Prasun Dutta, Andrea Talenti, Rachel Young, Siddharth Jayaraman, Rebecca Callaby, Santosh Kumar Jadhav, Velu Dhanikachalam, Mayakannan Manikandan, Bhim B. Biswa, Wai Y. Low, John L. Williams, Elizabeth Cook, Phil Toye, Eileen Wall, Appolinaire Djikeng, Karen Marshall, Alan L. Archibald, Suresh Gokhale, Satish Kumar, David A. Hume & James G. D. Prendergast

Nature Communications volume 11, Article number: 4739 (2020)

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

See https://www.nature.com/articles/s41467-020-18550-1

Figure 4: Identity by state phylogenetic tree of the set of 294 cattle whole genomes used in this analysis.

The tree represents the IBS-based distance between samples when restricting to the 8,339,626 biallelic variants with a minor allele frequency >5%. Nodes are colour coded by the geographic origin of the animals (red: African indicine, purple: subcontinent indicine, pink: East-Asian indicine, blue: East-Asian taurine, green: European taurine, brown: African taurine, yellow: Central Asian taurine) and the marker shape represents the confidence in that node (Hexagon: confidence of 90–100%, star: 75–90%, square: 50–75%, circle: <50).