2026 Volume 30 Issue 1 Pages 19-26
Advances in whole-genome resequencing (WGS) have transformed conservation genetics by making it possible to obtain high-resolution assessments of genetic diversity, inbreeding and demographic history in endangered species, even from limited samples. This review synthesizes recent developments in genome-wide analyses, focusing on three key components: genome-wide heterozygosity, inbreeding estimation based on homozygosity-by-descent (HBD) and runs of homozygosity (ROH), and effective population size (Ne) inference. Genome-wide heterozygosity provides a robust measure of genetic diversity and can reveal delayed genetic erosion associated with recent population declines. Inbreeding analyses based on HBD and ROH enable the detection of both recent and historical inbreeding and their functional consequences, including mutation load and inbreeding depression. Meanwhile, Ne reconstruction using coalescent- and SFS-based approaches makes it possible to infer past demographic processes, bridging current genomic patterns with historical population dynamics. Importantly, this review highlights the limitations of relying on single metrics such as Ne or the Ne/N ratio alone, which can fail to detect cryptic genetic risks in both small and seemingly large populations. By integrating genome-wide diversity, inbreeding and demographic history, genomic approaches provide a comprehensive framework for identifying latent extinction risks arising from genetic erosion. Despite remaining challenges, including sample acquisition, DNA quality and assembly requirements, ongoing technological advances and collaborative frameworks support the application of genomic data in conservation. This integrative approach provides a foundation for evidence-based conservation management within a One Plan framework, enhancing the long-term viability of endangered species.
