An instantaneous coalescent method insensitive to population structure |
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Authors: | Zeqi Yao Kehui Liu Shanjun Deng Xionglei He |
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Affiliation: | 1. Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA;2. Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA;1. Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818 Japan;2. Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818 Japan;3. Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;1. Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;2. The Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China;3. Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;4. Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan;5. Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou 310058, China;6. MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;1. Department of Rehabilitation Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China;2. Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;3. Tsinghua-Peking Center for Life Sciences, Beijing 100084, China;4. National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China |
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Abstract: | Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms. |
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Keywords: | Coalescent Population structure Demographic history Population size Phylogenetic tree |
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