On the genealogy of large populations

Kingmán, J. F. C.

doi:10.1017/s0021900200034446

Cited by 710 publications

(866 citation statements)

References 14 publications

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“…The method derives from coalescence theory (Kingman, 1982), as the shape of a genealogy depends on the demographic history. More specifically, the generalized skyline plot uses a step function and the genealogy to represent estimated changes in effective population size (Ne) over time.…”

Section: Mtdna-igsmentioning

confidence: 99%

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

Coyer¹,

Hoarau²,

Costa³

et al. 2011

Molecular Phylogenetics and Evolution

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Section: Mtdna-igsmentioning

confidence: 99%

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

Coyer¹,

Hoarau²,

Costa³

et al. 2011

Molecular Phylogenetics and Evolution

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“…Moreover, this probability distribution on trees is precisely the same as that given by a quite different process, namely Kingman's coalescent process [9] in population genetics, which starts at the leaves and successively combines pairs of elements, provided that, once again, we ignore branch lengths ( [1]). …”

Section: Cladesmentioning

confidence: 92%

Clades, clans, and reciprocal monophyly under neutral evolutionary models

Zhu

Degnan

Steel

2011

Theoretical Population Biology

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The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the probability of finding one or more groups of taxa as clades in a rooted tree, or as 'clans' in an unrooted tree. Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics.

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“…Meuwissen and Goddard [13] inferred pair-wise IBD probabilities between haplotypes using the coalescent theory, which is an approximate representation of genealogies [7,8]. The coalescent recreates the phylogenetic tree among current population members proceeding backwards in time, until a single expected common ancestor is reached, and all lineages have merged.…”

Section: A Coalescent-based Methodsmentioning

confidence: 99%

“…These parameters were not used in Meuwissen and Goddard's work, instead, the coalescent theory was applied [7,8], and henceforth their method will be called the coalescent (-based) method (CM). Our method uses a regression approach, henceforth called regression (-based) method (RM), to predict IBD L as a function of θ k , p and IBS at markers (x).…”

Section: Introductionmentioning

confidence: 99%

Prediction of IBD based on population history for fine gene mapping

2006

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-A novel multiple regression method (RM) is developed to predict identity-bydescent probabilities at a locus L (IBD L ), among individuals without pedigree, given information on surrounding markers and population history. These IBD L probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T ), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM. QTL fine mapping/ identity-by-descent

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On the genealogy of large populations

Cited by 710 publications

References 14 publications

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

Clades, clans, and reciprocal monophyly under neutral evolutionary models

Prediction of IBD based on population history for fine gene mapping

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