Similarity of DNA Fingerprints Due to Chance and Relatedness

Li, C.C.; Weeks, Daniel E.; Chakravarti, A.

doi:10.1159/000154113

Cited by 266 publications

(271 citation statements)

References 7 publications

(9 reference statements)

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“…Several different estimators of relatedness (R) based on genotype and population allele frequency data have been proposed (e.g., Queller and Goodnight, 1989;Lynch and Ritland, 1999), as have estimators based on multilocus DNA fingerprints (e.g., Lynch, 1988Lynch, , 1990Li et al, 1993). Van de Casteele et al (2001) compared the performance of several microsatellite-based estimators of relatedness using simulation models, and found that, depending on allele frequency distributions at the different loci under investigation, certain estimators more accurately reconstructed "true" relatedness.…”

Section: Basic Analytical Methodsmentioning

confidence: 99%

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction

Fiore

2003

Am. J. Phys. Anthropol.

106

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In the past several decades, the development of novel molecular techniques and the advent of noninvasive DNA sampling, coupled with the ease and speed with which molecular analyses can now be performed, have made it possible for primatologists to directly examine the fitness effects of individual behavior and to explore how variation in behavior and social systems influences primate population genetic structure. This review describes the theoretical connections between individual behavior and primate social systems on the one hand and population genetic structure on the other, discusses the kinds of molecular markers typically employed in genetic studies of primates, and summarizes what primatologists have learned from molecular studies over the past few decades about dispersal patterns, mating systems, reproductive strategies, and the influence of kinship on social behavior. Several important conclusions can be drawn from this overview. First, genetic data confirm that, in many species, male dominance rank and fitness are positively related, at least over the short term, though this relationship need not simply be a reflection of malemale contest competition over mates. More importantly, genetic research reveals the significance of female choice in determining male reproductive success, and documents the efficacy of alternative mating tactics among males. Second, genetic data suggest that the presumed importance of kinship in structuring primate social relationships needs to be evaluated further, at least for some taxa such as chimpanzees in which demographic factors may be more important than relatedness. I conclude this paper by offering several suggestions of additional ways in which molecular techniques might be employed in behavioral and ecological studies of primates (e.g., for conducting "molecular censuses" of unhabituated populations, for studying disease and host-parasite interactions, or for tracking seed fate in studies of seed dispersal) and by providing a brief introduction to the burgeoning field of nonhuman primate behavioral genetics. Yrbk Phys Anthropol 46:62-99, 2003.

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Section: Basic Analytical Methodsmentioning

confidence: 99%

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction

Fiore

2003

Am. J. Phys. Anthropol.

106

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“…The similarity index (SI), denoted S xy (Li et al 1993) is here defined as the average fraction of alleles at a locus in a reference individual X for which there is another allele in the proband Y that is IBS (Lynch and Ritland 1999). Let x and y be the genotypes of individuals X and Y, respectively, and let a, b, c, and d denote alternative alleles.…”

Section: Simentioning

confidence: 99%

“…A commonly used measure of relatedness is the coancestry coefficient (Wright 1922). Many estimators for pairwise relatedness have been developed for the case where the loci are unlinked and the individuals are not inbred, for example the maximum likelihood (ML) estimator of Thompson (1975), and a variety of method of moments (MOM) estimators (Li et al 1993;Lynch and Ritland 1999;Queller and Goodnight 1989;Ritland 1996a;Wang 2002). Milligan (2003) compared the statistical properties of these estimators and concluded that the ML estimator exhibits a smaller standard error but is more biased than the others are.…”

Section: Introductionmentioning

confidence: 99%

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

et al. 2008

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Several estimators have been proposed that use molecular marker data to infer the degree of relatedness for pairs of individuals. The objective of this study was to evaluate the performance of seven estimators when applied to marker data of a set of 33 key individuals from a large complex apple pedigree. The evaluation considered different scenarios of allele frequencies and different numbers of marker loci. The method of moments estimators were Similarity, Queller-Goodknight, Lynch-Ritland and Wang. The maximum likelihood estimators were Thompson, Anderson-Weir and Jacquard. The pedigree-based coancestry coefficients were taken as the point of reference in calculating correlations and root mean square error (RMSE). The marker data comprised 86 multi-allelic SSR markers on 17 linkage groups, covering 11 Morgans. Additionally, we simulated 10 datasets conditional on the real pedigree to support the results on the real dataset. None of the estimators outperformed the others. Knowledge of allele frequencies appeared to be the most influential, i.e., the highest correlations and lowest RMSE were found when frequencies from the founder population were available. When equal allele frequencies were used, all estimators resulted in very similar, but on average lower, correlations. The use of allele frequencies estimated from the set of 33 individuals gave, on average, the poorest results. The maximum likelihood estimators and the Lynch-Ritland estimator were the most sensitive to allele frequencies. The results from the simulation study fully supported the trends in results of the real dataset. This study indicated that high correlations (up to 0.90) and small RMSE (below 0.03), may be obtained when population allelic frequencies are available. In this scenario, the performances of the various estimators were similar, but seemed to favor the maximum likelihood estimators. In the absence of reliable allele frequencies the method of moments estimators were shown to be more robust. The number of marker loci influenced the average performance of the estimators; however, the ranking was not affected. Correlations up to 0.80 were obtained when two markers per chromosome and appropriate allele frequencies were available. Adding more markers to the current dataset may lead to marginal improvements.

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“…These methods can generate an unbiased estimation of relatedness, including either r directly (that is, Queller and Goodnight, 1989;Li et al, 1993;Ritland, 1996), or both r and Δ (four-gene coefficient, the probability that both genes of one individual are identical by descent (IBD) to both genes of another individual) simultaneously (that is, Lynch and Ritland, 1999;Wang, 2002;Thomas, 2010). Here we define r as the probability that an allele sampled from one individual at a locus is IBD to one of the alleles from the other individual.…”

Section: Introductionmentioning

confidence: 99%

A maximum-likelihood estimation of pairwise relatedness for autopolyploids

et al. 2014

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Relatedness between individuals is central to ecological genetics. Multiple methods are available to quantify relatedness from molecular data, including method-of-moment and maximum-likelihood estimators. We describe a maximum-likelihood estimator for autopolyploids, and quantify its statistical performance under a range of biologically relevant conditions. The statistical performances of five additional polyploid estimators of relatedness were also quantified under identical conditions. When comparing truncated estimators, the maximum-likelihood estimator exhibited lower root mean square error under some conditions and was more biased for non-relatives, especially when the number of alleles per loci was low. However, even under these conditions, this bias was reduced to be statistically insignificant with more robust genetic sampling. We also considered ambiguity in polyploid heterozygote genotyping and developed a weighting methodology for candidate genotypes. The statistical performances of three polyploid estimators under both ideal and actual conditions (including inbreeding and double reduction) were compared. The software package POLYRELATEDNESS is available to perform this estimation and supports a maximum ploidy of eight.

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Similarity of DNA Fingerprints Due to Chance and Relatedness

Cited by 266 publications

References 7 publications

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

A maximum-likelihood estimation of pairwise relatedness for autopolyploids

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