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Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this data set, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average FST=0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. In addition, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy–Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.

Made available in DSpace on 2018-11-26T17:48:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-22 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) PROPE/UNESP The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F-ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme. Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Univ Santiago Compostela, Vet Fac, Lugo, Spain Sao Paulo State Univ, Sch Sci, Bauru, Brazil Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Sao Paulo State Univ, Sch Sci, Bauru, Brazil FAPESP: 2014/03772-7 FAPESP: 2014/05732-2 CNPq: 446779/2014-8 CNPq: 305916/2015-7

Made available in DSpace on 2018-11-26T17:06:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-08-30 Investigador-FCT contract from the Portuguese Foundation for Science and Technology (FCT, Fundacao para a Ciencia e Tecnologia) - EU European Social Fund Programa Operacional Potencial Humano Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The 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. Univ Estadual Paulista, Lab Biol & Genet Peixes, Botucatu, SP, Brazil Univ Fed Sao Paulo, Inst Marine Sci, Lab Genet Pesqueira & Conservacao, Santos, SP, Brazil Valencia Coll, Lake Nona Campus, Orlando, FL USA Univ Florida, Florida Museum Nat Hist, Florida Program Shark Res, Gainesville, FL 32611 USA Portuguese Inst Ocean & Atmosphere, IPMA, Algarve, Portugal Univ Estadual Paulista, Lab Biol & Genet Peixes, Botucatu, SP, Brazil Programa Operacional Potencial Humano: IF/00253/2014 FAPESP: 2013/14555-4 FAPESP: BIOTA 2011/23787-0

Made available in DSpace on 2018-12-11T17:03:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-01 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 (τ) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ØST = 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. Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP) Instituto Português Do Mar e DaAtmosfera (IPMA) Centro de Ciências Do Mar (CCMAR) Universidade Algarve School of Marine and Atmospheric Science Stony Brook University Microwave Telemetry Inc. Shark Research and Conservation Program Cape Eleuthera Institute Manta Trust Catemwood House Department of Biology and Environmental Science Linnaeus University Blue Resources Departamento de Pesca e Aquicultura Universidade Federal Rural de Pernambuco Laboratório de Genética Pesqueira e Conservação Instituto Do Mar Universidade Federal de São Paulo (UNIFESP) Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP)