Genome-wide markers redeem the lost identity of a heavily managed gamebird

Abstract

Heavily managed wildlife may suffer from genetic homogenization and reshuffling of locally adapted genotypes with non-native ones. This phenomenon often affects natural populations by reducing their evolutionary potential and speeding up the ongoing biodiversity crisis. For decades, the red-legged partridge ( Alectoris rufa ), an intensively managed gamebird of conservation concern and considerable socio-economic importance, has been subjected to extensive releases of farm-reared hybrids with the chukar partridge ( Alectoris chukar ) and translocations irrespective of subspecific affinity. These practices have led to serious concerns that the genetic integrity and biogeographic structure of most red-legged partridge populations are irreversibly affected, as suggested by previous studies based on few genetic markers. Using over 168 000 genome-wide loci and a sampling across the entire A. rufa range, we detected unexpectedly limited and spatially uneven chukar introgression as well as significant intraspecific structure. We demonstrate that species widely feared to have irretrievably lost their genetic identity are likely to be much less affected by unsuitable management practices than previously assumed. Our results spell the need for a radical re-think on animal conservation, possibly restoring native status to populations long treated as compromised. Our study exemplifies how the application of innovative conservation-genomic methods is key to solving wildlife management problems dealing with introgressive hybridization worldwide.

Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations

“…Our results suggest that the impact of long-term natural processes (such as Quaternary climatic fluctuations, range expansions, natural selection), as well as the prolonged geographic isolation of Italy determined by the Alps and the Mediterranean Sea, might still affect the phylogeographic structure of a number of species, prevailing over the effects of human manipulations in shaping WB genetic diversity patterns. Similar results were recently found in a genomic study on managed populations of red-legged partridges (Alectoris rufa, Forcina et al, 2021).…”

Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations

“…Such contamination can also be seen in A. rufa and A. greaca in Europe, which appears to be related to A. chukar , previously introduced into the Mediterranean Basin via the Silk Road [ 24 , 30 , 78 , 79 , 178 ]. Subsequently, the breeding of A. chukar -contaminated individuals with farm-reared chukars for hunting purposes contaminated the local gene pools of A. rufa and A. greaca in Europe, with A. chukar genes at a dangerous level [ 182 , 183 , 184 , 185 ].…”

Evidence for Genetic Hybridization between Released and Wild Game Birds: Phylogeography and Genetic Structure of Chukar Partridge, Alectoris chukar, in Turkey

“…These captive partridges threaten the genetic integrity of wild populations. A number of studies unveiled the anthropogenic hybridization involving A. rufa X A. chukar [14,15,[18][19][20][21]24,[40][41][42][43][44][45], A. graeca X A. chukar [21] as well as intraspecific hybridization in Chukar Partridge [46,47].…”