Biology subjects

Allman, E. S.

Publications and source records attributed to Allman, E. S..

8 recordsLinked to original sources

bioRxiv2026

Consensus methods for trees of blobs and level-1 phylogenetic networks

Phylogenetic networks are increasingly used to represent evolutionary histories involving hybridization, introgression, and other reticulate processes that cannot be captured by a single tree. Recent advances have produced numerous methods for inferring networks from genomic data. These methods may produce multiple plausible networks due to optimality ties, bootstrap analyses, Bayesian posterior samples, or differences in tools, datasets, and parameters. While consensus methods are well established for trees and some approaches exist for rooted networks, no consensus framework currently exists for semi-directed (unrooted) networks. We address this gap by introducing a new consensus framework for phylogenetic networks, rooted or semi-directed. We first develop a method for constructing a consensus tree of blobs, taking as input networks of any complexity. Building on this approach, we construct a consensus for level-1 networks (i.e., networks with non-overlapping cycles). This method, called 'L1N consensus', takes a collection of level-1 networks as input and returns a level-1 network. The different components of this consensus network (e.g., blobs, hybrid clades, and edges) have support values that correspond to the frequency of the given component among the input networks. These methods are implemented in PhyloSummaries, building on the foundation of PhyloNetworks. We evaluate the performance of L1N consensus using large-scale simulated data. Our results demonstrate that L1N consensus outperforms existing methods in the rooted setting in terms of informativity and accuracy. Similar results are obtained in the semi-directed setting. Applying L1N consensus to Leopardus and HIV datasets confirms these findings and demonstrates the usefulness of the method.

bioinformatics↗

bioRxiv2026

Statistical inference of the Tree of Blobs of a phylogenetic network from quartet concordance factors

A phylogenetic network represents evolutionary relationships involving hybridization, gene flow, or admixture. While the full network may not be identifiable from genomic data under common coalescent models, its tree of blobs, depicting only the tree-like portions of the network structure, is. We introduce ECToBlob (Edge Contraction for Tree of Blobs), a new statistically-consistent algorithm to estimate the tree of blobs from quartet concordance factors. Starting from a resolved tree, ECToBlob successively contracts edges which statistical tests indicate do not belong in the tree of blobs, due to reticulate or polytomous signal. We show that ASTRAL provides a valid starting tree under common assumptions, in that, asymptotically in the number of loci, trees optimizing ASTRALs criterion refine the tree of blobs. We describe several algorithm variants, differing in how evidence from multiple tests are combined to determine if the edge should be contracted, and provide software implementations. Relevance to Life SciencesHybridization, gene flow, or admixture are now recognized as important aspects of evolutionary history, but their genomic signal is confounded with that from a coalescent process, creating substantial challenges for inferring phylogenetic networks. The networks tree of blobs identifies areas where reticulation occurred, separated by tree-like branching. ECToBlob quickly estimates the tree of blobs using quartet concordance factors from gene trees, and provides a measure of statistical support for its result. Performance is illustrated through simulation and on empirical data, using an implementation in the R package MSCquartets. While the presence of a blob may be all that can be inferred in some cases, in others ECToBlob offers a robust and principled way to focus further analyses on more local reticulate structure. Mathematical ContentThis work makes contributions to mathematical phylogenetics in optimization, combinatorics, and statistics. We show that any tree maximizing quartet support (the criterion underlying ASTRAL) is a refinement of the networks tree of blobs under the coalescent model. Second, we give a concise proof that whether a network has a cut-edge corresponding to a given split is determined by information in certain subcollections of its 4-taxon subnetworks (quarnets). Finally, we propose valid statistical approaches for combining p-values across multiple quarnet hypothesis tests, proving that their use with specific decreasing test levels leads to statistically consistent inference as the number of loci grows. MSC codes05C90, 60J95, 62-04, 62F07, 92D15

evolutionary biology↗

bioRxiv2024

NANUQ+: A divide-and-conquer approach to network estimation

Inference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of the Tree of Blobs of a network, showing only the networks cut edges, can be performed for any network by TINNiK, suggesting a divide-and-conquer approach to network inference where the trees multifurcations are individually resolved to give more detailed structure. Here we develop a method, NANUQ+, to quickly perform such a level-1 resolution. Viewed as part of the NANUQ pipeline for fast level-1 inference, this gives tools for both understanding when the level-1 assumption is likely to be met and for exploring all highly-supported resolutions to cycles.

evolutionary biology↗

bioRxiv2024

TINNiK: Inference of the Tree of Blobs of a Species Network Under the Coalescent

The tree of blobs of a species network shows only the tree-like aspects of relationships of taxa on a network, omitting information on network substructures where hybridization or other types of lateral transfer of genetic information occur. By isolating such regions of a network, inference of the tree of blobs can serve as a starting point for a more detailed investigation, or indicate the limit of what may be inferrable without additional assumptions. Building on our theoretical work on the identifiability of the tree of blobs from gene quartet distributions under the Network Multispecies Coalescent model, we develop an algorithm, TINNiK, for statistically consistent tree of blobs inference. We provide examples of its application to both simulated and empirical datasets, utilizing an implementation in the MSCquartets 2.0 R package. MSC Classification92D15, 92D20

evolutionary biology↗

bioRxiv2023

Anomalous networks under the multispecies coalescent: theory and prevalence

AO_SCPLOWBSTRACTC_SCPLOWReticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of 32-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods.

evolutionary biology↗

bioRxiv2023

PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow

AO_SCPLOWBSTRACTC_SCPLOWWe 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.

evolutionary biology↗

bioRxiv2020

MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

MSCquartets is an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package includes the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model.

bioinformatics↗

bioRxiv2020

Gene tree discord, simplex plots, and statistical tests under the coalescent

AO_SCPLOWBSTRACTC_SCPLOWA simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees appears to be in accord with the MSC, the plots may reveal when substantial incomplete lineage sorting is present and coalescent based species tree inference is preferred over concatenation approaches. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.

evolutionary biology↗