An exploration of the phylogeography and genetic relationships of the extinct Sardinian dhole with other canids.

The Sardinian dhole (Cynotherium sardous) was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene. Given its peculiar dental morphology, small body size and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor. Morphometric analyses have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the land-bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.

撒丁岛野犬（Sardinian dhole，*Cynotherium sardous*）是一类极具标志性且独特的犬科物种，曾特有于撒丁岛与科西嘉岛，直至晚更新世末期走向灭绝。鉴于其特殊的牙齿形态、小巧的体型与极高的特有性，学界曾提出多种现生犬科类群作为其近缘类群的候选，其中包括亚洲野犬（Asian dhole）与非洲野犬的祖先类群。此前的形态计量学分析始终未能明确其与其他犬科类群的演化亲缘关系。本研究对一具距今约21100年的撒丁岛野犬遗骸进行了全基因组测序，以期解析其基因组演化历史并明确其系统发育位置。研究结果显示，撒丁岛野犬与欧亚大陆、非洲及北美洲的所有现生犬科类群均为独立演化的类群；其谱系与亚洲野犬的分化时间约为88.5万年前（885 ka）。本研究还检测到撒丁岛野犬与亚洲野犬谱系间曾存在历史基因交流，该交流约在50万至30万年前终止——彼时撒丁岛与意大利本土之间的陆桥早已断裂，二者的种群连通性被彻底切断。与其他现生犬科类群相比，本次研究的撒丁岛野犬样本展现出较低的全基因组遗传多样性，这大概率是长期地理隔离所致，而该特征可能推动了撒丁岛野犬的后续灭绝。