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Inbreeding effective population size and parentage analysis without parents
Author(s) -
WAPLES ROBIN S.,
WAPLES RYAN K.
Publication year - 2011
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.1755-0998.2010.02942.x
Subject(s) - inbreeding , biology , sample size determination , offspring , statistics , population , estimator , pairwise comparison , genetics , effective population size , mathematics , demography , genetic variation , pregnancy , sociology , gene
An important use of genetic parentage analysis is the ability to directly calculate the number of offspring produced by each parent ( k i ) and hence effective population size, N e . But what if parental genotypes are not available? In theory, given enough markers, it should be possible to reconstruct parental genotypes based entirely on a sample of progeny, and if so the vector of parental k i values. However, this would provide information only about parents that actually contributed offspring to the sample. How would ignoring the ‘null’ parents (those that produced no offspring) affect an estimate of N e ? The surprising answer is that null parents have no effect at all. We show that: (i) The standard formula for inbreeding N e can be rewritten so that it is a function only of sample size and ; it is not necessary to know the total number of parents ( N ). This same relationship does not hold for variance N e . (ii) This novel formula provides an unbiased estimate of N e even if only a subset of progeny is available, provided the parental contributions are accurately determined, in which case precision is also high compared to other single‐sample estimators of N e . (iii) It is not necessary to actually reconstruct parental genotypes; from a matrix of pairwise relationships (as can be estimated by some current software programs), it is possible to construct the vector of k i values and estimate N e . The new method based on parentage analysis without parents (PwoP) can potentially be useful as a single‐sample estimator of contemporary N e , provided that either (i) relationships can be accurately determined, or (ii) can be estimated directly.