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Coalescence 2.0: a multiple branching of recent theoretical developments and their applications
Author(s) -
Tellier Aurélien,
Lemaire Christophe
Publication year - 2014
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.12755
Subject(s) - coalescent theory , biology , evolutionary biology , population , natural selection , population genetics , population genomics , effective population size , neutral theory of molecular evolution , ecology , population size , genome , genomics , genetics , phylogenetics , genetic variation , gene , demography , sociology
Population genetics theory has laid the foundations for genomic analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNP s under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the K ingman coalescent theory based on the W right‐ F isher population model. However, these theoretical models rely on biological and life history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so‐called multiple merger coalescent models are reviewed here (Λ‐coalescent, beta‐coalescent, B olthausen‐Sznitman, Ξ‐coalescent). We explain how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as (i) the skew in offspring production typical of marine species, (ii) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, (iii) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles and (iv) the high rates of extinction‐recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNP s under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.