Revising how the computer program <scp>cervus</scp> accommodates genotyping error increases success in paternity assignment

Molecular Ecology - Tập 16 Số 5 - Trang 1099-1106 - 2007
Steven T. Kalinowski1, Mark L. Taper1, Tristan Marshall2
1Department of Ecology, Montana State University, Bozeman, MT 59717, USA,
2Field Genetics Limited, 23a Oaklands Grove, London W12 0JD, UK

Tóm tắt

AbstractGenotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program cervus to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of cervus to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of cervus (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com.

Từ khóa


Tài liệu tham khảo

10.1016/S0169-5347(03)00225-8

10.1111/j.1365-294X.2004.02346.x

10.1023/B:COGE.0000031146.51681.b0

10.1046/j.1439-0310.2003.00880.x

10.1046/j.1365-294X.2001.01262.x

10.2307/3677249

10.1046/j.1365-294X.2003.01868.x

10.1016/S0379-0738(00)00158-4

KalinowskiST TaperML(2006)Maximum likelihood estimation of the frequency of null alleles at microsatellite loci.Conservation Genetics 7 991–995.

10.1007/s10592-005-9024-6

KalinowskiST SawayaM TaperML(2006b)Individual identification and distributions of genotypic differences.Journal of Wildlife Management 70 148–150.

KalinowskiST WagnerAP TaperML(2006c)ml‐relate: software for estimating relatedness and relationship from multilocus genotypes.Molecular Ecology Notes 6 576–579.

10.1046/j.1365-294x.1998.00374.x

10.1111/j.1365-294X.2005.02708.x

10.1038/nrg1707

10.1017/S0016672397002851

10.1093/beheco/arh148

10.1046/j.1365-294x.2000.00930.x

10.1086/338920

10.1111/j.1471-8286.2005.01167.x

WagnerAP CreelS KalinowskiST(2006)Maximum likelihood estimation of relatedness and relationship using microsatellite loci with null alleles.Heredity 97 336–345.

10.1093/genetics/166.4.1963

Thông tin
Thông tin xuất bản

Molecular Ecology

Tập 16 Số 5

1099-1106

Thông tin tác giả