On the genealogy of large populations

Kingmán, J. F. C.

doi:10.2307/3213548

Cited by 1,164 publications

(450 citation statements)

References 18 publications

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“…As per coalescent theory, a neutrally evolving population of size 2000 will have a shared common ancestor after approximately 4000 generations (Kingman, 1982). We thus ran the simulator for 14000 generations to ensure that this criterion is met.…”

Section: Methodsmentioning

confidence: 99%

Tests of Selection in Pooled Case-Control Data: An Empirical Study

Udpa¹,

Zhou²,

Haddad³

et al. 2011

Front. Gene.

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For smaller organisms with faster breeding cycles, artificial selection can be used to create sub-populations with different phenotypic traits. Genetic tests can be employed to identify the causal markers for the phenotypes, as a precursor to engineering strains with a combination of traits. Traditional approaches involve analyzing crosses of inbred strains to test for co-segregation with genetic markers. Here we take advantage of cheaper next generation sequencing techniques to identify genetic signatures of adaptation to the selection constraints. Obtaining individual sequencing data is often unrealistic due to cost and sample issues, so we focus on pooled genomic data. We explore a series of statistical tests for selection using pooled case (under selection) and control populations. The tests generally capture skews in the scaled frequency spectrum of alleles in a region, which are indicative of a selective sweep. Extensive simulations are used to show that these approaches work well for a wide range of population divergence times and strong selective pressures. Control vs control simulations are used to determine an empirical False Positive Rate, and regions under selection are determined using a 1% FPR level. We show that pooling does not have a significant impact on statistical power. The tests are also robust to reasonable variations in several different parameters, including window size, base-calling error rate, and sequencing coverage. We then demonstrate the viability (and the challenges) of one of these methods in two independent Drosophila populations (Drosophila melanogaster) bred under selection for hypoxia and accelerated development, respectively. Testing for extreme hypoxia tolerance showed clear signals of selection, pointing to loci that are important for hypoxia adaptation. Overall, we outline a strategy for finding regions under selection using pooled sequences, then devise optimal tests for that strategy. The approaches show promise for detecting selection, even several generations after fixation of the beneficial allele has occurred.

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Section: Methodsmentioning

confidence: 99%

Tests of Selection in Pooled Case-Control Data: An Empirical Study

Udpa¹,

Zhou²,

Haddad³

et al. 2011

Front. Gene.

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“…The most exciting recent development at the interface of evolutionary biology and epidemiology has come about from the proliferation of sequence data combined with methods capable of making inferences about the history of a sample of sequences from the structure of the genealogy underlying them. A key concept is the coalescent (Kingman, 1982), which describes the genealogy of a sample of sequences in terms of how often their lineages 'coalesce' or come together to form an internal node in the tree. Combined with a molecular clock that relates the accumulation of sequence divergence to time, this allows us to infer events that have happened in the history of the sequences, most notably and relevant for epidemiology, changes in population size.…”

Section: Phylodynamics and Using Dna Sequence To Study Transmissionmentioning

confidence: 99%

Pathogen Epidemiology

Hanage

2016

Encyclopedia of Evolutionary Biology

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“…The underlying Kingman coalescent model [35,36] is used with two basic assumptions. At a speciation event (internal node on the species tree; Figure 1) travelling past to present, the population splits into two isolated populations.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, all species (past and present) have a constant population size. Now sampling a number of alleles from different individuals of a single species and tracing the genetic lineages backward in time, we have a traditional Kingman coalescent process with exponential waiting time between gene coalescent events within a species [28,35,36]. The rate with which two genetic lineages in a population coalesce is proportional to 1/ θ where θ is a measure of the effective population size.…”

Section: Introductionmentioning

confidence: 99%

Rooted triple consensus and anomalous gene trees

et al. 2008

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BackgroundAnomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.ResultsBased on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny.ConclusionEvidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.

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On the genealogy of large populations

Cited by 1,164 publications

References 18 publications

Tests of Selection in Pooled Case-Control Data: An Empirical Study

Tests of Selection in Pooled Case-Control Data: An Empirical Study

Pathogen Epidemiology

Rooted triple consensus and anomalous gene trees

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