Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs

By Steven T. Kalinowski. Conservation Genetics, 2004

744 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0e5892b3212e1695e41c58831da27942eb8cb10f

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In Genetics

Citations in the corpus

Molecular tracing of confiscated pangolin scales for conservation and illegal trade monitoring in Southeast Asia (2015, methodology): “The second approach involved the use of rarefaction (Kalinowski, 2004) to quantify the number of haplotypes that would be expected to be observed in samples of size n = 1 through n = N − 1, where N is the original number of individuals included in the sequence analyses.”
Genetic discontinuity among regional populations of Lophelia pertusa in the North Atlantic Ocean (2011, methodology): “As sample sizes at different localities varied, allelic richness, or the number of alleles per locality, was calculated by rarefaction (Kalinowski 2004) to compensate for unequal sample sizes using the program HP-Rare (Kalinowski 2005).”
Estimating allelic richness and its diversity (2006, background): “Kalinowsky (2004) has recently extended the rarefaction procedure to count private alleles.”
hp-rare 1.0: a computer program for performing rarefaction on measures of allelic richness (2005, methodology): “Kalinowski (2004) recently extended the rarefaction method to count private alleles and to accommodate hierarchical sampling designs that had two levels.”
Molecular characterization of breeds and its use in conservation. (2009, methodology): “An extension of the rarefaction method to count private alleles (alleles present in a given breed but absent from all the others) was defined by Kalinowski (2004) as”
The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia (2008, methodology): “One way to alleviate this problem is through rarefaction to the smallest sample size (Petit et al. 1998, Leberg 2002, Kalinowski 2004).”
ADZE: a rarefaction approach for counting alleles private to combinations of populations (2008, methodology): “Using this notation, the estimated private allelic richness for a sample size g from population j can be written as π̂ (j)g = I∑ i=1 Pijg J∏ j′=1 j′ =j Qij′g , (3) where J is the total number of populations (Kalinowski, 2004).”