Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong

Area of Science:

• Population Genetics
• Conservation Biology
• Genomics

Background:

• Heterozygosity is a key metric for genetic diversity, crucial in conservation.
• Estimates using single nucleotide polymorphisms (SNPs) are prone to biases from study design and filtering.
• Existing methods to correct SNP-based heterozygosity bias are often insufficient.

Purpose of the Study:

• To enhance the reliability and comparability of heterozygosity estimates.
• To investigate the impact of sample size and missing data thresholds on autosomal heterozygosity calculations.
• To assess how excluding tri- and tetra-allelic sites biases genetic diversity interpretations.

Main Methods:

• Investigated the influence of sample size and missing data thresholds on heterozygosity calculations.
• Analyzed autosomal heterozygosity across three diverse taxa: a frog, a tree, and a grasshopper.
• Compared heterozygosity estimates with and without the exclusion of tri- and tetra-allelic sites.

Main Results:

• Heterozygosity estimates were significantly affected by sample size and missing data thresholds.
• The exclusion of tri- and tetra-allelic sites introduced inconsistencies and biases in estimates.
• More diverse populations exhibited more severe biases, potentially altering conservation conclusions.

Conclusions:

• A modified framework for heterozygosity calculation is proposed to reduce bias and improve utility.
• Existing population genetic pipelines require adjustments to include all genetic sites (tri- and tetra-allelic).
• Accurate heterozygosity measures are vital for reliable genetic diversity assessments in conservation.