Evaluating and accelerating the multispecies coalescent
Evaluating, Accelerating and Extending the Multispecies Coalescent Model of Evolution
... the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for bet- ter ...
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Statistical Inference under the Multispecies Coalescent: Methods and Theory
... 4.4 Consistency Simulation As the covariances, and therefore distances, cannot be estimated without error, we present simulations to show as the amount of information increases, the error in estimation decreases, and the ...
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Preliminary framework for DNA barcoding, incorporating the multispecies coalescent
... genes was chosen for both practical purposes, and because it is the minimum number needed for coalescent-based barcoding. G ENERATING U NKNOWNS F OR T ESTING We wanted to test whether an unknown specimen could be ...
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A preliminary framework for DNA barcoding, incorporating the multispecies coalescent
... genes was chosen for both practical purposes, and because it is the minimum number needed for coalescent-based barcoding. G ENERATING U NKNOWNS F OR T ESTING We wanted to test whether an unknown specimen could be ...
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Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
... We suggest that the utility of summary vs. full-likelihood methods will depend on the nature of the species tree esti- mation problem. For easy problems with long internal branches in the species tree and little ...
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Efficient Bayesian species tree inference under the multispecies coalescent
... the multispecies coalescent (MSC) ...Bayesian coalescent-based method is statistically more efficient than heuristic methods based on summary statistics, and that our implementation is computationally ...
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DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Abstract.
... The coalescent prior on the gene trees will affect them in a way that single recent introgressions will be “pushed back” by other gene trees that reflect the “true” spe- ciation event, such that the ...
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Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent
... the multispecies coalescent Fang, Bohao ; Merilä, Juha ; Matschiner, Michael ; Momigliano, Paolo Abstract: Incomplete lineage sorting (ILS) can lead to biased divergence time ...the multispecies ...
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Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses
... the multispecies coalescent (MSC) model, which is a straightforward extension of the standard single-species coalescent (Kingman, 1982; Hudson, 1983; Tajima, 1983) to the case of multiple species ...
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Evaluating Ecosystem Response to Oyster Restoration and Nutrient Load Reduction With a Multispecies Bioenergetics Model
... TroSim comparison to other models and model predictions The effect of bivalves on food web dynamics has been examined in several systems, however the focus has largely been on changes in benthic-pelagic coupling and ...
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Counting Coalescent Histories
... those coalescent histories that are ...resources evaluating whether or not each proposed coalescent history is ...valid coalescent histories could simply be ...valid coalescent ...
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Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae)
... multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets ...multi-species ...
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The Segregated Lambda-Coalescent
... Kingman’s coalescent was generalized, independently but in the same spirit, by Donnelly and Kurtz (1999), Pitman (1999) and Sagitov ...- coalescent starts with a countable infinity of particles, with each ...
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The Coalescent With Gene Conversion
... informative site to be a site where at least two different obtained in the coalescent with recombination. The covariance between trees relating two distinct positions nucleotides are present in at least two ...
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The Coalescent Process With Selfing
... When the process leaves this state (because the two alleles find themselves in the same ancestral individual), the common ancestral allele is found, and thus the process [r] ...
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Multispecies virial expansions
... The article is organised as follows. In Section 2 we give the general setting of the virial expansion in the context of formal power series. The main theorem proposes sufficient conditio[r] ...
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For a Politicized Multispecies Ethnography
... politicized multispecies ethnogra- phy aims to understand these power-laden entangle- ments among species; humans, too, are a species (in- deed, a species that thoroughly and routinely shapes the lives of farmed ...
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Multispecies hybridization in birds
... Dong et al. 2014; Pons et al. 2014; Battey and Klicka 2017; Morales et al. 2017; Shipham et al. 2017). Species might thus occasionally benefit from intro- gression. When multiple lineages are interbreeding, the adaptive ...
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A unified multi-resolution coalescent: Markov lumpings of the Kingman-Tajima n-coalescent
... Tajima’s evolutionary relationships have been formalized into an n-coalescent whose realizations are g-sequences that are in bijection with ranked tree shapes. Kingman’s unla- beled n-coalescent has been ...
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The coalescent process in models with selection.
... Two essential features of the selectively neutral infinite sites model proposed by KIMURA (1969) are (1) each segregating site in a random sample genes is the result of [r] ...
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