Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach

Genetica
Zihao YuanZhanjiang Liu

Abstract

The inference of historical demography of a species is helpful for understanding species' differentiation and its population dynamics. However, such inference has been previously difficult due to the lack of proper analytical methods and availability of genetic data. A recently developed method called Pairwise Sequentially Markovian Coalescent (PSMC) offers the capability for estimation of the trajectories of historical populations over considerable time periods using genomic sequences. In this study, we applied this approach to infer the historical demography of the common carp using samples collected from Europe, Asia and the Americas. Comparison between Asian and European common carp populations showed that the last glacial period starting 100 ka BP likely caused a significant decline in population size of the wild common carp in Europe, while it did not have much of an impact on its counterparts in Asia. This was probably caused by differences in glacial activities in East Asia and Europe, and suggesting a separation of the European and Asian clades before the last glacial maximum. The North American clade which is an invasive population shared a similar demographic history as those from Europe, consistent with the idea tha...Continue Reading

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Citations

Jun 22, 2019·Scientific Data·Shengyong XuTianxiang Gao
May 28, 2021·Molecular Ecology·Henry L NorthChris D Jiggins

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Software Mentioned

PSMC
SAMtools
BWA mem
fq2psmcfa

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