Journal article

Unbiased population heterozygosity estimates from genome-wide sequence data

Thomas L Schmidt, Moshe-Elijah Jasper, Andrew R Weeks, Ary A Hoffmann

METHODS IN ECOLOGY AND EVOLUTION | WILEY | Published : 2021

Abstract

Heterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome-wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis with these markers may depend heavily on ‘upstream’ filtering decisions. Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected hete..

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