The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

Yu, Yun; Degnan, J.H.; Nakhleh, Luay

doi:10.1371/journal.pgen.1002660

Cited by 221 publications

(296 citation statements)

References 55 publications

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“…2 in this work. Using this formulation, the pmf pðG i jΨ; ΓÞ, when G i is the gene genealogy's topology alone, is computable using the algorithms of Yu et al (16,17). In Results, we derive the pdf of gene genealogies (with branch lengths), given a phylogenetic network.…”

Section: Modelmentioning

confidence: 99%

“…First, we devise a search heuristic that searches the phylogenetic network space in layers. Second, we explore the use of cross-validation as a method to ameliorate overfitting the data, which adds to the array of other methods (e.g., information criteria) that have already been used (12,16). Finally, to assess the fit of the inferred phylogenetic network to the data, we devise a parametric bootstrap approach that allows us to quantify branch support for the phylogenetic network.…”

Section: Modelmentioning

confidence: 99%

“…However, these methods are all applicable to simple scenarios of species evolution and mostly assume a known hypothesis about the topology of the phylogenetic network. As reported (16,17), we devised methods for computing the likelihood of a phylogenetic network, given a set of gene tree topologies. Still, these methods did not allow for inference of phylogenetic networks (they assume a given phylogenetic network topology and compute its likelihood).…”

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confidence: 99%

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Maximum likelihood inference of reticulate evolutionary histories

Yu¹,

Dong²,

Liu

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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260

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Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships. reticulate evolution | incomplete lineage sorting | phylogenetic networks | maximum likelihood P hylogenetic trees have long been a mainstay of biology, providing an interpretive model of the evolution of molecules and characters and a backdrop against which comparative genomics and phenomics are conducted. Nevertheless, some evolutionary events, most notably horizontal gene transfer in prokaryotes and hybridization in eukaryotes, necessitate going beyond trees (1). These events result in reticulate evolutionary histories, which are best modeled by phylogenetic networks (2). The topology of a phylogenetic network is given by a rooted, directed, acyclic graph (rDAG) that is leaf-labeled by a set of taxa ( Fig. 1; more details are provided in Model and SI Appendix). Reticulation events result in genomic regions with local genealogies that are incongruent with the speciation pattern. Several methods and heuristics use this incongruence as a signal for inferring reticulation events and reconstructing phylogenetic networks from local genealogies. These methods, which are surveyed elsewhere (2-4), assume that reticulation events are the sole cause of all incongruence among the gene trees and seek phylogenetic networks to explain all of the incongruence. A serious limitation of these methods is that they would grossly overestimate the amount of reticulation in a dataset when other causes of incongruence are at play. Indeed, several recent studies (5-9) have shown that detecting hybridization in practice can be complicated by the presence of incomplete lineage sorting (ILS) (Fig. 1).Recently, a set of methods was devised to analyze data where reticulation and ILS might both be simultaneously at play (10-15). However, these methods are all applicable to simple scenarios of species evolution and mostly assume a known hypothesis about the topol...

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Section: Modelmentioning

confidence: 99%

Section: Modelmentioning

confidence: 99%

mentioning

confidence: 99%

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Maximum likelihood inference of reticulate evolutionary histories

Yu¹,

Dong²,

Liu

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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260

389

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“…tritici and B.g. triticale are hybrids and four alternative models in which there is no hybridization or only one of the two formae speciales is a hybrid [15][16][17][18] . The model depicted in Figure 3 with two hybridizations seems to be the most likely (Supplementary Fig.…”

Section: Openmentioning

confidence: 99%

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

et al. 2016

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“…SWGE and ALF include complex evolutionary processes not simulated in TreeToReads, such as recombination across lineages and heterogeneity of the evolutionary model across the genome. While recombination and horizontal gene transfer (HGT) can be important processes, the expectations are challenging to parameterize, as even a few HGT events can lead to phylogenetic networks generating extremely complex ancestral recombination graphs [25]. In order to simulate shifts in relationships along chromosomes it is possible to independently input into TreeToReads different tree topologies for different genomic regions, and then combine the reads for these simulations and attempt inference.…”

Section: Resultsmentioning

confidence: 99%

TreeToReads - a pipeline for simulating raw reads from phylogenies

McTavish

Pettengill

Davis

et al. 2016

Preprint

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Background: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered. Results: To resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree. Conclusions: Such critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings.

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The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

Cited by 221 publications

References 55 publications

Maximum likelihood inference of reticulate evolutionary histories

Maximum likelihood inference of reticulate evolutionary histories

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

TreeToReads - a pipeline for simulating raw reads from phylogenies

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