Genetic diversity and kinship analysis in Squalus acanthias sharks (Chondrichthyes: Squalidae) in the Atlantic Ocean, using SNPs

Author(s)

Beatriz Rochitti Boza

• Document type: Master's Dissertation
• Press: Botucatu. 2022-04-01.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu
• Defense date: 2022-02-10
• Advisor: Claudio Oliveira; Vanessa Paes Cruz

Abstract

Overfishing influences changes in the life strategy of populations of aquatic organisms, especially elasmobranchs (sharks and rays). The knowledge and identification of stocks of populations represent a fundamental point for the management and conservation of the species. The species Squalus acanthias is a small shark, belonging to the genus Squalus, popularly known as the spiny dogfish, widely distributed, migratory and susceptible to overfishing. In Argentina, there is a high occurrence of fishing on S. acanthias, which is currently classified as Vulnerable (VU) on the IUCN (International Union for Conservation of Nature) red list. In this context, the present work aims to study samples of S. acanthias, trying to track SNP markers for population and kinship studies, study the genetic composition of a population and study the occurrence of multiple paternity. The ddRADSeq library was performed with females and six litters, ranging from three to 12 pups/mother, totaling 40 samples from Mar del Plata (n=17) and Puerto de Santa Cruz (n=23), Argentina. After sequencing, marker screening was performed, resulting in 4.157 SNPs. The genetic diversity indices were moderate (for observed heterozygosity and expected heterozygosity), in addition, the inbreeding coefficient (FIS) was negative for both analyzed localities, indicating an excess of heterozygotes and absence of inbreeding. The pairwise FST was 0.042 between the regions of Mar del Plata and Puerto de Santa Cruz, demonstrating the absence of population structure. The analyzes with the STRUCTURE and DAPC programs indicated that the analyzed individuals are distributed in three genetic clusters, in addition, a high gene flow was found between individuals from different locations, with a low effective population size (Ne). Kinship analyzes revealed genetically well-related individuals. In the COLONY program, 35 full-sibling relationships were identified, distributed in eight groups that varied in size from two to five individuals, and 45 half-sibling relationships, and multiple paternity was detected in three of the six litters analyzed. This is the first study that evaluated the genetic diversity, population structure and multiple paternity in the S. acanthias species off the coast of Argentina with SNPs markers. The results obtained show evidence of the occurrence of a single panmitic unit on the coast of Argentina and the occurrence of multiple paternity in the species, which may be helping to maintain the genetic variability. (AU)

• FAPESP's process: 19/15131-0 - Genetic diversity and multiple paternity analysis in sharks of the genus Squalus (Chondrichthyes: Squalidae) using of SNPs
• Grantee: Beatriz Rochitti Boza
• Support Opportunities: Scholarships in Brazil - Master