Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (F_IS and F_ROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Mismatches between Morphology and DNA in Italian Partridges May Not Be Explained Only by Recent Artificial Release of Farm-Reared Birds

Translocations and releases of farm-reared birds are considered among the major drivers of genetic pollution with consequent loss of genetic diversity in wild populations. In this study, we aimed to assess the extent of hybridization and introgression in the Italian partridges as a consequence of translocation. We surveyed two mitochondrial markers and one nuclear marker of Alectoris and Perdix from collections (museums and private collections), extant wild populations and farms. Consistent with previous studies, we found haplotypes of allochthonous species within the same genus, likely due to introductions for hunting activities. In addition, we found hybrids between Perdix and Alectoris species with genetic markers from both genera in single individuals. Such introgression was bidirectional and in both mitochondrial and nuclear markers. Counterintuitively, most of the hybrid samples came from collections before the 1950s, when large-scale translocations started, from wild populations where Grey Partridge (Perdix perdix) and Rock Partridge (Alectoris graeca) overlap in their distribution, whereas only one hybrid occurred among the farmed birds. Our results suggest that Perdix and Alectoris species can hybridize in nature and that artificial translocations and releases of farm-reared birds for restocking or reintroduction purposes may be only partially responsible for the genomic mismatches of Italian partridges.

Characterisation of Toll-like receptors 4, 5 and 7 and their genetic variation in the grey partridge

Toll-like receptors (TLRs) are a cornerstone of vertebrate innate immunity. In this study, we identified orthologues of TLR4, TLR5 and TLR7 (representing both bacterial- and viral-sensing TLRs) in the grey partridge (Perdix perdix), a European Galliform game bird species. The phylogeny of all three TLR genes follows the known phylogeny of Galloanserae birds, placing grey partridge TLRs (PePeTLRs) in close proximity to their turkey and pheasant orthologues. The predicted proteins encoded by the PePeTLR genes were 843, 862-863 and 1,047 amino acids long, respectively, and clearly showed all TLR structural features. To verify functionality in these genes we mapped their tissue-expression profiles, revealing generally high PePeTLR4 and PePeTLR5 expression in the thymus and absence of PePeTLR4 and PePeTLR7 expression in the brain. Using 454 next-generation sequencing, we then assessed genetic variation within these genes for a wild grey partridge population in the Czech Republic, EU. We identified 11 nucleotide substitutions in PePeTLR4, eight in PePeTLR5 and six in PePeTLR7, resulting in four, four and three amino acid replacements, respectively. Given their locations and chemical features, most of these non-synonymous substitutions probably have a minor functional impact. As the intraspecific genetic variation of the three TLR genes was low, we assume that either negative selection or a bottleneck may have reduced TLR population variability in this species.