Simultaneous Estimation of Null Alleles and Inbreeding Coefficients
TLDR
2 formerly described approaches, population inbreeding model and individual inbreedingmodel, can be applied for simultaneous estimation of null allele frequencies and of the inbreeding coefficient and it is shown that they outperform the commonly used approaches in the estimation ofnull allele frequencies based on genotypic data.Abstract:
Although microsatellites are a very efficient tool for many population genetics applications, they may occasionally produce "null" alleles, which, when present in high proportion, may affect estimates of key parameters such as inbreeding and relatedness coefficients or measures of genetic differentiation. In order to account for the presence of null alleles, it is first necessary to estimate their frequency within studied populations. However, the commonly used null allele frequency estimators are not of general applicability because they can produce upwardly biased estimates when a population under study experiences some inbreeding. In such a case, 2 formerly described approaches, population inbreeding model and individual inbreeding model, can be applied for simultaneous estimation of null allele frequencies and of the inbreeding coefficient. In this study, we demonstrate the properties and utility of these 2 methods and show that they outperform the commonly used approaches in the estimation of null allele frequencies based on genotypic data. The methods are applied to empirical data from a natural population of European beech (Fagus sylvatica L.), and results are briefly discussed. The methods presented in this paper are implemented in the Windows-based user-friendly INEST computer program (available free of charge at http://genetyka.ukw.edu.pl/INEst10_setup.exe).read more
Citations
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Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology
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Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths.
Xaymara M. Serrano,Iliana B. Baums,Katherine E. O’Reilly,Tyler B. Smith,Ross Jones,Tonya L. Shearer,Flavia L. D. Nunes,Flavia L. D. Nunes,Andrew C. Baker +8 more
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Genome–environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica
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Long distance dispersal and vertical gene flow in the Caribbean brooding coral Porites astreoides
Xaymara M. Serrano,Iliana B. Baums,Tyler B. Smith,Ross Jones,Tonya L. Shearer,Andrew C. Baker +5 more
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No gene flow across the Eastern Pacific Barrier in the reef‐building coral Porites lobata
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References
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Journal ArticleDOI
A measure of population subdivision based on microsatellite allele frequencies.
TL;DR: It was found that, under the generalized stepwise mutation model, R( ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long.
Journal ArticleDOI
Microsatellite Null Alleles and Estimation of Population Differentiation
TL;DR: F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes, and the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction.
Journal ArticleDOI
Coefficients of Inbreeding and Relationship
TL;DR: The importance of having a coefficient by means of which the degree of inbreeding may be expressed has been brought out by Pearl' in a number of papers published between 1913 and 1917.
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