RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

Abstract

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.

Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals

“…We deployed a large panel of neutral microsatellites to test for inbreeding effects on mortality due to bacterial infection. In line with recent studies based on both microsatellites (Stoffel et al, ) and genomic data (Humble et al, ), we obtained a significantly positive g 2 estimate, which is indicative of variance in inbreeding within the study population. This is to be expected given the highly polygynous breeding system of Antarctic fur seals (Hoffman, Boyd, & Amos, ) and their extreme site fidelity (Hoffman et al, ; Hoffman & Forcada, ).…”

A 90K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony

“…Genome-wide distributed nuclear SNPs were discovered using RAD sequencing as described by Humble et al . (2018).…”

“…The transcriptome was assembled in multiple iterations using 454 and Illumina sequence data from three different cDNA libraries (Hoffman 2011; Hoffman et al . 2013b; Humble et al . 2018).…”

“…We also added to our list of probe sequences a further set of SNPs that were previously demonstrated to be polymorphic in the study colony. These included 40 SNPs derived from RAD sequencing data that were validated using Sanger sequencing (Humble et al . 2018), 102 transcriptomic SNPs that were validated using Illumina’s GoldenGate assay (Hoffman et al .…”

“…This paper describes the development of a 90K Affymetrix Axiom genotyping array for the Antarctic fur seal. As our longer-term aims are to investigate the mechanism(s) behind the population decline as well as more generally to explore the genetic architecture of fitness-related traits, we developed a genome-wide panel of nuclear SNPs based on RAD sequencing data from a recent study (Humble et al 2018). We additionally made use of another desirable property of SNP arrays, the possibility of incorporating candidate gene markers, by tiling over ten thousand polymorphisms from a transcriptome assembly (Humble et al .…”