Statistical confidence for likelihood-based paternity inference in natural populations
TL;DR: This study derives likelihood ratios for paternity inference with codominant markers taking account of typing error, and defines a statistic Δ for resolving paternity, and demonstrates the method is robust to their presence under commonly encountered conditions.
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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TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Abstract: DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.
9,953 citations
TL;DR: This paper showed 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.
Abstract: Genotypes 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.
4,562 citations
TL;DR: This synthesis presents a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike and aims to encourage the use and consistent reporting of thorough marker screening to ensure high quality data.
Abstract: Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike.
1,601 citations
Cites methods from "Statistical confidence for likeliho..."
...The effect of error on measures of genetic structure can be estimated using a bootstrapping technique developed by Adams et al. (2004), and the parentage program CERVUS can estimate error rate while also accounting for mutation (Marshall et al. 1998)....
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TL;DR: A protocol for estimating error rates is proposed and it is recommended that these measures be systemically reported to attest the reliability of published genotyping studies.
Abstract: Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.
1,143 citations
TL;DR: This work reviews the recent application of restricted maximum-likelihood "animal models" to multigenerational data from natural populations, and shows how the estimation of variance components and prediction of breeding values using these methods offer a powerful means of tackling the potentially confounding effects of environmental variation.
Abstract: Estimating the genetic basis of quantitative traits can be tricky for wild populations in natural environments, as environmental variation frequently obscures the underlying evolutionary patterns. I review the recent application of restricted maximum-likelihood "animal models" to multigenerational data from natural populations, and show how the estimation of variance components and prediction of breeding values using these methods offer a powerful means of tackling the potentially confounding effects of environmental variation, as well as generating a wealth of new areas of investigation.
1,062 citations
Cites background or methods from "Statistical confidence for likeliho..."
...However, paternity assignment using genetic data will also be imperfect: for example, levels of statistical certainty in paternity assignment (Marshall et al. 1998) in the ungulate studies discussed here involve error rates of 20% (Kruuk et al. 2000; Coltman et al. 2001) or 5% (Milner et al. 2000;…...
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...For field studies of wild vertebrate populations, errors in maternal identity are rare: for example, maternity is determined by field observations with complete reliability for the ungulate populations discussed here (Marshall et al. 1998), and there is no evidence of intraspecific brood parasitism among the passerine bird populations discussed (e....
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...The ones that I will discuss in particular here are studies of a wild ungulate and a passerine bird population: the red deer (Cervus elaphus) population in the North Block of the Isle of Rum, northwest Scotland (Clutton-Brock et al. 1982), and the collared flycatcher (Ficedula albicollis) population on the island of Gotland, Sweden (Gustafsson 1986; Merilä et al. 2001b; Sheldon et al. 2003)....
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...However, paternity assignment using genetic data will also be imperfect: for example, levels of statistical certainty in paternity assignment (Marshall et al. 1998) in the ungulate studies discussed here involve error rates of 20% (Kruuk et al....
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...For example, the software package Cervus (Marshall et al. 1998) uses a ML approach to identify the most likely father among a set of candidate males, and assigns paternity to that male if, and only if, he is significantly more probable than any rival male....
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References
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Book•
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
15,840 citations
Book•
01 Jan 1982
TL;DR: Red Deer: Behavior and Ecology of Two Sexes is the most extensive study yet available of reproduction in wild vertebrate and reveals the extent of sex differences in behavior, reproduction, and ecology.
Abstract: Red Deer: Behavior and Ecology of Two Sexes is the most extensive study yet available of reproduction in wild vertebrate. The authors synthesize data collected over ten years on a population of individually recognizable red deer, usually regarded as conspecific with the American elk. Their results reveal the extent of sex differences in behavior, reproduction, and ecology and make a substantial contribution to our understanding of sexual selection.
2,317 citations
"Statistical confidence for likeliho..." refers background in this paper
...Detailed descrip- tions of the study site are available in Clutton-Brock et al. (1982) and Clutton-Brock & Albon (1989)....
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1,339 citations
"Statistical confidence for likeliho..." refers background in this paper
...For example, high values of linkage disequilibrium are likely for a series of loci known to lie within a single gene cluster (e.g. the Major Histocompatibility Complex) or in zones of hybridization between two populations, subspecies or species (Barton & Gale 1993)....
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TL;DR: Many evolutionary studies, particularly kinship studies, have been limited by the availability of segregating genetic marker loci, and microsatellites promise to alleviate these problems.
Abstract: 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.
842 citations
"Statistical confidence for likeliho..." refers background in this paper
...When microsatellite markers are used, mutations (Queller et al. 1993) and null alleles (Callen et al. 1993; Phillips et al. 1993; Pemberton et al. 1995) may also generate mismatches between genuine relatives at measurable frequencies....
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...When microsatellite markers are used, mutations (Queller et al. 1993) and null alleles (Callen et al....
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Book•
01 Jun 1995TL;DR: In this article, the authors present a review of uncertainty in forensic science, focusing on the evaluation of evidence and its application in the field of forensic science. But they do not discuss the use of DNA profiling.
Abstract: Preface to the first edition. Preface to the second edition. Uncertainty in forensic science. Variation. The evaluation of evidence. Historical review. Bayesian inference. Sampling. Interpretation. Transfer evidence. Discrete data. Continuous data. Multivariate analysis. Fibres. DNA profiling. Bayesian networks. References. Notation. Cases.
724 citations