Analysis of population structure and genetic diversity in low-variance Saimaa ringed seals using low-coverage whole-genome sequence data

This protocol demonstrates how a fragmented reference genome and low-coverage sequencing data can be efficiently utilized for population genetic analyses of a species with highly reduced genetic diversity. Focusing on endangered Saimaa ringed seals, we detail the steps for data preparation and conventional analyses and then extend the latter by combining genomic and geospatial data. In addition, we introduce coancestry as a measure of genetic identity and describe accessible tools for the quantification of across-genome variation in genetic diversity. For complete details on the use and execution of this protocol, please refer to Löytynoja et al. (2023).(1).