Marker densities and the mapping of ancestral junctions

MacLeod, Andy; Haley, Chris; Woolliams, John; Stam, P.

doi:10.1017/s0016672305007329

Cited by 25 publications

(38 citation statements)

References 15 publications

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“…At the extreme, an allele responsible for adaptation in one parental taxon will be in complete linkage disequilibrium with all markers that have fixed allele differences between parental lineages, even those not physically linked to the causal locus. Recombination in admixed individuals will reduce the extent of linkage disequilibrium [64][65][66]. A variety of different approaches have been developed to control statistically for genome-wide admixture and ancestry in modeling phenotypes [12,13,15,67].…”

Section: Statistical Methods and Data Acquisitionmentioning

confidence: 99%

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Admixture as the basis for genetic mapping

Buerkle

Lexer

2008

Trends in Ecology & Evolution

162

204

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Section: Statistical Methods and Data Acquisitionmentioning

confidence: 99%

“…Regions of each chromosome with different colors represent genomic regions with ancestry in each of the parental taxa. The size of these ancestry blocks and the linkage disequilibrium between neighboring molecular markers decays with additional generations (t) of recombination (u) at a rate proportional to (1 À u) t [64][65][66].…”

Section: Glossarymentioning

confidence: 99%

Admixture as the basis for genetic mapping

Buerkle

Lexer

2008

Trends in Ecology & Evolution

162

204

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“…In the terminology of Fisher (1954), it is the mapping of 'junctions', points of recombination between nonidentical segments, that is important. Theory of the number of recognisable junctions in a finite population has been given by Stam (1980) (see also Macleod et al, 2005). As mentioned above, the Hapmap study provides information at a sufficiently detailed level to allow determination of such junctions.…”

Section: Junctions and Identity Of Chromosome Regionsmentioning

confidence: 99%

Linkage Disequilibrium and Its Expectation in Human Populations

Sved¹

2009

Twin Res Hum Genet

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L inkage disequilibrium (LD), the association in populations between genes at linked loci, has achieved a high degree of prominence in recent years, primarily because of its use in identifying and cloning genes of medical importance. The field has recently been reviewed by Slatkin (2008). The present article is largely devoted to a review of the theory of LD in populations, including historical aspects.

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“…Regional IBD is conceptually linked to Fisher's (1953) junction theory. As junctions were defined as recombination events delimiting different IBD regions, there must be a link between the number of junctions and the regional IBD obtained in this work (e.g., MacLeod et al 2005).…”

Section: Resultsmentioning

confidence: 99%

Prediction of Multilocus Identity-by-Descent

Hill

Hernández-Sánchez

2007

Genetics

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Previous studies have enabled exact prediction of probabilities of identity-by-descent (IBD) in randommating populations for a few loci (up to four or so), with extension to more using approximate regression methods. Here we present a precise predictor of multiple-locus IBD using simple formulas based on exact results for two loci. In particular, the probability of non-IBD X ABC at each of ordered loci A, B, and C can be well approximated by X ABC ¼ X AB X BC /X B and generalizes to X 123. . .k ¼ X 12 X 23. . . X kÀ1,k /X kÀ2 , where X is the probability of non-IBD at each locus. Predictions from this chain rule are very precise with population bottlenecks and migration, but are rather poorer in the presence of mutation. From these coefficients, the probabilities of multilocus IBD and non-IBD can also be computed for genomic regions as functions of population size, time, and map distances. An approximate but simple recurrence formula is also developed, which generally is less accurate than the chain rule but is more robust with mutation. Used together with the chain rule it leads to explicit equations for non-IBD in a region. The results can be applied to detection of quantitative trait loci (QTL) by computing the probability of IBD at candidate loci in terms of identity-by-state at neighboring markers. I N a recent article formulas for computing probabilities of identity-by-descent (IBD) at multiple loci in random-mating populations were obtained (Hill and Weir 2007) by extending methods of Cockerham (1969, 1974) for a haploid model. Recurrence equations were presented for multilocus non-IBD, from which IBD can be computed; but the number of terms involved quickly becomes impracticably large to compute. For example, prediction of nonidentity at three loci requires recurrence equations for a total of 16 non-IBD measures defined for loci sampled on two, three, four, five, and six different haplotypes. For four loci the number of measures rises to 139 (Hill and Weir 2007). Hernández-Sánchez et al. (2004) have developed approximations based on multiple regression to compute IBD at multiple loci from that at two loci, but the formulas become increasingly less tractable and accurate as the number of loci increases.Here we develop a straightforward method (the chain rule) for predicting probabilities of multilocus non-IBD, and thus IBD, which uses exact results only on two-locus non-IBD probabilities. Assuming a known population history, this predictor can be very precise for many loci and can enable IBD for a whole chromosome region to be computed. We also develop simple approximate recurrence equations that are generally less precise, except in the presence of mutation.An application of multiple-locus extensions of Wright's inbreeding coefficient is in gene or quantitative trait loci (QTL) mapping on the basis of the association between phenotypic similarity of individuals and shared IBD at a particular genomic region (Meuwissen et al. 2002;Hernández-Sánchez et al. 2006). The magnitude of IBD at a QTL is c...

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Marker densities and the mapping of ancestral junctions

Cited by 25 publications

References 15 publications

Admixture as the basis for genetic mapping

Admixture as the basis for genetic mapping

Linkage Disequilibrium and Its Expectation in Human Populations

Prediction of Multilocus Identity-by-Descent

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