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On the Apportionment of Population Structure

View ORCID ProfileYaron Granot, Omri Tal, View ORCID ProfileSaharon Rosset, View ORCID ProfileKarl Skorecki
doi: https://doi.org/10.1101/033852
Yaron Granot
1Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, and Rambam Medical Center, Haifa, Israel
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Omri Tal
2Max Planck Institute for Mathematics in the Sciences, Inselstr. 22-26, 04103 Leipzig, Germany
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Saharon Rosset
3School of Mathematical Sciences Tel Aviv University, Tel Aviv, Israel
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Karl Skorecki
1Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, and Rambam Medical Center, Haifa, Israel
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Abstract

Measures of population differentiation, such as FST, are traditionally derived from the partition of diversity within and between populations. However, the emergence of population clusters from multilocus analysis is a function of genetic structure (departures from panmixia) rather than of diversity. If the populations are close to panmixia, slight differences between the mean pairwise distance within and between populations (low FST) can manifest as strong separation between the populations, thus population clusters are often evident even when the vast majority of diversity is partitioned within populations rather than between them. For any given FST value, clusters can be tighter (more panmictic) or looser (more stratified), and in this respect higher FST does not always imply stronger differentiation. In this study we propose a measure for the partition of structure, denoted EST, which is more consistent with results from clustering schemes. Crucially, our measure is based on a statistic of the data that is a good measure of internal structure, mimicking the information extracted by unsupervised clustering or dimensionality reduction schemes. To assess the utility of our metric, we ranked various human (HGDP) population pairs based on FST and EST and found substantial differences in ranking order. In some cases examined, most notably among isolated Amazonian tribes, EST ranking seems more consistent with demographic, phylogeographic and linguistic measures of classification compared to FST. Thus, EST may at times outperform FST in identifying evolutionary significant differentiation.

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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 May 25, 2016.
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On the Apportionment of Population Structure
Yaron Granot, Omri Tal, Saharon Rosset, Karl Skorecki
bioRxiv 033852; doi: https://doi.org/10.1101/033852
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On the Apportionment of Population Structure
Yaron Granot, Omri Tal, Saharon Rosset, Karl Skorecki
bioRxiv 033852; doi: https://doi.org/10.1101/033852

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