Gallus
Mahendra Mariadassou, Marie Suez, Sathya Sathyakumar, Alain Vignal, Mariangela Arca, Pierre Nicolas, Thomas Faraut, Diane Esquerré, Masahide Nishibori, Agathe Vieaud, Chih-Feng Chen, Hung Manh Pham, Frédéric Hospital, Tatiana Zerjal, Xavier Rognon, and Michèle Tixier-Boichard. Unraveling the history of the genus
Gallus through whole genome sequencing, 2020. Molecular Phylogenetics and Evolution, In Press.
Abstract:
The genus
Gallus is distributed across a large part of Southeast Asia and has received special interest because the domestic chicken,
Gallus gallus domesticus, has spread all over the world and is a major protein source for humans. There are four species: the red junglefowl (
G. gallus), the green junglefowl (
G. varius), the Lafayette’s junglefowl (
G. lafayettii) and the grey junglefowl (
G. sonneratii). The aim of this study is to reconstruct the history of these species by a whole genome sequencing approach and resolve inconsistencies between well supported topologies inferred using different data and methods.
Using deep sequencing, we identified over 35 million SNPs and reconstructed the phylogeny of the
Gallus genus using both distance (BioNJ) and maximum likelihood (ML) methods. We observed discrepancies according to reconstruction methods and genomic components. The two most supported topologies were previously reported and were discriminated by using phylogenetic and gene flow analyses, based on ABBA statistics. This led to support a scenario with
G. gallus as the basal species of the
Gallus genus, instead of
G. varius. We discuss the probable causes for the discrepancy. A likely one is that
G. sonneratii samples from parks or private collections are all recent hybrids, with roughly 10% of their autosomal genome originating from
G. gallus. The removal of those regions is needed to provide reliable data, which was not done in previous studies. We took care of this and additionally included two wild
G. sonneratii samples from India, showing no trace of introgression. This reinforces the importance of carefully selecting and validating samples and genomic components in phylogenomics.
