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Ghosts of a structured past: Impacts of ancestral patterns of isolation-by-distance on divergence-time estimation

Zachary B. Hancock, Heath Blackmon
doi: https://doi.org/10.1101/2020.03.24.005736
Zachary B. Hancock
1Department of Biology at Texas A&M University
2Ecology & Evolutionary Biology Interdisciplinary Program at Texas A&M University
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  • For correspondence: zhancock@bio.tamu.edu
Heath Blackmon
1Department of Biology at Texas A&M University
2Ecology & Evolutionary Biology Interdisciplinary Program at Texas A&M University
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Abstract

Isolation by distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to the potential for allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the product of the population size and the deme number. Next, we simulate whole genomes to obtain SNPs, and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. We conclude that studies estimating divergence times be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 25, 2020.
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Ghosts of a structured past: Impacts of ancestral patterns of isolation-by-distance on divergence-time estimation
Zachary B. Hancock, Heath Blackmon
bioRxiv 2020.03.24.005736; doi: https://doi.org/10.1101/2020.03.24.005736
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Ghosts of a structured past: Impacts of ancestral patterns of isolation-by-distance on divergence-time estimation
Zachary B. Hancock, Heath Blackmon
bioRxiv 2020.03.24.005736; doi: https://doi.org/10.1101/2020.03.24.005736

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