The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations

Thomas, Stuart C.

doi:10.1098/rstb.2005.1675

Cited by 59 publications

(57 citation statements)

References 72 publications

(104 reference statements)

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“…Thomas (2005) reviewed different approaches to relationship estimation with particular attention on optimizing the use of this relationship information in subsequent heritability estimation. A real data example in Soay sheep (Thomas et al 2002) using a set of 12 markers, did not result in reliable heritability estimates probably because of the low average relatedness in the population (Thomas et al 2002).…”

Section: Subsequent Analysismentioning

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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Section: Subsequent Analysismentioning

confidence: 99%

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

et al. 2008

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“…The majority of these are moment-based estimators derived from expectations of allelic identity at single markers (Queller and Goodnight 1989;Ritland 1996;Lynch and Ritland 1999;Wang 2002). Despite the superior performance of maximum-likelihood estimators (Milligan 2003) these less-biased estimators of relatedness are often preferred in the estimation of heritability (Thomas 2005). Since unrelated individuals have kinship coefficient 0, the maximum-likelihood estimator can never be unbiased, whereas moment-based estimators that permit negative estimates can be so.…”

Section: Estimators Of Relatednessmentioning

confidence: 99%

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

2013

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Gene identity by descent (IBD) is a fundamental concept that underlies genetically mediated similarities among relatives. Gene IBD is traced through ancestral meioses and is defined relative to founders of a pedigree, or to some time point or mutational origin in the coalescent of a set of extant genes in a population. The random process underlying changes in the patterns of IBD across the genome is recombination, so the natural context for defining IBD is the ancestral recombination graph (ARG), which specifies the complete ancestry of a collection of chromosomes. The ARG determines both the sequence of coalescent ancestries across the chromosome and the extant segments of DNA descending unbroken by recombination from their most recent common ancestor (MRCA). DNA segments IBD from a recent common ancestor have high probability of being of the same allelic type. Non-IBD DNA is modeled as of independent allelic type, but the population frame of reference for defining allelic independence can vary. Whether of IBD, allelic similarity, or phenotypic covariance, comparisons may be made to other genomic regions of the same gametes, or to the same genomic regions in other sets of gametes or diploid individuals. In this review, I present IBD as the framework connecting evolutionary and coalescent theory with the analysis of genetic data observed on individuals. I focus on the high variance of the processes that determine IBD, its changes across the genome, and its impact on observable data.The descent and ancestry of DNA At a given location in the genome, the descent of DNA as described by Mendel's first law (Mendel 1866) provides the framework for analyses of the genetic consequences of coancestry among individuals. This fundamental law of inheritance is phrased in probabilistic terms. In a diploid individual, at each location in the genome, a random one of the two homologous copies of the DNA at that location is the DNA copied to the offspring gamete. Additionally, all meioses are independent; the random choice is made independently for each offspring, independently in the two parents of an individual, and independently from generation to generation in an ancestral lineage.DNA in different current gametes that is a copy of a single piece of DNA in some ancestral individual is said to be identical by descent or IBD from that ancestor. There is no absolute measure of IBD; IBD is always relative to some ancestral reference population. Many experimental or agricultural populations have a natural founding stock, as do some natural populations, and IBD may be measured relative to this founder population. More generally, IBD may be measured relative to the population at some past time point, with the implication that more remote coancestry of current gametes is ignored. In pedigrees, IBD is well defined relative to the specified founders of the pedigree. The fact of IBD does not depend on whether pedigree relationships are known. Specification of a pedigree relationship merely imposes a specific prior distribution o...

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“…Relatedness itself may be the subject of interest in selective breeding or conservation applications. The growing importance of this type of analysis is indicated in recent surveys, including Blouin (2003), Jones and Ardren (2003), Garant and Kruuk (2005) and Thomas (2005). Relatedness inference can vary in level of detail, ranging from aggregate measures of relatedness, pairwise estimates of relatedness type, or fully specified pedigrees (ie.…”

Section: Introductionmentioning

confidence: 99%

A graphical approach to relatedness inference

Almudevar

2007

Theoretical Population Biology

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The estimation of relatedness structure in natural populations using molecular marker data has become an important tool in population biology, resulting in a variety of estimation procedures for specific sampling scenarios. In this article a general approach is proposed, in which the detailed relationship structure, typically a pedigree graph or partition, is considered to be the object of inference. This makes available tools used in complex model selection theory which have demonstrated effectiveness. An important advantage of this approach is that it permits a fully Bayesian approach to the problem, providing a principled and accessible way to measure statistical error. The approach is demonstrated by applying the minimum description length principle. This technique is used in model selection to provide a rational way of comparing models of varying complexity. We show how the resulting score may be interpreted and applied as a Bayesian posterior density.

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The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations

Cited by 59 publications

References 72 publications

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

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

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

A graphical approach to relatedness inference

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