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Effective number of different populations: a new concept and how to use it
  • Evsey Kosman,
  • Frida Feijen,
  • Jukka Jokela
Evsey Kosman
Tel Aviv University The George S Wise Faculty of Life Sciences
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Frida Feijen
Eawag, Department of Aquatic Ecology Dubendorf, Zürich, CH
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Jukka Jokela
ETH Zurich Department of Environmental Systems Science

Corresponding Author:[email protected]

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Abstract

1. Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. 2. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated as a combination of the diversity and dispersion. ENDP estimates β-variation independently of within-sample α-variation. This new concept differs from the existing standard where β-diversity is estimated based on the ‘partition of variation’ scheme (beta=gamma-alpha or beta=gamma/alpha). 3. Estimates of ENDP are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. 4. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. Analysis is complicated by two coexisting cryptic sister clades and the potentially mixed-mating system of this hermaphroditic parasite.
27 May 2024Submitted to Ecology and Evolution
28 May 2024Submission Checks Completed
28 May 2024Assigned to Editor
31 May 2024Review(s) Completed, Editorial Evaluation Pending
17 Jul 2024Editorial Decision: Revise Minor
05 Aug 20241st Revision Received
06 Aug 2024Submission Checks Completed
06 Aug 2024Assigned to Editor
06 Aug 2024Review(s) Completed, Editorial Evaluation Pending
31 Aug 2024Editorial Decision: Accept