A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

Flouris, Thomas; Jiao, Xiyun; Rannala, Bruce; Yang, Ziheng

doi:10.1101/766741

Cited by 3 publications

(2 citation statements)

References 58 publications

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“…Here we use the species tree of Thawornwattana et al (2018) (Fig. 7) and the parameter estimates from Flouris et al (2019) to confirm that under the MSci model the introgression rates affecting the autosomes are high enough to mislead species tree estimation.…”

Section: African Mosquito Data Examplementioning

confidence: 85%

The Impact of Cross-Species Gene Flow on Species Tree Estimation

et al. 2020

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Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]

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Section: African Mosquito Data Examplementioning

confidence: 85%

The Impact of Cross-Species Gene Flow on Species Tree Estimation

et al. 2020

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“…Accounting for and modeling potential sources of admixture is a next step for these parameter inference methods. It is worth noting that a preprint for an extension of BPP implementing the full MSC with introgression (MSci) has recently been released [7]. Identifying locations of admixture and fitting admixture branches to a species tree are left to future work for COAL PHYRE.…”

Section: Run Timesmentioning

confidence: 99%

COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory

Guerra

Nielsen

2020

Preprint

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2AbstractGenome-scale data are increasingly being used to infer phylogenetic trees. A major challenge in such inferences is that different regions of the genome may have local topologies that differ from the species tree due to incomplete lineage sorting (ILS). Another source of gene tree discrepancies is estimation errors arising from the randomness of the mutational process during sequence evolution. There are two major groups of methods for estimating species tree from whole-genome data: a set of full likelihood methods, which model both sources of variance, but do not scale to large numbers of independent loci, and a class of faster approximation methods which do not model the mutational variance.To bridge the gap between these two classes of methods, we present COAL_PHYRE (COmposite Approximate Likelihood for PHYlogenetic REconstruction), a composite likelihood based method for inferring population size and divergence time estimates of rooted species trees from aligned gene sequences. COAL_PHYRE jointly models coalescent variation across loci using the MSC and variation in local gene tree reconstruction using a normal approximation. To evaluate the accuracy and speed of the method, we compare against BPP, a powerful MCMC full-likelihood method, as well as ASTRAL-III, a fast approximate method. We show that COAL_PHYRE’s divergence time and population size estimates are more accurate than ASTRAL, and comparable to those obtained using BPP, with an order of magnitude decrease in computational time. We also present results on previously published data from a set of Gibbon species to evaluate the accuracy in topology and parameter inference on real data, and to illustrate the method’s ability to analyze data sets which are prohibitively large for MCMC methods.

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The Impact of Cross-Species Gene Flow on Species Tree Estimation

Jiao

Flouris

Rannala³

et al. 2019

Preprint

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Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree inference. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multi-locus sequence data. Our results suggest that the majority-vote method is more robust to gene flow than the UPGMA method and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. A small amount of introgression or migration can mislead species tree methods if the species diverged through speciation events separated by short time intervals. Estimates of parameters under the MSC with gene flow suggest the Anopheles gambia African mosquito species complex is an example where gene flow greatly impacts species phylogeny.

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A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

Cited by 3 publications

References 58 publications

The Impact of Cross-Species Gene Flow on Species Tree Estimation

The Impact of Cross-Species Gene Flow on Species Tree Estimation

COAL_PHYRE: A Composite Likelihood Method for Estimating Species Tree Parameters from Genomic Data Using Coalescent Theory

The Impact of Cross-Species Gene Flow on Species Tree Estimation

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