A model for the length of tracts of identity by descent in finite random mating populations

Chapman, Nicola H.; Thompson, E. A.

doi:10.1016/s0040-5809(03)00071-6

Cited by 51 publications

(63 citation statements)

References 10 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

155

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

155

204

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“…(see Chapman and Thompson 2003) for more accurate formulae for varying population sizes). Figure 4 shows that when a bottleneck occurred, there is a linear relationship between the frequency of IBD tracts (on a log scale) and the length of IBD tracts, and this linear relationship fails for a constant-size population (Gusev et al, 2012).…”

Section: Identical By Descent (Ibd) Segments and Runs Of Homozygositymentioning

confidence: 99%

Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

2013

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Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data.

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“…Any inference made on a population's history using the theory of junctions will necessarily be made using genetic markers. Whilst the results of Stam (1980) and Chapman & Thompson (2003) give a precise record of the make-up of each chromosome, this would not be available if markers alone were examined. Indeed Stam states (p. 143), with reference to his results, that using spaced markers 'may result in an underestimation of the number of junctions '.…”

Section: Introductionmentioning

confidence: 99%

Marker densities and the mapping of ancestral junctions

et al. 2005

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SummaryIn any partially inbred population, ' junctions' are the loci that form boundaries between segments of ancestral chromosomes. Here we show that the expected number of junctions per Morgan in such a population is linearly related to the inbreeding coefficient of the population, with a maximum in a completely inbred population corresponding to the prediction given by Stam (1980). We further show that high-density marker maps (fully informative markers with average densities of up to 200 per cM) will fail to detect a significant proportion of the junctions present in highly inbred populations. The number of junctions detected is lower than that which would be expected if junctions were distributed randomly along the chromosome, and we show that junctions are not, in fact randomly spaced. This non-random spacing of junctions significantly increases the number of markers that is required to detect 90 % of the junctions present on any chromosome : a marker count of at least 12 times the number of junctions present will be needed to detect this proportion.

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A model for the length of tracts of identity by descent in finite random mating populations

Cited by 51 publications

References 10 publications

Admixture as the basis for genetic mapping

Admixture as the basis for genetic mapping

Inferring population size changes with sequence and SNP data: lessons from human bottlenecks

Marker densities and the mapping of ancestral junctions

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