Statistical confidence for likelihood‐based paternity inference in natural populations

Molecular Ecology - Tập 7 Số 5 - Trang 639-655 - 1998
Tristan Marshall1, Jon Slate1, Loeske E. B. Kruuk1, J. M. Pemberton1
1Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK,

Tóm tắt

Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error‐prone genetic data typical of large‐scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic Δ for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for Δ that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows‐based computer program,CERVUS, described in this study is available from the authors.CERVUScan be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.

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Tài liệu tham khảo

Aickin M, 1984, Some fallacies in the computation of paternity probabilities, American Journal of Human Genetics, 36, 904

AitkinCGG(1995)Statistics And The Evaluation Of Evidence For Forensic Scientists. John Wiley & Sons Chichester UK.

Ashton GC, 1980, Mismatches in genetic markers in a large family study, American Journal of Human Genetics, 32, 601

10.1038/hdy.1995.47

BartonNH&GaleKS(1993) Genetic analysis of hybrid zones. In:Hybrid Zones and the Evolutionary Process (ed. Harrison RG) pp. 13–45 . Oxford University Press New York.

10.1093/genetics/145.2.535

BuchananFC&CrawfordAM(1993) Ovine microsatellites at the OarFCB11 Oar FCB128 OarFCB193 OarFCB266 and OarFCB304 loci.Animal Genetics 24 145.

Callen DF, 1993, Incidence and origin of ‘null’ alleles in the (AC)n microsatellite markers, American Journal of Human Genetics, 52, 922

10.1093/genetics/118.3.527

Chakraborty R, 1974, Exclusion of paternity: the current state of the art, American Journal of Human Genetics, 26, 477

ChakravartiA&LiCC(1983) The effect of linkage on paternity calculations. In:Inclusion Probabilities In Parentage Testing (ed. Walker RH) pp. 411–422. American Association of Blood Banks Arlington Virginia.

Clutton‐BrockTH&AlbonSD(1989)Red Deer In The Highlands. BSB Professional Books Oxford.

Clutton‐BrockTH GuinnessFE AlbonSD(1982)Red Deer – Behavior And Ecology Of Two Sexes. Edinburgh University Press Edinburgh.

ColtmanDW BowenWD WrightJM(1998)Male mating success in an aquatically mating pinniped the harbour seal (Phoca vitulina) determined by microsatellite DNA markers.Molecular Ecology 7 627–638.

10.1007/BF00265336

10.1111/j.1365-2052.1995.tb02655.x

EdwardsAWF(1972)Likelihood. Cambridge University Press Cambridge.

Elston RC, 1986, Probability and paternity testing, American Journal of Human Genetics, 39, 112

Elston RC, 1986, Some fallacious thinking about the paternity index: comments, American Journal of Human Genetics, 39, 670

Foltz DW, 1981, Analysis of the mating system in the black‐tailed prairie dog (Cynomys ludovicianus) by likelihood of paternity, Journal of Mammalogy, 62, 706, 10.2307/1380592

GeorgesM&MasseyJ(1992)Polymorphic DNA Markers In Bovidae. World Intellectual Property Org. Geneva.

10.1007/s002650050361

10.1038/hdy.1965.54

10.1111/j.1365-2052.1994.tb00401.x

10.1046/j.1365-294X.1997.00173.x

10.1046/j.1365-294X.1997.00178.x

Lathrop GM, 1983, Evaluating pedigree data. I. The estimation of pedigree error in the presence of marker mistyping, American Journal of Human Genetics, 35, 241

Li CC, 1985, Basic fallacies in the formulation of the paternity index, American Journal of Human Genetics, 37, 809

Li CC, 1986, Some fallacious thinking about the paternity index: a reply to Dr Jack Valentin's comments, American Journal of Human Genetics, 38, 586

10.1086/284554

10.1111/j.1365-294X.1994.tb00125.x

NeiM(1987)Molecular Evolutionary Genetics. Columbia University Press New York.

10.1111/j.1558-5646.1988.tb02511.x

10.1111/j.1365-294X.1994.tb00127.x

10.1111/j.1365-294X.1995.tb00214.x

10.1098/rstb.1996.0069

10.1016/0168-9525(94)90257-7

10.1159/000133570

10.1016/0169-5347(93)90256-O

10.2307/2531483

10.1017/S0016672397002851

10.1093/genetics/136.1.313

10.1111/j.1365-2052.1991.tb00692.x

SwarbrickPA&CrawfordAM(1992) Ovine dinucleotide repeat polymorphism at the MAF109 locus.Animal Genetics 23 84.

10.1046/j.1365-294X.1997.00146.x

10.1111/j.1469-1809.1975.tb00120.x

10.1177/053901847601500214

10.2307/1425927

Thompson EA, 1986, Likelihood inference of paternity, American Journal of Human Genetics, 39, 285

10.2307/2531997

10.1093/genetics/133.3.737

Valentin J, 1980, Exclusions and attributions of paternity: practical experiences of forensic genetics and statistics, American Journal of Human Genetics, 32, 420

Valentin J, 1986, Some fallacious thinking about the paternity index, American Journal of Human Genetics, 38, 582

ValsecchiE(1996)Genetic Analysis Of The Humpback Whale (Megaptera novaeangliae) Using Microsatellites. PhD thesis University of Cambridge UK.

WalkerRH(1983)Inclusion Probabilities In Parentage Testing. American Association of Blood Banks Arlington Virginia.

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Molecular Ecology

Tập 7 Số 5

639-655

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