Luo, S.-J. | bioRxiv Science

bioRxiv2020

Genomic Evidence for the Chinese Mountain Cat as a Wildcat Conspecific (Felis silvestris bieti) and Its Introgression to Domestic Cats

The enigmatic Chinese mountain cat, endemic to the Qinghai-Tibet Plateau, has a controversial taxonomic status, whether a true species or conspecific with the wildcat (Felis silvestris) and whether it may have contributed to the domestication of cats (F. s. catus) in Asia. Here, we sampled 270 domestic and wild cats across China, sequenced 51 nuclear genomes, 55 mitogenomes, and multi-locus regions from modern and museum specimens. Genome-wide phylogenies supported taxonomic classification of the Chinese mountain cat as wildcat subspecies, F. s. bieti. No involvement of F. s. bieti in cat domestication in East Asia was detected, confirming that domestic cats shared a single origin from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats in the Tibetan region, raises the prospect of disrupting the genetic integrity of F. s. bieti, an issue with profound conservation implications.

evolutionary biology↗

bioRxiv2020

The Genetics and Evolution of Eye Color in Domestic Pigeons (Columba livia)

The avian eye color, generally referred to the color of the iris, results from both pigments and structural coloration. Avian iris colors exhibit striking interspecific and, in some domestic species, intraspecific variations, suggesting unique evolutionary and ecological histories. Here we tackled the genetic basis of the pearl (white) iris color in domestic pigeons (Columba livia), to elucidate the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) in 92 pigeons, we mapped the pearl iris trait to a 9 kb region and a facilitative glucose transporter gene SLC2A11B. A nonsense mutation W49X leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss-of-function may downregulate the xanthophore-differentiation gene CSF1R, and a key gene GCH1 involved in biosynthesis of pteridine, whose absence results in pearl iris. Coalescence and phylogenetic analyses indicated the mutation originated about 5,400 years ago coinciding with the onset of pigeon domestication, while positive selection was detected likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in 10 species from six distinct lineages correlated to their signature brown or blue eyes. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that, during and after avian divergence from reptile ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated due to feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.

genetics↗