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      Statistical confidence for likelihood-based paternity inference in natural populations.

      1 , , ,

      Molecular ecology

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          Abstract

          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 delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta 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. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.

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          Most cited references 8

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          Microsatellites and kinship.

          Many evolutionary studies, particularly kinship studies, have been limited by the availability of segregating genetic marker loci. Microsatellites promise to alleviate these problems. Microsatellite loci are segments of DNA with very short sequence motifs repeated in tandem; their often numerous alleles differ in the number of these repeat units. They are very common in eukaryotic DNA and can be amplified by the polymerase chain reaction, which allows the use of minute or degraded DNA samples. The alleles can be scored consistently and compared unambiguously, even across different gels. Copyright © 1993. Published by Elsevier Ltd.
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            Analysis of Paternity within a Natural Population of Chamaelirium luteum. 1. Identification of Most-Likely Male Parents

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              Mating in bighorn sheep: frequent male reproduction via a high-risk "unconventional" tactic

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                Author and article information

                Journal
                Mol. Ecol.
                Molecular ecology
                0962-1083
                0962-1083
                May 1998
                : 7
                : 5
                Affiliations
                [1 ] Institute of Cell, Animal and Population Biology, University of Edinburgh, UK. tristan.marshall@ed.ac.uk
                Article
                9633105

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