Genetic composition of ray viola Pseudobatos percellens (elasmobranchii: rhinobatidae) using SNPs

Author(s)

Bruno de Campos Souza

• Document type: Master's Dissertation
• Press: Botucatu. 2022-01-12.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu
• Defense date: 2021-11-12
• Advisor: Fausto Foresti

Abstract

Marine biodiversity is a growing threat in the face of countless environmental changes. Understanding how organisms respond to such changes is a major concern for scientists, especially involving studies of genetic diversity that can be better elucidated to with the recent development of technologies in genomics. Next-generation sequencing has transformed the field of functional genomics, enabling the identification of single nucleotide polymorphisms (SNPs) throughout the genome. An interesting model for the application of this methodology is represented by the guitarfish species Pseudobatos percellens, popularly known as “guitarfish”, since the lack of studies involving populations of this species addressing mainly issues of structuring and genetic diversity. This work aimed to genetically characterize the populations of P. percellens that occur on the Brazilian coast, in investigations that involved the identification of possible occurrence of genetic structuring in the is species using molecular markers such as SNPs, in addition to identifying connections, differences and similarities between populations with the application of statistical analyzes used in population genetics. Fifty-two samples of P. percellens obtained from localities in the coastal region of the states of Amapá, Pará, Pernambuco, São Paulo and Paraná were used. Filtering the SNPs resulted in a final set of 3,329 markers of this type. For all localities the observed heterozygosity (Ho) had a higher value than the expected heterozygosity (He) and the values for the fixation index or coefficient of inbreeding (Fis) were negative for all sampled localities, indicating that there was no inbreeding in these groups and an excess of heterozygotes. The results indicate a population structure with significant Fst and the F statistics (ΦST estimates) generated by AMOVA revealed the existence of significant genetic heterogeneity, with a partition of genetic variation. Bayesian and DAPC analysis revealed at least two distinct genetic groupings of P. percellens. The migration rates calculated through migrant’s number estimated returned high connectivity between North (Amapá e Pará) and Northeast regions by the existence of gene flow among the individuals of these regions. In the same way, high connectivity between Southeast (São Paulo) e South (Paraná) areas was observed. However, the values of genetic flow between these two groups (Norte/Nordeste vs. Sudeste/Sul) were low. Therefore, it is considered that the mobility behavior of P. percellens could be an influential factor in the genetic diversity found with the application of the analyzed SNPs markers. Evidence of new genetic stocks is critical to strengthen conservation policies in this group of organisms that has a large number of threatened species. (AU)

• FAPESP's process: 18/25429-3 - Genetic composition of stingrays of the genus Pseudobatos (Chondrichthyes, Rhinobatidae) and search for SNPs associated with environmental adaptation
• Grantee: Bruno de Campos Souza
• Support Opportunities: Scholarships in Brazil - Master