Modeling Hybridization Under the Network Multispecies Coalescent

Degnan, J.H.

doi:10.1093/sysbio/syy040

Cited by 97 publications

(98 citation statements)

References 109 publications

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“…If the probability distributions of the data are identical for two sets of parameter values (Θ and Θ ), with f (X|Θ) = f (X|Θ ) for all possible data X, then Θ is unidentifiable given data X. Previous studies of identifiability have mostly focused on the use of gene tree topologies as data (Degnan, 2018;Zhu and Degnan, 2017). Note that a model unidentifiable given gene tree topologies alone may be identifiable given gene trees with branch lengths (Zhu and Degnan, 2017).…”

Section: Identifiability Of Msci Modelsmentioning

confidence: 99%

“…The second set of simulation was to compare BPP with summary methods. Most methods are designed to test for the presence of gene flow (hybridization or migration) (Degnan, 2018). Here we used two methods that can estimate the introgression probability under a fixed introgression model: SNAQ (Solis-Lemus and Ane, 2016) implemented in the program PhyloNetworks (Solis-Lemus et al, 2017) and HYDE (Blischak et al, 2018).…”

Section: Simulation Studymentioning

confidence: 99%

“…The third set of simulation explores the performance of BPP under models that are unidentifiable using SNAQ and HYDE. An MSci model may be identifiable given the gene trees with coalescent times but unidentifiable given gene tree topologies only (Degnan, 2018). We simulated and analyed data using BPP under two models: model D of Fig.…”

Section: Simulation Studymentioning

confidence: 99%

“…Most use summaries of the multi-locus sequence data such as the frequencies of estimated gene tree topologies (Solis-Lemus and Ane, 2016;Solis-Lemus et al, 2017) or the counts of parsimony-informative site patterns (Blischak et al, 2018;Durand et al, 2011;Green et al, 2010). See Degnan (2018) and Folk et al (2018) for recent reviews. We focus on coalescent-based full-likelihood models for closely related species.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper we extend the MSC model in the BPP program (Burgess and Yang, 2008;Rannala and Yang, 2003;Yang, 2015) to accommodate introgression, resulting in the multispecies-coalescent-with-introgression model, or MSci (Degnan, 2018). The MSci model can be used to estimate species divergence times and the number, timings and intensities of introgression events.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

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

Flouris

Jiao

Rannala³

et al. 2019

Preprint

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Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation.Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispeciescoalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

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Section: Identifiability Of Msci Modelsmentioning

confidence: 99%

Section: Simulation Studymentioning

confidence: 99%

Section: Simulation Studymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Flouris

Jiao

Rannala³

et al. 2019

Preprint

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Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys

Schrago

Seuánez²

2019

American J Primatol

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The phylogenetic position of owl monkeys, grouped in the genus Aotus, has been a controversial issue for understanding Neotropical primate evolution. Explanations of the difficult phylogenetic assignment of owl monkeys have been elusive, frequently relying on insufficient data (stochastic error) or scenarios of rapid speciation (adaptive radiation) events. Using a coalescent‐based approach, we explored the population‐level mechanisms likely explaining these topological discrepancies. We examined the topological variance of 2,192 orthologous genes shared between representatives of the three major Cebidae lineages and the outgroup. By employing a methodological framework that allows for reticulated tree topologies, our analysis explicitly tested for non‐dichotomous evolutionary processes impacting the finding of the position of owl monkeys in the cebid phylogeny. Our findings indicated that Aotus is a sister lineage of the callitrichines. Most gene trees (>50%) failed to recover the species tree topology, although the distribution of gene trees mismatching the true species topology followed the standard expectation of the multispecies coalescent without reticulation. We showed that the large effective population size of the common ancestor of Aotus and callitrichines was the most likely factor responsible for generating phylogenetic uncertainty. On the other hand, fast speciation scenarios or introgression played minor roles. We propose that the difficult phylogenetic placement of Aotus is explained by population‐level processes associated with the large ancestral effective size. These results shed light on the biogeography of the early cebid diversification in the Miocene, highlighting the relevance of evaluating phylogenetic relationships employing population‐aware approaches.

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Hybridization in palms (Arecaceae)

Bacon,

Hill

2024

Ecology and Evolution

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Hybridization has significant evolutionary consequences across the Tree of Life. The process of hybridization has played a major role in plant evolution and has contributed to species richness and trait variation. Since morphological traits are partially a product of their environment, there may be a link between hybridization and ecology. Plant hybrid species richness is noted to be higher in harsh environments, and we explore this hypothesis with a keystone tropical plant lineage, palms (Arecaceae). Leveraging a recent literature review of naturally occurring palm hybrids, we developed a method to calculate hybrid frequency, and then tested if there is phylogenetic signal of hybrids using a phylogeny of all palms. Further, we used phylogenetic comparative methods to examine the interaction between hybrid frequency and presence in dry environments, on islands, and the species richness of genera. Phylogenetic generalized least squares models had stronger support than models of random association, indicating phylogenetic signal for the presence of hybrids in dry and island environments. However, all p‐values were >.05 and therefore the correlation was poor between hybridization and the trait frequencies examined. Presence in particular environments are not strongly correlated to hybrid frequency, but phylogenetic signal suggests a role in its distribution in different habitats. Hybridization in palms is not evenly distributed across subfamilies, tribes, subtribes yet plays an important role in palm diversity, nonetheless. Increasing our understanding hybridization in this economically and culturally important plant family is essential, particularly since rates are projected to increase with climate change, reconfiguring the dynamics and distribution of biodiversity.

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Modeling Hybridization Under the Network Multispecies Coalescent

Cited by 97 publications

References 109 publications

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

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

Large ancestral effective population size explains the difficult phylogenetic placement of owl monkeys

Hybridization in palms (Arecaceae)

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