Coalescent: an open-science framework for importance sampling in coalescent theory [PDF]
PeerJ, 2015 Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but ...
Susanta Tewari, John L. Spouge
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Extending coalescent theory to autotetraploids. [PDF]
Genetics, 2012 Abstract We develop coalescent models for autotetraploid species with tetrasomic inheritance. We show that the ancestral genetic process in a large population without recombination may be approximated using Kingman’s standard coalescent, with a coalescent effective population size 4N.
Arnold B, Bomblies K, Wakeley J.
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Coalescent Theory of Migration Network Motifs. [PDF]
Mol Biol Evol, 2019 Abstract Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small ...
Alcala N +3 more
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Coalescent: an open-source and scalable framework for exact calculations in coalescent theory [PDF]
BMC Bioinformatics, 2012 Background Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either.
Tewari Susanta, Spouge John L
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Coalescent theory of the ψ directionality index. [PDF]
G3 (Bethesda)Abstract The ψ directionality index was introduced by Peter and Slatkin (Evolution 67: 3274–3289, 2013) to infer the direction of range expansions from single-nucleotide polymorphism variation. Computed from the joint site frequency spectrum for two populations, ψ uses shared genetic variants to measure the difference in the amount of
Lappo E, Rosenberg NA.
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Moonshine.jl: a Julia package for genome-scale model-based ancestral recombination graph inference [PDF]
Frontiers in GeneticsThe ancestral recombination graph (ARG) is the model of choice in statistical genetics to model population ancestries. Software capable of inferring ARGs on a genome scale within a reasonable amount of time are now widely available for most practical use
Patrick Fournier, Fabrice Larribe
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HIV classification using the coalescent theory. [PDF]
Bioinformatics, 2010 Abstract Motivation: Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise.
Bulla I +7 more
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Genomic perspectives on the inference of evolutionary changes in ecological life-history traits [PDF]
Quantitative Plant BiologyGenome-wide polymorphism data are increasingly used in conservation biology, and new developments in theoretical population genomics generate refined statistical inference methods.
Lukas Metzger +3 more
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Theory and applications of a deterministic approximation to the coalescent model [PDF]
Theoretical Population Biology, 2014 Under the coalescent model, the random number nt of lineages ancestral to a sample is nearly deterministic as a function of time when nt is moderate to large in value, and it is well approximated by its expectation E[nt]. In turn, this expectation is well approximated by simple deterministic functions that are easy to compute.
Noah Rosenberg
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Combining population genomics, larval dispersal modelling and graph theory to reveal connectivity patterns of the black-lipped pearl oyster in French Polynesia [PDF]
Scientific ReportsUnravelling the mechanisms driving marine connectivity in open ocean environments remains a challenge, particularly for bentho-pelagic species, where larval dispersal further complicates analysis.
Antoine Gradel +5 more
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