing the mtDNA control region obtained from the mitogenomes to sequences reported previously for Brazil, the Caribbean lineage remained highly divergent. These results support the existence of a discrete population in Central America due to a phylogeographic break separating the Caribbean Sea from the western North Atlantic, Gulf of Mexico and South America.

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Introduction: Isla del Coco is an important protected area for marine fauna in the Eastern Tropical Pacific. In this area, the species that inhabit the intertidal zone have been subject to few studies. One of the species inhabiting these areas is the clingfish Gobiesox adustus (Gobiesocidae). Objective: To analyze for the first time the mitochondrial gene cytochrome oxidase subunit 1 (cox1) of G. adustus' population from Isla del Coco and compare it with those of continental coast of Costa Rica and Ecuador. Methods: We constructed a haplotype network for these samples. Genetic diversity, distance and structure were calculated by several software. The historical demography of Isla del Coco samples was assessed with the method Bayesian skyline plot as implemented in BEAST2. Results: The samples segregate into three haplogroups: one consisting of the Isla del Coco samples, a second consisting of a subset of the Ecuador samples, and a third consisting of Costa Rica and the remaining Ecuador samples. The genetic distances between the three haplogroups range between 1.6% and 2.1% (uncorrected p-distance), and pairwise ΦST and AMOVA results between the three haplogroups show high and significant values. Conclusions: The Isla del Coco haplogroup showed a Pleistocene population growth, which agrees with demographic patterns found in other marine organisms. The history of isolation of the G. adustus population from Isla del Coco demonstrates the evolutionary independence of this population.

Introducción: Isla del Coco es un área protegida importante para la fauna marina en el Pacifico Oriental Tropical. En esta área, las especies que habitan la zona intermareal han sido objeto de pocos estudios. Una de las especies que habitan en estas áreas es el clingfish Gobiesox adustus (Gobiesocidae). Objetivo: Analizar por primera vez el gen mitocondrial citocromo oxidasa sub unidad 1 (cox1) de poblaciones de Isla del Coco y compararlo con las de la zona continental de Costa Rica y Ecuador. Métodos: Se construyó una red de haplotipos. La diversidad, la distancia y la estructura genética fueron calculadas por diversos programas. La demografía histórica de las muestras de Isla del Coco fue evaluada con el método Bayesian skyline plot implementado en BEAST2. Resultados: Las muestras se agruparon en tres haplogrupos: en un haplogrupo se incluyó a los individuos de Isla del Coco, otro haplogrupo integró las muestras de Ecuador y un tercer grupo incluyó las muestras restantes de Costa Rica y Ecuador. Las distancias genéticas entre los tres haplogrupos oscilan entre 1.6% y 2.1% (p-distancia, no corregida), las distancias ΦST y los resultados de AMOVA entre los tres haplogrupos muestran valores altos y significativos. Conclusiones: El haplogrupo de Isla del Coco mostró un crecimiento poblacional datado en el Pleistoceno, coincidiendo con la demografía poblacional encontrada en otros organismos marinos. La historia de aislamiento de la población de G. adustus de Isla del Coco demostró la independencia evolutiva de esta población.

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We assessed the spatial pattern of genetic structure of smooth hammerhead shark Sphyrna zygaena in 10 localities from the Northern Mexican Pacific. A total of 35 haplotypes were identified in 129 sequences of the mtDNA control region. The results showed slight but significant genetic structure among localities (ΦST = 0.044, P < 0.001). In addition, the localities with highest number of juveniles were genetically different (ΦST = 0.058, P < 0.024), which may be representative of nursery areas. The genetic differentiation pattern can be associated to female philopatry and preference for particular birthing sites. Finally, historical demography shows that S. zygaena populations present a recent demographic expansion that occurred during glacial events in the late Pleistocene to early Holocene.

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The genus Rhinoptera is composed of eight species widely distributed in tropical, subtropical and temperate coastal waters, which inhabit bays, estuaries and river mouths. Cownose ray Rhinoptera bonasus has been reported to inhabit the Western Atlantic including the Gulf of Mexico and the Caribbean, whereas the Brazilian cownose ray R. brasiliensis has been considered endemic to the coast of Brazil. Recent reports of R. brasiliensis in the Gulf of Mexico bring about the question of whether the species has a wider range than previously reported. Here, the mitochondrial genes COI, Cytb, NADH2 and the nuclear gene RAG1 were used to distinguish among species and to confirm the presence of R. brasiliensis in the Gulf of Mexico. R. brasiliensis specimens collected along the southern Gulf of Mexico showed a remarkable genetic and morphological affinity when compared with R. brasiliensis specimens from Brazil, supporting the presence of the species in Mexico (from Veracruz through Campeche) and providing evidence that its distribution ranges from Brazil to the Caribbean Sea and the Gulf of Mexico. Both species overlap geographically to a large degree, leading to a reassessment of their conservation status. Our results also show that R. bonasus distribution in the Gulf of Mexico may be restricted to the northern portion, in US waters.

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The structure of the mitochondrial genome for the Pacific red snapper, Lutjanus peru, and the spotted rose snapper, Lutjanus gutattus, of specimens collected in the eastern Pacific is similar to the reported for other teleosts and shares the same configuration with other members of the family Lutjanidae. It has a total length of 16 502 and 16 508 base pairs (bp) for Lutjanus peru and L. gutattus, respectively; on average the base composition was A (27.9%), T (24.8%) C (30.9%), and G (16.4%), containing 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes; and the leucine (Leu) tRNA is duplicated.

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