Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

Mikkel-Holger S Sinding,Marta M Ciucani,Jazmín Ramos-Madrigal,Alberto Carmagnini,Jacob Agerbo Rasmussen,Shaohong Feng,Guangji Chen,Filipe G Vieira,Valeria Mattiangeli,Rajinder K Ganjoo,Greger Larson,Thomas Sicheritz-Pontén,Bent Petersen,Laurent Frantz,M Thomas P Gilbert,Daniel G Bradley

doi:10.1016/j.isci.2021.103226

Abstract

SummaryThe evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.

Highlights

The genera Bos and Bison form a complex group of closely related wild species including several domesticated forms (Table 1)
We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus
We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow

Summary

Introduction

The genera Bos and Bison form a complex group of closely related wild species including several domesticated forms (Table 1). Other hypotheses argue it may have originated as a hybrid, for example, between B. javanicus and zebu cattle (Edmond-Blanc, 1947; Bohlken, 1958; Galbreath et al, 2006) (but see Hassanin and Ropiquet, 2007a; Galbreath et al, 2007; Hedges et al, 2007), or between B. javanicus and either B. gaurus or water buffalo Bubalus bubalis (Edmond-Blanc, 1947) Both its presence in the Pleistocene fossil record (Vithayanon and Bhumpakphan, 2004) and the results of a genetic analysis of eight loci (three autosomal, two Y chromosome, and three mitochondrial) (Hassanin and Ropiquet, 2007b) have been used to support the argument that B. sauveli is a distinct, non-hybrid lineage within the genus Bos, the ability of such analyses to reconstruct species trees and assess levels of potential hybridization is much less than can be achieved using nuclear genome-scale datasets

Methods

Results

Conclusion