Integrative Conservation Genomics

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.