Statistical Properties of Two Teststhat Use Multilocus Data Sets to Detect Population Expansions

Reich, DE; Feldman, M. W.; Goldstein, DB

doi:10.1093/oxfordjournals.molbev.a026127

Cited by 107 publications

(166 citation statements)

References 10 publications

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“…The mode-shift indicator test, although not a statistical test per se, was also performed because stable populations are expected to show larger proportions of alleles at low frequency (Cornuet and Luikart, 1997). We used the intra-locus kurtosis test (k-test) and the inter-locus variance test (gtest) (Reich and Goldstein, 1998;Reich et al, 1999) to search for signatures of population expansions. Both tests (k and g) were performed using the macro program "KGTESTS" (Bilgin, 2007) implemented in Microsoft Excel ® .…”

Section: Statistical Analysesmentioning

confidence: 99%

Genetic diversity and structure of goats within an early livestock dispersal area in Eastern North Africa

Elbeltagy¹,

Aboul-Naga²,

Hassen³

et al. 2016

Afr. J. Biotechnol.

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In this study we genotyped 14 microsatellites to assess genetic diversity, population stratification and demographic dynamics using Egyptian local goats (Zaraibi, Baladi, Saidi and Barki) and the Shami (Damascus) goat from the Middle East and West Asia close to the geographic center of goat domestication. We observed high levels of allelic and genetic diversity that was partitioned into six gene pools. Cluster analyses separated Zaraibi and Shami, which were identified with independent gene pools of potential ancestral backgrounds. The analyses provided further evidence for extensive sharing of genetic variation, revealing, varying levels of admixture among the study populations. This finding was supported by AMOVA analysis, which indicated that the proportion of genetic variation due to differences among populations was 7.06%. Our results most likely indicate that multiple waves of introduction of diverse gene pools and recent flock intermixing has created and maintained a unique set of caprine biodiversity in Eastern North Africa emphasizing the importance of the region as one of the hotbeds of African animal biodiversity.

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Section: Statistical Analysesmentioning

confidence: 99%

Genetic diversity and structure of goats within an early livestock dispersal area in Eastern North Africa

Elbeltagy¹,

Aboul-Naga²,

Hassen³

et al. 2016

Afr. J. Biotechnol.

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“…Obviously, there are a number of additional caveats in the comparisons -the different provenance of the samples, the types of demographic model considered, and the methods of analysis -but it would appear that the Y-chromosome microsatellite data are not compatible with either the autosomal microsatellite data or the SNP data, whereas the two autosomal data sets, despite substantial differences in the types of markers and modelling assumptions, appear to be compatible, generally suggesting weak evidence of population expansion. With respect to the details of the expansion models, it should be noted that the results in Beaumont (1999) and Reich et al (1999) suggest that inferences about population growth are relatively insensitive to the details of how population size changes, provided that the changes are monotonic. A further observation is that if data from geographically separated populations are pooled, ignoring the effects of population structure, as in the Y-chromosome data here, any signal of population growth will tend to be weakened (Reich et al, 1999;Wakeley et al, 2001;Ptak and Przeworski, 2002), yet the observation of population growth is very strong in this data set.…”

Section: Applicationsmentioning

confidence: 99%

“…With respect to the details of the expansion models, it should be noted that the results in Beaumont (1999) and Reich et al (1999) suggest that inferences about population growth are relatively insensitive to the details of how population size changes, provided that the changes are monotonic. A further observation is that if data from geographically separated populations are pooled, ignoring the effects of population structure, as in the Y-chromosome data here, any signal of population growth will tend to be weakened (Reich et al, 1999;Wakeley et al, 2001;Ptak and Przeworski, 2002), yet the observation of population growth is very strong in this data set. The observations in Beaumont (1999) suggest that the genealogies associated with the region of highest posterior density in the Y chromosome data set have long recent branches ('star genealogies'), whereas the genealogies associated with the region of highest posterior density in the other two data sets are more similar to those in stable populations.…”

Section: Applicationsmentioning

confidence: 99%

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Beaumont

2004

Heredity

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Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of singlenucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.

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“…for the design of tests for bottlenecks using diploid data such as microsatellites (Cornuet and Luikart, 1996;Kimmel et al, 1998;Luikart and England, 1999;Reich et al, 1999;Garza and Williamson, 2001). This method is the first time that this possibility has been investigated for haploid DNA sequences.…”

Section: Björklundmentioning

confidence: 99%

“…It is well known that historic changes in population size can have profound effects on the patterns of genetic variation in a population, and, given the remarkable technical development of easy-to-use molecular techniques, a variety of methods have been developed to test the possible occurrence of a bottleneck (Cornuet and Luikart, 1996;Kimmel et al, 1998;Luikart and England, 1999;Reich et al, 1999;Garza and Williamson, 2001). All these methods were mainly designed for use with microsatellite data.…”

Section: Introductionmentioning

confidence: 99%

Test for a population expansion after a drastic reduction in population size using DNA sequence data

Björklund

2003

Heredity

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Populations may, during their evolutionary history, go through drastic changes in population size due to bottlenecks or founder events upon colonization of new areas. This involves a subsample of haplotypes, causing the allele frequencies to be different from the original population. In addition, the period of recovery after a bottleneck can be of considerable length. If reproduction is unequal among individuals but random with regard to haplotype, large deviations from the patterns expected in a stable population may result. By means of computer simulation, I have analysed the patterns arising when populations undergo bottlenecks and then slowly recover, and used two new statistical tests for the detection of the bottleneck. A test based on the variance of the relative frequency of haplotypes had generally high power even at low sample size (n ¼ 25). This statistic was most powerful after very strong bottlenecks and lost power with increasing propagule size. A test based on the variance of the pairwise differences shows slightly less power. As expected, power was reduced when migration into the founder population was allowed from the source population. This suggests that the test is particularly suited for detecting relatively recent and strong bottlenecks, and thus may be a valuable tool for identifying population events on a fine temporal scale, such as colonisations after the last glaciation.

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Statistical Properties of Two Teststhat Use Multilocus Data Sets to Detect Population Expansions

Cited by 107 publications

References 10 publications

Genetic diversity and structure of goats within an early livestock dispersal area in Eastern North Africa

Genetic diversity and structure of goats within an early livestock dispersal area in Eastern North Africa

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Test for a population expansion after a drastic reduction in population size using DNA sequence data

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