On spatial coalescents with multiple mergers in two dimensions

Heuer, Benjamin; Sturm, Anja

doi:10.1016/j.tpb.2012.11.006

Cited by 10 publications

(10 citation statements)

References 33 publications

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“…In these cases, gene genealogies are often expected to be starlike [ 61 ] but other factors (like the reduction of number of individuals due to overfishing) can explain while at the single deme level we find only a slight expansion (anyway recent) and not in all stations. Finally we note that pooling lineages for several demes in a meta-population (mimicking a scatter sample sensu Wakeley 1999 [ 53 ]) overcome the effect of the skew in offspring production [ 63 ]. Therefore, we argue that the finding of an expansion of 50,000 years B.P.…”

Section: Discussionmentioning

confidence: 99%

Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

et al. 2015

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Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i) the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii) a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from “virgin” deeper grounds not affected by fishing to upper fishing areas support an effective ‘rescue effect’ contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman’s coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be particularly relevant to sample the deepest ones directly.

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Section: Discussionmentioning

confidence: 99%

Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

et al. 2015

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“…Both approaches model proliferation of lineages over time. Further examples include β-coalescent [32], Λ-coalescent [33,34], Ξ-coalescent [35,36], and Galton-Watson theory [37,38]. Technical mathematical treatments tend to assume the foundations of ancestral processes.…”

Section: Coalescent Theory Of Branching Processesmentioning

confidence: 99%

Linearization of the Kingman Coalescent

Slade

2018

Mathematics

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Kingman's coalescent process is a mathematical model of genealogy in which only pairwise common ancestry may occur. Inter-arrival times between successive coalescence events have a negative exponential distribution whose rate equals the combinatorial term ( n 2 ) where n denotes the number of lineages present in the genealogy. These two standard constraints of Kingman's coalescent, obtained in the limit of a large population size, approximate the exact ancestral process of Wright-Fisher or Moran models under appropriate parameterization. Calculation of coalescence event probabilities with higher accuracy quantifies the dependence of sample and population sizes that adhere to Kingman's coalescent process. The convention that probabilities of leading order N −2 are negligible provided n N is examined at key stages of the mathematical derivation. Empirically, expected genealogical parity of the single-pair restricted Wright-Fisher haploid model exceeds 99% where n ≤ √ N/6. The fractional cubic root criterion is practicable, since although it corresponds to perfect parity and to an extent confounds identifiability it also accords with manageable conditional probabilities of multi-coalescence.

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“…Interestingly, in a model assuming a Λ‐coalescent in each deme, the genealogy underlying a species‐wide sampling of individuals (Städler et al . ), that is, reflecting the collecting phase, tends to converge to the classic Kingman coalescent (Heuer & Sturm ). It follows that the collecting phase may be well approximated by the classic Kingman coalescent, even though MMC genealogies occur locally within each deme.…”

Section: Current and Potential Applications Of Multiple Merger Coalesmentioning

confidence: 99%

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

2014

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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 SNPs 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 Kingman coalescent theory based on the Wright-Fisher 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, Bolthausen-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 SNPs 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.

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On spatial coalescents with multiple mergers in two dimensions

Cited by 10 publications

References 33 publications

Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

Linearization of the Kingman Coalescent

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

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