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

Rhodes, J. A.; Allman, E. S.; Ane, C.; Banos, H.

doi:10.64898/2026.05.28.728501

Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.05.28.728501

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

Rhodes, J. A.·Allman, E. S.·Ane, C.·Banos, H.

View original source ↗Export metadata ↓

Abstract

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

Explore related subjects

evolutionary biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Rhodes, J. A., Allman, E. S., Ane, C., Banos, H.. 2026-05-31. Statistical inference of the Tree of Blobs of a phylogenetic network from quartet concordance factors. https://doi.org/10.64898/2026.05.28.728501

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ocean current models predict spatial structure for coastal biodiversity

Genomic diversity provides the raw material through which all evolutionary processes occur. Accurately describing how environmental features affect patterns of diversity shows promise in predicting the resilience of populations and entire communities to dynamic environments and novel stressors. Identifying the contribution of purely neutral responses to environmental effects can be difficult, especially across large spatial ranges with many covarying environmental features. Using an individual-based model of larvae carried by ocean currents, we predict patterns of neutral genomic diversity in a passively dispersed coastal species, suggesting large geographic regions of relative homogeneity with ancestry determined by the nearest "upstream" population with limited larval input. The genomic identity that dominates each region sharply transitions at the next such interruption, generating hierarchical structure and violating assumptions of isolation-by-distance. We call these upstream populations "lineage source regions" (LSRs), and we find strong concordance between LSR model predictions and an empirical population genomic survey of a keystone salt marsh mussel (Geukensia demissa). We quantitatively validate model performance and goodness-of-fit, updating baseline predictions of genomic diversity patterns from the classic isolation-by-distance model to this LSR framework. This spatially explicit coastal ancestry model has potential for generalization across passive dispersing species.

evolutionary biology↗

bioRxiv2026

TaxaAudit: A statistical model of consensus in phylogenetics identifies non-monophyletic taxa

Interpreting variation in genes and traits across species requires understanding their evolutionary relationships. Taxonomic hierarchies provide a practical approximation of the tree of life, with the NCBI taxonomy linking this framework directly to public sequence data. Some named groups, however, are not evolutionary clades, and recognizing these exceptions requires knowledge scattered across the phylogenetics literature. Here we introduce TaxaAudit, a statistical model that identifies taxonomic groups whose monophyly is repeatedly contradicted by published phylogenies. The model accounts for background taxonomic conflict and the ability of each study's species sampling to expose non-monophyly. Applied to 5,865 molecular phylogenies from TimeTree, TaxaAudit flagged 516 NCBI taxa at family rank and below for significant recurrent contradiction of monophyly. Excluding these taxa's monophyly requirements improved the taxonomy's agreement with independent phylogenomic reference trees and phylogenies withheld from discovery. Flagged taxa were also 3.61 times as likely as matched controls to have their monophyly challenged in publications outside the discovery set. In tree-inference experiments, excluding these monophyly constraints improved agreement with reference phylogenies relative to enforcing the unmodified taxonomy. By identifying groups whose monophyly should not be assumed, TaxaAudit lets researchers draw on published phylogenetic knowledge without reviewing the specialist literature for every taxon. This supports broader use of the NCBI taxonomy as an evolutionary framework for biological comparisons.

evolutionary biology↗

bioRxiv2026

Shared landscape, divergent genomes: Comparative population genomics of co-occurring flora in an isolated Australian mountain range

Understanding how landscape heterogeneity shapes genomic variation is key to conserving biodiversity and evolutionary potential. Yet conservation genomics is typically conducted at the single species level, limiting our ability to identify shared genomic patterns or understand how co-occurring taxa differ in their response to common environmental gradients. We assessed spatial patterns of genomic variation and their associations with geographic and environmental features among populations of nine co-existing plant species with contrasting life-histories and ecological traits across Gariwerd, a threatened biodiversity hotspot in south-eastern Australia. All species exhibited weak overall genetic structure, although the magnitude and spatial distribution of differentiation varied among species. Despite this variation, broadly consistent spatial trends were apparent, with higher genomic divergence largely concentrated in central zones and higher genomic diversity localised in southern regions of the landscape. Significant associations between genetic differentiation and geographic distance were observed in three species, while another species showed associations with environmental distance. These findings demonstrate that coexisting species can show overlapping spatial patterns in genomic variation while differing markedly in their associations with geographic and environmental variation across the same landscape. This comparative approach provides a basis for spatial prioritisation and conservation planning, while highlighting the complex eco-evolutionary processes operating across heterogeneous landscapes.

evolutionary biology↗