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Recent mixing of Vibrio parahaemolyticus populations

By Chao Yang, Xiaoyan Pei, Yarong Wu, Lin Yan, Yanfeng Yan, Yuqin Song, Nicola Coyle, Jaime Martinez-Urtaza, Christopher Quince, Qinghua Hu, Min Jiang, Edward Feil, Dajin Yang, Yajun Song, Dongsheng Zhou, Ruifu Yang, Daniel Falush, Yujun Cui

Posted 25 Jun 2018
bioRxiv DOI: 10.1101/354761 (published DOI: 10.1038/s41396-019-0461-5)

Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1,103 genomes, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if dispersal between oceans has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping and aquatic products trade, are responsible for the change of distribution pattern of this marine species.

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