Quartet Inference from SNP Data Under the Coalescent Model

Chifman, Julia; Kubatko, Laura

doi:10.1093/bioinformatics/btu530

Cited by 975 publications

(838 citation statements)

References 27 publications

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“…Some of these summary methods are created on the basis of the multispecies coalescent model (20) and are statistically consistent under that model (12,13), which means they will reconstruct the true species tree with high probability given a sufficiently large number of estimated gene trees that are error-free (12,13,17,18). A new type of coalescent-based method estimates the species tree directly from unlinked markers without also estimating gene trees (21)(22)(23).…”

Section: Resultsmentioning

confidence: 99%

“…However, binning without attempting to evaluate whether genes have a common tree [as used in the "naïve binning" technique (28)] may not provide the improvements in accuracy seen here. Statistical binning is not likely to be useful for methods that estimate species trees directly from sequence data [e.g., (21)(22)(23)], because binning reduces the amount of data given to the method and can only be beneficial if it also improves the quality of the input data.…”

Section: Treementioning

confidence: 99%

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab

Bayzid

Boussau

et al. 2014

Science

242

247

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Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life.

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Section: Resultsmentioning

confidence: 99%

Section: Treementioning

confidence: 99%

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab

Bayzid

Boussau

et al. 2014

Science

242

247

View full text Add to dashboard Cite

show abstract

“…We first inferred phylogenetic relationships with singular value decomposition scores for species quartets (SVD quartets) (42), sampling all possible quartets and allowing for up to 30% of missing data. Node support was estimated with 1,000 bootstrap replicates.…”

Section: Methodsmentioning

confidence: 99%

Inferring responses to climate dynamics from historical demography in neotropical forest lizards

Prates

Xue

Brown

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

105

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We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.phylogeography | population genomics | Amazon Forest | Atlantic Forest | climate change

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“…On the coalescence front, single nuclear polymorphism (SNP) methods such as SVDquartets [94] provide an alternative to fully parametric and shortcut coalescence methods that depend on gene trees. An important advantage of SNP methods is that they avoid problems with the recombination ratchet [10].…”

Section: Morphology Moleculesmentioning

confidence: 99%

Mammal madness: is the mammal tree of life not yet resolved?

Foley

Springer

Teeling

2016

Phil. Trans. R. Soc. B

209

195

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One contribution of 15 to a discussion meeting issue 'Dating species divergences using rocks and clocks'. Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

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Quartet Inference from SNP Data Under the Coalescent Model

Abstract: The method to infer the phylogenetic relationship among quartets is implemented in the software SVDquartets, available at www.stat.osu.edu/∼lkubatko/software/SVDquartets.

Cited by 975 publications

References 27 publications

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Inferring responses to climate dynamics from historical demography in neotropical forest lizards

Mammal madness: is the mammal tree of life not yet resolved?

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