Demographic history shapes North American gray wolf genomic diversity and informs species’ conservation

Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. Further, if isolated, the only natural process that introduces new variation into the gene pool is de novo mutation rate. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 81,595 RADseq SNPs genotyped in 437 gray wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, gray wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and has declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct gray wolf populations in North America, which ranged between N e ~141–226 since 1990. We provide data that informs managers regarding the status and importance of effective population size estimates for gray wolf conservation, which are on average 5.2–9.3% of census estimates for this species. We show that while gray wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to avoid long-term risk of extinction.