ADZE: a rarefaction approach for counting alleles private to combinations of populations

By Zachary A. Szpiech, Mattias Jakobsson, Noah A. Rosenberg. Bioinform., 2008

686 citations recorded by the source corpus.

Motivation: Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups. Results: We introduce a generalized rarefaction approach for counting alleles private to combinations of populations. Our method evaluates the number of alleles found in each of a set of populations but absent in all remaining populations, considering equal-sized subsamples from each population. Applying this method to a worldwide human microsatellite dataset, we observe a high number of alleles private to the combination of African and Oceanian populations. This result supports the possibility of a migration out of Africa into Oceania separate from the migrations responsible for the majority of the ancestry of the modern populations of Asia, and it highlights the utility of our approach to sample size correction in evaluating hypotheses about population history. Availability: We have implemented our method in the computer pro-gram ADZE, which is available for download at http://rosenberglab.bioinformatics.med.umich.edu/adze.html. Contact: szpiechz@umich.edu

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/d33528d1d85910562a2e5500fbcd636d0491b5fc

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In Genetics

Citations in the corpus

Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China (2017, methodology): “Allelic richness and private allele richness for a sample size of six were estimated with ADZE (Szpiech et al., 2008).”
Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers (2016, methodology): “…(see below) was compared to the genetic diversity of the initial population (dessert and cider) by considering the heterozygosity parameters (H o and H e ) and the allelic richness calculated using a rarefaction framework with the program ADZE 1.0 (Gross et al. 2014; Szpiech et al. 2008).”
Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection (2012, methodology): “Expected heterozygosity (He) and the inbreeding coefficient (F) were estimated using PLINK [52], while allelic richness (Ar) and private allele richness (pAr) were estimated by ADZE [54].”