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Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters, such as divergence times and population sizes, they form a generative process of molecular sequence evolution. Early work on computational methods for phylogenetic network inference focused exclusively on reticulations and sought networks with the fewest number of reticulations to fit the data. As processes such as incomplete lineage sorting (ILS) could be at play concurrently with hybridization, work in the last decade has shifted to computational approaches for phylogenetic network inference in the presence of ILS. In such a short period, significant advances have been made on developing and implementing such computational approaches. In particular, parsimony, likelihood, and Bayesian methods have been devised for estimating phylogenetic networks and associated parameters using estimated gene trees as data. Use of those inference methods has been augmented with statistical tests for specific hypotheses of hybridization, like the D-statistic. Most recently, Bayesian approaches for inferring phylogenetic networks directly from sequence data were developed and implemented. In this chapter, we survey such advances and discuss model assumptions as well as methods’ strengths and limitations. We also discuss parallel efforts in the population genetics community aimed at inferring similar structures. Finally, we highlight major directions for future research in this area.
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Assessing the fit of the multi-species network coalescent to multi-locus data
Abstract Motivation With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These phylogenetic networks include events like hybridization, gene flow or horizontal gene transfer explicitly. However, the most accurate network inference methods are computationally heavy. Methods that scale to larger datasets do not calculate a full likelihood, such that traditional likelihood-based tools for model selection are not applicable to decide how many past hybridization events best fit the data. We propose here a goodness-of-fit test to quantify the fit between data observed from genome-wide multi-locus data, and patterns expected under the multi-species coalescent model on a candidate phylogenetic network. Results We identified weaknesses in the previously proposed TICR test, and proposed corrections. The performance of our new test was validated by simulations on real-world phylogenetic networks. Our test provides one of the first rigorous tools for model selection, to select the adequate network complexity for the data at hand. The test can also work for identifying poorly inferred areas on a network. Availability and implementation Software for the goodness-of-fit test is available as a Julia package at https://github.com/cecileane/QuartetNetworkGoodnessFit.jl. Supplementary information Supplementary data are available at Bioinformatics online.
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- PAR ID:
- 10225145
- Editor(s):
- Russell, Schwartz
- Date Published:
- Journal Name:
- Bioinformatics
- ISSN:
- 1367-4803
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/bioinformatics/btaa863
