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Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation
Author(s) -
TOMIUK JÜRGEN,
GULDBRANDTSEN BERNT,
LOESCHCKE VOLKER
Publication year - 2009
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2009.02623.x
Subject(s) - biology , intraspecific competition , similarity (geometry) , genetic similarity , evolutionary biology , computational biology , genetics , zoology , artificial intelligence , genetic diversity , computer science , population , demography , sociology , image (mathematics)
Abstract For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST . The program provides maximum‐likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared ‘bands’ in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band‐sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum‐likelihood estimator or the band‐sharing measure.