Low genetic variability and high isolation of a post-harvest South American pinniped population as revealed by genome-wide SNPs

Abstract

Otaria flavescenshas been one of the most heavily exploited pinnipeds during the last 200 years with depletions of about 90% in some colonies. After the prohibition on sealing in South America, populations became stabilized except for the Uruguayan population, which showed a constant decrease. The underlying causes of its decline have remained unknown. This study used the RAD-seq approach to assess the variability and connectivity of some of the most overexploited sea lion colonies in the Atlantic Ocean. Our results revealed low allelic richness, nucleotide diversity and heterozygosity in the Uruguayan population and evidence of complete isolation from the Argentinean populations under study. In contrast, the Patagonian populations showed a high degree of connectivity, which could explain their recovery and high levels of current diversity. Our research emphasizes the precarious genetic status of the Uruguayan sea lion population, calling for the immediate implementation of conservation measures.

A rapid approach for sex assignment by RAD-seq using a reference genome

“…Dispersion plot of both indexes based on the dataset from Peralta et al . [34]. Red dots: males; black points: females.…”

“…The RAD-seq library from Peralta et al . [34] was constructed according to the protocol described in Roesti et al . [36,37], adopted from Hohenlohe et al .…”

“…This may be linked to the origin of the samples and the extent of DNA degradation, as indicated in Supplementary Table 2. Specifically, only one of the samples from the dataset of Peralta et al [34] was obtained from a live animal while the remaining ones corresponded to deceased animals at different stages of decomposition. In this regard, we found that Index X requires an average coverage depth above 10X to correctly assign the sex of samples; below this value it tended to fail, with a bias toward males.…”

“…Moreover a detailed sequential overview of the methodological procedure is available at: https://github.com/Dieggarp/sexing. RAD-seq sequence reads belonging to Peralta et al [34] are deposited in GenBank under the BioProject Accession no. : PRJNA1022835.…”

A rapid approach for sex assignment by RAD-seq using a reference genome

“…Thus, we developed two indexes aiming at identifying the sex of animals with heteromorphic XY/ZW sex chromosomes, based on a closely related genome assembled at the chromosome level. The combination of both indexes allowed us to accurately assign sex to the fur seal dataset from Stovall et al [25] and to the sea lion dataset from Peralta et al [34].…”