Browsing by Author "Foresti, Fausto"
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- Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus)Publication . Domingues, Rodrigo R.; Mastrochirico-Filho, Vito Antonio; Mendes, Natalia J.; Hashimoto, Diogo T.; Coelho, Rui; da Cruz, Vanessa Paes; Antunes, Agostinho; Foresti, Fausto; Mendonca, Fernando F.The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark found worldwide in tropical and subtropical waters. However, the understanding of its biology at molecular level is still incipient. We sequenced the messenger RNA isolated from eye and liver tissues. De novo transcriptome yielded a total of 705,940 transcripts. A total of 3774 genes were differentially expressed (DEGs), with 1612 in the eye and 2162 in the liver. Most DEGs in the eye were related to structural and signaling functions, including nonocular and ocular opsin genes, whereas nine out of ten most overexpressed genes in the liver were related to tumor suppression, wound healing, and human diseases. Furthermore, DEGs findings provide insights on the monochromatic shark vision and a repertory of cancer-related genes, which may be insightful to elucidate shark resistance to cancer. Therefore, our results provide valuable sequence resources for future functional and population studies.
- Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)Publication . Domingues, Rodrigo R.; Mastrochirico-Filho, Vito Antonio; Mendes, Natalia J.; Hashimoto, Diogo T.; Coelho, Rui; Antunes, Agostinho; Foresti, Fausto; Mendonça, Fernando F.The shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two massive parallel sequencing approaches, double digest restriction site-associated DNA sequencing (ddRAD) and RNA sequencing (RNAseq), for single nucleotide polymorphism (SNP) discovery in the shortfin mako. The ddRAD yielded a total of 82,676 putative SNPs. For RNAseq, a total of 129,663 putative SNPs were found. After the stricter filtering procedure, 405 SNPs from ddRAD and 1165 SNPs from RNAseq were retained and suitable for further analysis. Annotation analysis of SNPs from ddRAD revealed a total of 55 gene associated SNP markers, of which 32 SNPs (58.2%) are associated with diseases and defense responses, 9 SNPs (16.4%) are associated with developmental process, and 3 SNPs (5.4%) are present in genes involved in the reproductive function. For RNAseq, 739 SNPs were annotated and associated to relevant functions amongst which 10 SNPs (0.53%) were related with reproduction, 6 SNPs (0.32%) with growth, and 9 (0.48%) with locomotion. Overall, the genotyping of the SNPs was followed by the validation of 255 SNPs from ddRAD and 646 for RNAseq in 31 individuals from the Atlantic and Indian oceans. Our results provide valuable sequence resources for future population genomics analysis, comparative genomics, phylogenomics, and molecular evolution of the globally endangered shortfin mako shark.
- Global phylogeography of sailfish: deep evolutionary lineages with implications for fisheries managementPublication . da Silva Ferrette, Bruno Lopes; Mourato, Bruno; Vieira Hazin, Fabio Hissa; Arocha, Freddy; Williams, Samuel Mackey; Rodrigues Junior, Carlos Egberto; Porto-Foresti, Fabio; de Amorim, Alberto Ferreira; Rotundo, Matheus Marcos; Coelho, Rui; Hoolihan, John P.; Sow, Fambaye Ngom; Diaha, N'guessan Constance; Romanov, Evgeny, V; Domingues, Rodrigo Rodrigues; Oliveira, Claudio; Foresti, Fausto; Mendonca, Fernando FernandesSince the Miocene profound climatic changes have influenced the biology and ecology of species worldwide, such as their connectivity, genetic population structure, and biogeography. The goal herein is to evaluate the phylogeography of sailfish Istiophorus platypterus between the Atlantic, Indian, and Pacific oceans. Our results evidenced a high genetic diversity and three distinct populations among the ocean basins with limited gene flow among them. In addition, the species is characterized by two deep evolutionary lineages that diverged during the Miocene/Pliocene transition, one of them is circumtropical while the other is restricted to the Atlantic Ocean. These lineages evolved along the successive glacial-interglacial cycles from the Pleistocene and remained isolated from each other in glacial refugium until deglaciation. Assessments of sailfish suggest it may be subject to overfishing and the results herein imply the need to re-evaluate the current stock delimitations and management measures adopted by the Regional Fisheries Management Organizations, especially in the Atlantic and the Indo-Western Pacific oceans to effectively manage the species. In addition, this work highlights that both lineages should at least be treated as two distinct management units in the Atlantic Ocean until their taxonomic status is fully resolved, given their high genetic divergence.
- Global phylogeography of the smooth hammerhead shark: glacial refugia and historical migration patternsPublication . Lopes da Silva Ferrette, Bruno; Coelho, Rui; Peddemors, Victor Marten; Ovenden, Jennifer R.; De Franco, Bruno Alexandre; Oliveira, Claudio; Foresti, Fausto; Mendonça, Fernando FernandesExtreme climate changes during the Cenozoic Era strengthened different biogeographical barriers that decreased the connectivity among populations, triggering lineage diversification of different species worldwide. The mitochondrial DNA control region was employed to explore the phylogeography of Sphyrna zygaena, a globally distributed species threatened by unsustainable, illegal, unreported and unregulated fisheries triggered by the international shark fin trade. It is listed as 'Vulnerable' by the IUCN Red List and its trade is regulated by CITES Appendix II. Only 13 haplotypes were found with low genetic diversity levels (hd = 0.686 +/- 0.014; pi = 0.00206 +/- 0.00004) compared with other species of the Sphyrnidae family. The species has a very strong phylogeographic population structure among the Atlantic, Indian and Pacific Oceans (phi(ST) = 0.79132). Worldwide, there are six distinct populations with some haplotype sharing. These populations are probably connected by a stepping-stone dispersal of a small number of migrants per generation from the Indo-Pacific towards the Atlantic. Modelling suggests that S. zygaena diverged into two lineages around 6.96 million years ago which have been isolated in glacial refuges in the Atlantic and Indo-Pacific oceans; and after deglaciation, a population expansion probably permitted secondary contact. Conservation plans to establish differentiated management units should be adopted in each of the identified populations. Among these, the Eastern Central Atlantic and West Indo-Pacific are the most important areas for the species considering the historical migration routes that act as a bridge connecting the Atlantic and Indo-Pacific Oceans while the Gulf of Guinea connects the Atlantic populations. Still, further studies are required to know if these populations are also linked with nursery areas for the species. The results herein can help to delimit the main evolutionarily significant units to implement effective policies to establish differentiated management units as starting points to genetic monitoring programmes for Sphyrna zygaena.
- High connectivity of the Crocodile Shark between the Atlantic and Southwest Indian Oceans: highlights for conservationPublication . da Silva Ferrette, Bruno Lopes; Mendonca, Fernando Fernandes; Coelho, Rui; Vasconcelos de Oliveira, Paulo Guilherme; Vieira Hazin, Fabio Hissa; Romanov, Evgeny V.; Oliveira, Claudio; Santos, Miguel Neves; Foresti, FaustoAmong the various shark species that are captured as bycatch in commercial fishing operations, the group of pelagic sharks is still one of the least studied and known. Within those, the crocodile shark, Pseudocarcharias kamoharai, a small-sized lamnid shark, is occasionally caught by longline vessels in certain regions of the tropical oceans worldwide. However, the population dynamics of this species, as well as the impact of fishing mortality on its stocks, are still unknown, with the crocodile shark currently one of the least studied of all pelagic sharks. Given this, the present study aimed to assess the population structure of P. kamoharai in several regions of the Atlantic and Indian Oceans using genetic molecular markers. The nucleotide composition of the mitochondrial DNA control region of 255 individuals was analyzed, and 31 haplotypes were found, with an estimated diversity Hd = 0.627, and a nucleotide diversity pi = 0.00167. An analysis of molecular variance (AMOVA) revealed a fixation index phi(ST) = -0.01118, representing an absence of population structure among the sampled regions of the Atlantic Ocean, and between the Atlantic and Indian Oceans. These results show a high degree of gene flow between the studied areas, with a single genetic stock and reduced population variability. In panmictic populations, conservation efforts can be concentrated in more restricted areas, being these representative of the total biodiversity of the species. When necessary, this strategy could be applied to the genetic maintenance of P. kamoharai.
- Microsatellite loci in the tiger shark and cross-species amplification using pyrosequencing technologyPublication . Mendes, Natalia J.; Cruz, Vanessa P.; Ashikaga, Fernando Y.; Camargo, Samia M.; Oliveira, Claudio; Piercy, Andrew N.; Burgess, George H.; Coelho, Rui; Santos, Miguel N.; Mendonca, Fernando F.; Foresti, FaustoThe tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide.
- A new map of the tiger shark (Galeocerdo cuvier) genetic population structure in the western Atlantic Ocean: Hypothesis of an equatorial convergence centrePublication . Carmo, Camila B.; Ferrette, Bruno L.S.; Camargo, Sâmia M.; Roxo, Fábio F.; Coelho, Rui; Garla, Ricardo C.; Oliveira, Claudio; Piercy, Andrew N.; Bornatowski, Hugo; Foresti, Fausto; Burgess, George H.; Mendonça, Fernando F.The tiger shark (Galeocerdo cuvier) is a common widespread coastal–pelagic shark species whose population genetic structure has only recently been the object of genetic studies. In this study, the tiger's shark mitochondrial DNA control region was sequenced for a sample of 172 individuals from the western Atlantic and from Australia's east coast in the Pacific Ocean. The results show a moderate variation in genetic diversity (h = 0.615 ± 0.038, π = 0.00184 ± 0.00021) with a strong population structure between Atlantic areas (ΦST = 0.28141, P = 0.00001). The maternal lineage has high site fidelity, which paradoxically is coupled with connectivity across open ocean stretches to Fernando de Noronha Archipelago, which is identified as an important hotspot for this species. These results help with the understanding of what drives the displacement of this shark, at intra‐ and/or inter‐ocean basins levels, and can help inform the implementation of future conservation and management measures. We recommend that the conservation of genetic diversity should be maintained at a global level and its maintenance should be pursued diligently in all populations of tiger shark. As the Fernando de Noronha region in the western Atlantic appears to contain the largest global genetic diversity of the species, this area should be treated as a marine reserve or ecological refuge for the tiger shark.
- Population genetics of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans: implications for conservationPublication . Morales, Millke Jasmine Arminini; Mendonça, Fernando Fernandes; Magalhães, Carolina Oliveira; Oliveira, Claudio; Coelho, Rui; Santos, Miguel Neves; Cruz, Vanessa Paes; Piercy, Andrew; Burgess, George; Hazin, Fabio Vieira; Foresti, FaustoPopulation structure and genetic connectivity are pivotal contributions to the establishment of conservation strategies for fisheries management, in particular for highly migratory species that are affected by commercial fisheries. This study used partial sequences of mitochondrial DNA control region to determine the genetic structure of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans. A total of 858 base pairs of mtDNA CR from 228 individuals were analyzed. The resulting nucleotide diversity (π) was 0.0011 ± 0.0008 and the haplotype diversity (h) was 0.127 ± 0.030. These are the lowest diversities registered in elasmobranchs with this genetic marker. Two genetically distinct lineages were identified, one of them represented by 3.9% of the analyzed individuals and none restricted to any particular area. Simulated scenarios of population structure, tested with AMOVA and pairwise ΦST did not result in significant values indicating high connectivity among all sampled groups. The absence of population structure, even between Atlantic and Indian Oceans, corroborates the high dispersal ability of this species. The low genetic diversity detected in this species and the identification of two historical lineages occurring in sympatry, one represented by a very small number of individuals, should be considered in the conservation efforts and management plans of A. superciliosus.
- Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNAPublication . Camargo, Samia M.; Coelho, Rui; Chapman, Demian; Howey-Jordan, Lucy; Brooks, Edward J.; Fernando, Daniel; Mendes, Natalia J.; Hazin, Fábio H. V.; Oliveira, Claudio; Santos, Miguel N.; Foresti, Fausto; Mendonca, Fernando F.Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (pi) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (phi(ST) = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.