Inferring Phylogenetic Networks Using PhyloNet

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

doi:10.1093/sysbio/syy015

Cited by 274 publications

(216 citation statements)

References 38 publications

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“…The Δ test was significant using multiple different subsamples of four taxa, suggesting multiple ancestral introgression events. An initial attempt to disentangle these events using Phylonet v3.8.0 [97,98] with the seven Papionini species and an outgroup was unsuccessful, as Phylonet failed to converge on an optimal network for these taxa. When there are multiple episodes of gene flow within a clade, even complex computational machinery may be unable to infer the correct combination of events.…”

Section: Resultsmentioning

confidence: 99%

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Vanderpool

Minh

Lanfear

et al. 2020

Preprint

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Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

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Section: Resultsmentioning

confidence: 99%

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Vanderpool

Minh

Lanfear

et al. 2020

Preprint

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“…We utilized neighbor‐net (Bryant & Moulton, ) to visualize overall patterns of molecular genetic diversity. Likelihood‐based methods (Solís‐Lemus & Ané, ; Solís‐Lemus et al ., ; Wen et al ., ; Zhang et al ., ) that we have utilized on smaller oak datasets (Eaton et al ., ; Hauser et al ., ; McVay et al ., ,b; Crowl et al ., ) proved computationally intractable for the current dataset. Consequently, we utilized a splits network inferred with SplitsTree v.14.3 (Huson & Bryant, ) based on the maximum‐likelihood (GTR+γ) pairwise distance matrix estimated in RAxML and the same datasets utilized for the singletons tree.…”

Section: Methodsmentioning

confidence: 99%

Genomic landscape of the global oak phylogeny

et al. 2019

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The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

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“…We also computed RF tree distance, because it is widely applied in the evaluation of species phylogenies 75 . We used PhyloNET software 76 to count the number of partitions that were common and different between the true and the inferred phylogeny. The RF distance is the number of differing partitions divided by the total number of partitions in the two phylogenies.…”

Section: Multi-labeled Tree Edit Distance (Mlted)mentioning

confidence: 99%

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

Miura

Deng

et al. 2020

Sci Rep

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tumors harbor extensive genetic heterogeneity in the form of distinct clone genotypes that arise over time and across different tissues and regions in cancer. Many computational methods produce clone phylogenies from population bulk sequencing data collected from multiple tumor samples from a patient. These clone phylogenies are used to infer mutation order and clone origins during tumor progression, rendering the selection of the appropriate clonal deconvolution method critical. Surprisingly, absolute and relative accuracies of these methods in correctly inferring clone phylogenies are yet to consistently assessed. Therefore, we evaluated the performance of seven computational methods. The accuracy of the reconstructed mutation order and inferred clone groupings varied extensively among methods. All the tested methods showed limited ability to identify ancestral clone sequences present in tumor samples correctly. The presence of copy number alterations, the occurrence of multiple seeding events among tumor sites during metastatic tumor evolution, and extensive intermixture of cancer cells among tumors hindered the detection of clones and the inference of clone phylogenies for all methods tested. Overall, CloneFinder, MACHINA, and LICHeE showed the highest overall accuracy, but none of the methods performed well for all simulated datasets. So, we present guidelines for selecting methods for data analysis.www.nature.com/scientificreports www.nature.com/scientificreports/ ignoring SNV frequencies by using a heuristic algorithm based on co-comparability graphs 38 . It addresses the minimum conflict-free row split problem, where row is tumor genotypes, and observed tumor genotypes are split into clone genotypes. Ultimately, all of these methods deconvolute individual clones from population bulk sequencing of multiple tumor samples acquired over time and/or different locations in a patient.Surprisingly, absolute and relative accuracies of clone phylogenies produced by these computational methods have not been assessed using the same collection of datasets, i.e., their performances are yet to be benchmarked. Such benchmarking is critical because of the biological relevance of the downstream inferences derived by using the results produced by these methods. For example, the accuracies of the order of driver mutations and the interrelationship of clones depend on the performance of current methods in accurately deconvoluting individual clone genotypes and reconstructing evolutionary events 13,34,36 . Accurate clone phylogenies are also critical for inferring migration paths. No previous study has evaluated the relative accuracy of clone phylogenies, because their focus has been on introducing and assessing the strengths of the new clone prediction method proposed 13,34-39 . Besides, the robustness of these computational methods to the complexity of clonal structures and evolutionary histories from different tumor sites is mostly unknown.Therefore, we evaluated the accuracy of clone phylogenies produced by seven methods t...

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Inferring Phylogenetic Networks Using PhyloNet

Cited by 274 publications

References 38 publications

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Genomic landscape of the global oak phylogeny

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

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