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1. Inference of species phylogenies from bi-allelic markers using pseudo-likelihood

   https://doi.org/10.1093/bioinformatics/bty295  

   Zhu, Jiafan ; Nakhleh, Luay ( June 2018 , Bioinformatics)

   Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses data that consist of bi-allelic markers (e.g. single nucleotide polymorphism data) and allows for exact likelihood computations of phylogenetic networks while numerically integrating over all possible gene trees per marker. While the approach has good accuracy in terms of estimating the network and its parameters, likelihood computations remain a major computational bottleneck and limit the method’s applicability.

   In this article, we first demonstrate why likelihood computations of networks take orders of magnitude more time when compared to trees. We then propose an approach for inference of phylogenetic networks based on pseudo-likelihood using bi-allelic markers. We demonstrate the scalability and accuracy of phylogenetic network inference via pseudo-likelihood computations on simulated data. Furthermore, we demonstrate aspects of robustness of the method to violations in the underlying assumptions of the employed statistical model. Finally, we demonstrate the application of the method to biological data. The proposed method allows for analyzing larger datasets in terms of the numbers of taxa and reticulation events. While pseudo-likelihood had been proposed before for data consisting of gene trees, the work here uses sequence data directly, offering several advantages as we discuss.

   The methods have been implemented in PhyloNet (http://bioinfocs.rice.edu/phylonet).

    

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2. Assessing the fit of the multi-species network coalescent to multi-locus data

   https://doi.org/10.1093/bioinformatics/btaa863  

   Cai, Ruoyi ; Ané, Cécile ( December 2020 , Bioinformatics)

   Russell, Schwartz (Ed.)

   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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3. PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow

   https://doi.org/10.1093/sysbio/syad030  

   Fogg, John ; Allman, Elizabeth S. ; Ané, Cécile ; Thomson, ed., Robert C. ( May 2023 , Systematic Biology)

   We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at https://github.com/cecileane/PhyloCoalSimulations.jl.

    

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4. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

   https://doi.org/10.1002/ajb2.1469  

   Larson, Drew A. ; Walker, Joseph F. ; Vargas, Oscar M. ; Smith, Stephen A. ( April 2020 , American Journal of Botany)

   Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.

   We used a hierarchical clustering approach, with tree‐based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene‐wise edge‐based analyses, concatenation, and coalescent‐based methods, and is summarized in a consensus framework.

   Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole‐genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.

   We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

    

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5. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

   https://doi.org/10.1111/mec.13544  

   Wen, Dingqiao ; Yu, Yun ; Hahn, Matthew W. ; Nakhleh, Luay ( March 2016 , Molecular Ecology)

   The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaineet al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of theAnopheles gambiaespecies complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co‐occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree‐based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse theAnophelesdata using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to captureILSand introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

    

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