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

被引:1
作者
Olkkonen, Emmi [1 ]
Loytynoja, Ari [1 ]
机构
[1] Univ Helsinki, Inst Biotechnol, HiLIFE, Helsinki 00790, Finland
来源
STAR PROTOCOLS | 2023年 / 4卷 / 04期
基金
芬兰科学院;
关键词
Evolutionary Biology; Genomics; Sequence Analysis;
D O I
10.1016/j.xpro.2023.102567
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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 endan-gered Saimaa ringed seals, we detail the steps for data preparation and conven-tional 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 Loytynoja et al. (2023).1
引用
收藏
页数:37
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