Mitochondrial DNA patterns describe the evolutionary history of the bonnethead shark Sphyrna tiburo (Linneus 1758) complex in the western Atlantic Ocean.

The apparent lack of physical barriers in the marine realm has created the conception that many groups have a constant gene flow. However, changes in ocean circulation patterns, glacial cycles, temperature, and salinity gradients are responsible for vicariant events in many fish species, including sharks. The bonnethead shark, Sphyrna tiburo, is an endangered small coastal shark species. Although considerable efforts have recently been undertaken, little remains known about the possible biogeographic scenario that can explain its actual distribution within the western Atlantic (WA). Here, we used 599 mitochondrial sequences to assess the phylogeographic structure and implement Bayesian phylogenetic analyses to obtain divergence times and reconstruct the ancestral geographic range. This allowed us to infer processes responsible for the diversification of S. tiburo into major divergent lineages. Our results indicated that S. tiburo in the WA represents three independent lineages, with Brazilian samples differentiated into a distinct genetic cluster. The posterior probability of ancestral range analysis indicated that the species likely originated in the northern region (Carolina Province and the southern Gulf of Mexico), where it colonized southward through the uplifting of the Central American Isthmus (CAI). The Northern and Caribbean genetic clusters appear to have arisen from the intensification of the Loop Current, which currently flows northward passing the Yucatan Peninsula, Gulf of Mexico, and east Florida. Following initial colonization, the Northeastern Brazil group differentiated from the Caribbean region due to the sediment and freshwater discharge of the Amazon-Orinoco Plume. Thus, the evolutionary history of the S. tiburo complex can be explained by a combination of dispersal and vicariance events that occurred over the last ~5 million years (MY). We established and confirmed the species and population limits, demonstrating that the Amazon-Orinoco Plume constitutes a significant dispersal barrier for coastal sharks. Finally, we discuss some recommendations for the conservation of the bonnethead shark.

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.

Genetic divergence at species boundaries of the dolphinfish (Coryphaena hippurus) in the Tropical Eastern Pacific.

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.

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.

Mitochondrial DNA genome evidence for the existence of a third divergent lineage in the western Atlantic Ocean for the bull shark (Carcharhinus leucas).

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.

Independent evolutionary lineage of the clingfish Gobiesox adustus (Gobiesocidae) from Isla del Coco, Costa Rica / Linaje evolutivo independiente del clingfish Gobiesox adustus (Gobiesocidae) de Isla del Coco, Costa Rica

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.

Possible female philopatry of the smooth hammerhead shark Sphyrna zygaena revealed by genetic structure patterns.

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.

Molecular evidence supporting the expansion of the geographical distribution of the Brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes: Rhinopteridae) in the western Atlantic.

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.

Complete mitogenome sequences of the pacific red snapper (Lutjanus peru) and the spotted rose snapper (Lutjanus gutattus).

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.

A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico.

We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP) following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.

Spatial and temporal genetic homogeneity of the Monterey Spanish mackerel, Scomberomorus concolor, in the Gulf of California.

The genetic homogeneity of the Monterey Spanish mackerel Scomberomorus concolor population in the Gulf of California was confirmed using nine nuclear microsatellite loci in combination with mitochondrial cytochrome b gene sequences. Samples were collected from the upper and central Gulf areas, representing the two main biogeographical regions of the Gulf. The analyses support the existence of a single panmictic population of S. concolor inhabiting the Gulf of California which in terms of fishery management represents a single genetic stock. Additionally, the contemporary effective population size estimated for the S. concolor population (Ne = 3056.9) was high and similar to another pelagic species. The gene flow seems to be bidirectional between the upper and central Gulf, which coincides with the seasonal movements between both regions related to spawning and feeding activities. A population expansion event was detected, which agrees with a colonization-expansion hypothesis of the S. concolor population in the Gulf.

Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs.

Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.

The complete mitochondrial DNA of white shark (Carcharodon carcharias) from Isla Guadalupe, Mexico.

The Isla Guadalupe white shark mitochondrial structure is similar to the one previously reported for a white shark individual from Taiwan with a total length of 16,745 and 16,742 bp respectively; the base composition of the genomes was as follow A (30.60%), T (28.67%), C (26.86%) and G (13.87%), contains 13 protein-coding genes and 24 tRNA genes and the non-coding control region. The tRNA genes range from 70-72 bp. Gene order is the same as in other vertebrates and teleosts.

The complete mitochondrial DNA of the bull shark (Carcharhinus leucas).

The bull shark mitochondrial structure is similar to that of other elasmobranchs; it has a total length of 16,100 bp, the base composition of the genomes was as follows: A (31.35%), T (31.35%), C (24.38%) and G (12.90%). It contains 13 protein-coding genes and 23 tRNA genes. The tRNA genes range from 70-72 bp. Gene order is the same as in other vertebrates and teleosts.