Bayesian Inference Of Phylogenetic Networks From Bi-allelic Genetic Markers

Zhu, Jiafan; Wen, Dingqiao; Yu, Yun; Meudt, Heidi M.; Nakhleh, Luay

doi:10.1101/143545

Cited by 13 publications

(35 citation statements)

References 40 publications

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“…The recent explosion of new methods to estimate phylogenetic species networks (e.g. Yu et al ., ; Yu & Nakhleh, ; Solís‐Lemus & Ané, ; Wen et al ., ; Wen & Nakhleh, ; Zhang et al ., ; Zhu et al ., ) will facilitate more comprehensive studies of reticulation in groups like Lachemilla . Moreover, with the emergence of approaches for performing phylogenetic comparative methods on networks (Jhwueng & O'Meara, ; Bastide et al ., ), we hope the results presented here will help us to investigate broad questions regarding trait evolution, biogeography, and diversification dynamics in Lachemilla , as well as an evolutionarily informed classification system that reflects the complex (reticulate) history of the group.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, methods to estimate phylogenetic species networks from sequence data that incorporate gene‐tree uncertainty and discordance due to ILS and gene flow have been developed (e.g. Yu et al ., ; Yu & Nakhleh, ; Solís‐Lemus & Ané, ; Wen et al ., ; Wen & Nakhleh, ; Zhang et al ., ; Zhu et al ., ). Although, these methods are still computationally intensive and limited to a small number of species and reticulation events (Hejase & Liu, ), their usage to detect patterns of reticulation is rapidly increasing (e.g.…”

Section: Introductionmentioning

confidence: 97%

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Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

2018

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Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

2018

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“…As evidence of reticulation (hybridization, horizontal gene transfer, etc.) in the evolutionary histories of diverse sets of species across the Tree (or, more appropriately in our context, Network) of Life continues to grow, increasingly sophisticated methods for phylogenetic network inference are being developed to incorporate processes such as incomplete lineage sorting (ILS), gene duplication and loss, and gene flow [20,21,15,16,24,28,27]. These methods, which are mostly statistical in nature, are computationally prohibitive due, in part, to the complex space of phylogenetic networks that is explored.…”

Section: Introductionmentioning

confidence: 99%

“…Several methods for inference of phylogenetic networks in the presence of incomplete lineage sorting have been devised. These include parsimony methods [18], maximum likelihood methods [19,20], maximum pseudo-likelihood methods [21,27], and Bayesian methods [15,16,24,28]. These methods have poor scalability in terms of time and memory requirements and are applicable to very small data sets.…”

Section: Introductionmentioning

confidence: 99%

Empirical Performance of Tree-based Inference of Phylogenetic Networks

Cao¹,

Nakhleh²

2019

Preprint

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Phylogenetic networks extend the phylogenetic tree structure and allow for modeling vertical and horizontal evolution in a single framework. Statistical inference of phylogenetic networks is prohibitive and currently limited to small networks. An approach that could significantly improve phylogenetic network space exploration is based on first inferring an evolutionary tree of the species under consideration, and then augmenting the tree into a network by adding a set of "horizontal" edges to better fit the data.In this paper, we study the performance of such an approach on networks generated under a birth-hybridization model and explore its feasibility as an alternative to approaches that search the phylogenetic network space directly (without relying on a fixed underlying tree). We find that the concatenation method does poorly at obtaining a "backbone" tree that could be augmented into the correct network, whereas the popular species tree inference method ASTRAL does significantly better at such a task. We then evaluated the tree-tonetwork augmentation phase under the minimizing deep coalescence and pseudo-likelihood criteria. We find that even though this is a much faster approach than the direct search of the network space, * the accuracy is much poorer, even when the backbone tree is a good starting tree.Our results show that tree-based inference of phylogenetic networks could yield very poor results. As exploration of the network space directly in search of maximum likelihood estimates or a representative sample of the posterior is very expensive, significant improvements to the computational complexity of phylogenetic network inference are imperative if analyses of large data sets are to be performed. We show that a recently developed divide-and-conquer approach significantly outperforms tree-based inference in terms of accuracy, albeit still at a higher computational cost.

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“…Species tree inference under the multispecies coalescent (MSC) model has gained much attention due to the fact that it allows for modeling gene tree heterogeneity that arises across the genome from incomplete lineage sorting (ILS; Degnan and Rosenberg, 2009). A wide array of methods that assume or are inspired by the MSC have been devised (Liu et al, 2010;Liu and Yu, 2011;Mirarab et al, 2014;Chifman and Kubatko, 2014;Wang and Nakhleh, 2018), including the Bayesian methods of Ogilvie et al (2017); Flouri et al (2018); Zhu et al (2018). The MSC was recently extended to the multispecies network coalescent (MSNC) to account for reticulation (in addition to ILS; see Yu et al, 2014) and Bayesian methods for inference under this model have been devised (Wen et al, 2016;Wen and Nakhleh, 2017;Wen et al, 2018;Zhu et al, 2018;Zhang et al, 2017;Bouckaert et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees

Wang

Ogilvie

Nakhleh

2019

Preprint

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Species tree inference from multi-locus data has emerged as a powerful paradigm in the post-genomic era, both in terms of the accuracy of the species tree it produces as well as in terms of elucidating the processes that shaped the evolutionary history. Bayesian methods for species tree inference are desirable in this area as they have been shown to yield accurate estimates, but also to naturally provide measures of confidence in those estimates. However, the heavy computational requirements of Bayesian inference have limited the applicability of such methods to very small data sets. In this paper, we show that the computational efficiency of Bayesian inference under the multispecies coalescent can be improved in practice by restricting the space of the gene trees explored during the random walk, without sacrificing accuracy as measured by various metrics. The idea is to first infer constraints on the trees of the individual loci in the form of unresolved gene trees, and then to restrict the sampler to consider only resolutions of the constrained trees. We demonstrate the improvements gained by such an approach on both simulated and biological data.

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Bayesian Inference Of Phylogenetic Networks From Bi-allelic Genetic Markers

Cited by 13 publications

References 40 publications

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

Empirical Performance of Tree-based Inference of Phylogenetic Networks

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees

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