Selective constraints in cold‐region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes |
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| Authors: | Jianhai Chen Pan Ni Thuy Nhien Tran Thi Evgeniy Varisovich Kamaldinov Valeriy Lavrentyevich Petukhov Jianlin Han Xiangdong Liu Nikica ?prem Shuhong Zhao |
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| Institution: | 1. Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China;2. The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China;3. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois;4. National Institute of Animal Sciences, Hanoi, Vietnam;5. Federal State Budgetary Educational Institution of Higher Education, Novosibirsk State Agrarian University, Novosibirsk, Russia;6. International Livestock Research Institute (ILRI), Nairobi, Kenya;7. CAAS‐ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China;8. Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia |
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| Abstract: | Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (Ne) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood‐ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch‐site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger Ne in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical Ne of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance. |
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| Keywords: | Ka/Ks ratio mitogenome purifying selection selective constraint
Sus scrofa
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