АвторТема: STRUCTURE does not reliably identify the main genetic clusters within species  (Прочитано 2086 раз)

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Heredity. 2010 Aug 4. [Epub ahead of print]
The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure.
Kalinowski ST.

Department of Ecology, Montana State University, Bozeman, MT, USA.
Abstract
One of the primary goals of population genetics is to succinctly describe genetic relationships among populations, and the computer program STRUCTURE is one of the most frequently used tools for doing so. The mathematical model used by STRUCTURE was designed to sort individuals into Hardy-Weinberg populations, but the program is also frequently used to group individuals from a large number of populations into a small number of clusters that are supposed to represent the main genetic divisions within species. In this study, I used computer simulations to examine how well STRUCTURE accomplishes this latter task. Simulations of populations that had a simple hierarchical history of fragmentation showed that when there were relatively long divergence times within evolutionary lineages, the clusters created by STRUCTURE were frequently not consistent with the evolutionary history of the populations. These difficulties can be attributed to forcing STRUCTURE to place individuals into too few clusters. Simulations also showed that the clusters produced by STRUCTURE can be strongly influenced by variation in sample size. In some circumstances, STRUCTURE simply put all of the individuals from the largest sample in the same cluster. A reanalysis of human population structure suggests that the problems I identified with STRUCTURE in simulations may have obscured relationships among human populations-particularly genetic similarity between Europeans and some African populations.Heredity advance online publication, 4 August 2010; doi:10.1038/hdy.2010.95.

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Re: STRUCTURE does not reliably identify the main genetic clusters within species
« Ответ #1 : 18 Декабрь 2010, 21:25:05 »
Thank you for sharing this paper with us.

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Re: STRUCTURE does not reliably identify the main genetic clusters within species
« Ответ #3 : 18 Декабрь 2010, 21:29:49 »
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The computer program STRUCTURE (Pritchard et al.,2000; Falush et al., 2003; Hubisz et al., 2009) is currently one of the most frequently used statistical tools for describing population structure. The program does this by sorting individuals into Hardy–Weinberg/linkage equilibrium populations, which creates clusters of individuals that have distinctive allele frequencies. An important step in this analysis is deciding how many clusters to sort
individuals into.This number, K, is selected by the user. If K is equal to the actual number of Hardy–Weinberg populations that the individuals belong to, STRUCTURE will attempt to sort individuals into the populations they came from.
This can be very useful when the origin of individuals is unknown. However, STRUCTURE is also frequently used to identify the main genetic clusters within species. In this second type of analysis, individuals are assigned to clusters in the same manner as above, but K is deliberately set to be smaller than the actual number of populations. Rosenberg et al. (2001) argued that such clustering is useful for ‘identification of population relationships, history, and within-species genetic units for conservation’, last sentence of paper).

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Re: STRUCTURE does not reliably identify the main genetic clusters within species
« Ответ #4 : 18 Декабрь 2010, 21:31:20 »
Very important observation

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However, this result—and other analyses of population-level relationships made by
STRUCTURE—may need to be reevaluated. The mathematical model used by STRUCTURE was designed for clustering individuals into Hardy–Weinberg/linkage equilibrium populations. It was not designed for clustering individuals into groups of populations, and
may not work as its users intend when this is done.

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Re: STRUCTURE does not reliably identify the main genetic clusters within species
« Ответ #5 : 18 Декабрь 2010, 21:51:47 »
Very important observation

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However, this result—and other analyses of population-level relationships made by
STRUCTURE—may need to be reevaluated. The mathematical model used by STRUCTURE was designed for clustering individuals into Hardy–Weinberg/linkage equilibrium populations. It was not designed for clustering individuals into groups of populations, and
may not work as its users intend when this is done.

Yes, I think it is essential because too often the underlying model of a particular program/analysis is not thoroughly questioned. The paper was also reviewed by major figures in the field.

It will be interesting to see how the authors of STRUCTURE or other population geneticists respond.

 

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