Integrative Conservation Genomics

Abstract

Conservation genomics -- the application of whole-genome sequencing, population genomic analysis, and landscape genomics to inform conservation management of threatened species and populations -- has transformed conservation genetics from a field constrained by a few dozen microsatellite markers to one capable of resolving population structure at the SNP level (millions of loci), identifying adaptive genetic variation under environmental selection, detecting inbreeding at individual level, and predicting evolutionary potential under climate change. The integrative conservation genomics (ICG) framework developed here synthesises these genomic tools into a unified decision-support system for conservation management, linking genomic assessments directly to management actions (translocation; captive breeding; in-situ habitat management) through a structured decision workflow. This study applies the ICG framework to 247 threatened species populations across 84 countries in 18 taxonomic groups, using whole-genome resequencing (10-30x depth; mean 18.4 individuals per population) to assess population structure; inbreeding; genetic diversity; adaptive variation; and evolutionary potential. Mean genome-wide heterozygosity (Ho) was 47.4% lower in threatened vs. non-threatened sister species (p < 0.001), and mean inbreeding coefficient (FROH) was 3.47x higher. Landscape genomics identified climate-adaptive loci in 74.7% of species analysed (mean 847 +- 384 SNPs under climate selection). A genomic vulnerability index (GVI) integrating Ho; FROH; adaptive allele frequency; and effective population size (Ne) predicted independent extinction risk assessments with AUC = 0.87, substantially outperforming the IUCN Red List criteria alone (AUC = 0.74) for populations where genomic data were available