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What Phylogenetic Tree Reconstruction got wrong, from 38 theses
Summary written by a model from the records below: The records describe methodological failures and algorithmic trade-offs across various phylogenetic tree reconstruction workflows. Researchers encountered significant difficulties when handling reticulate evolution, sparse marker sets, heuristic distance approximations, and lineage rate heterogeneity. These records come from graduate theses, 2021 to 2026, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 10 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Strict bifurcating tree models fail when lineages undergo hybridization reticulation or horizontal transfer
Evolutionary histories with horizontal gene flow, introgression, manuscript contamination, or dialect blending violate the core assumption of hierarchical tree branching. In these settings, bifurcating reconstructions produce non-monophyletic groupings, obscure reticulate relationships, or fail to place hybrid lineages.
Tried and failed
tree-based cladistic phylogenetic classification applied to dialect continuum classification. Outcome: did not generalise. Reason: horizontal transmission and overlapping features violate strict hierarchical branching assumptions
Tracing Dehlavi: The Origins of the Hindi-Urdu Lingua Franca · Penn · PhD
Tried and failed
unadmixed phylogenetic tree modeling applied to admixed population placement. Reason: the lineage violates bifurcating tree assumptions due to being an admixed allelic sink
Establishing a Genetic System for Studying Cannabis Domestication · Harvard · PhD
Tried and failed
strictly bifurcating phylogenetic tree inference applied to hybridising and introgressing lineages. Outcome: no signal. Reason: reticulate evolution and extensive introgression violate strict tree-like branching assumptions
Phylogeny, biogeography, and hybridization in Baptisia (Fabaceae) : genomic insights into evolutionary dynamics and species boundaries · UT Austin · PhD
Tried and failed
phylogenetic stemmatology and genealogical classification applied to historical manuscript variant networks. Outcome: did not generalise. Reason: hybrid or contaminated textual variants prevented placement into standard tree-based lineages
Das Buch von geistlicher Armut: Überlieferung, Armutskonzept, Rezeption · Harvard · PhD
Tried and failed
bifurcating tree phylogenetic reconstruction applied to lineages with rampant horizontal gene flow. Outcome: no signal. Reason: widespread introgression breaks the fundamental assumption of a strictly branching evolutionary history
Applications of Coalescent Theory to Introgression Inference and Analysis of Genomic Studies of Sex and Sexuality · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected standard haplotypic ancestral state reconstruction on bifurcating trees due to pervasive historical gene flow and incomplete lineage sorting.
The genomic basis of repeated adaptation in deer mice · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected standard bifurcating phylogenetic trees alone, adopting phylogenetic network analyses (SplitsTree Neighbor-Net) due to reticulate relationships and subgenome exchanges
Genotypes to Phenotypes: Genomic attributes that impact Genome-wide Associations in peanut (Arachis hypogaea. L). · Iowa State · PhD
Considered and rejected
Considered and rejected: Rejected dendrogram-based phylogenetic tree methods (e.g., ViPTree, GRAViTy) for classifying prophages because they flatten evolutionary relationships into a single hierarchy and cannot represent horizontal gene transfer and genome mosaicism.
Anti-phage defense as a driver of molecular innovation · MIT · PhD
Tried and failed
single-gene marker phylogenetic classification applied to bacterial strain taxonomic identification. Outcome: did not generalise. Reason: horizontal gene transfer and recombination caused single-marker phylogeny to produce non-monophyletic groups
Bacterial Plant Pathogen Identification using Genomics and Metagenomics · Virginia Tech · Doctorate
Tried and failed
strict phylogenetic cladistic tree modeling applied to dialect evolution with lateral transfer. Outcome: did not generalise. Reason: Strict hierarchical trees cannot capture lateral transfer, reticulation, or horizontal contact dynamics.
A Diachronic Analysis of Western Armenian Verbal Morphology · Penn · PhD
Isolated character partitions and single gene markers lack adequate phylogenetic resolution
Individual loci, isolated anatomical partitions, and short marker fragments often lack sufficient informative signal to resolve deeper lineages or distinct subfamilies. Relying on these restricted subsets leads to collapsed consensus trees, low nodal support, and homoplasy-driven misplacements that are resolved by whole genomes or transcriptomes.
Tried and failed
single-locus phylogenetic tree reconstruction applied to species tree inference in amphibians. Outcome: no signal. Reason: insufficient phylogenetic resolution leading to discordance and low posterior support
Adaptation during range expansion: a phylogenetic, population genetic, and physiological perspective · Cornell · PhD
Considered and rejected
Considered and rejected: Rejected individual nuclear gene trees as standalone phylogenetic markers due to polytomies and weak nodal support.
Exome analyses and species delimitations of the Heteromys pictus-spectabilis species complex · Texas Tech · PhD
Tried and failed
phylogenetic reconstruction using internal coding sequences applied to endogenous retrovirus subfamily classification. Outcome: no signal. Reason: coding sequences provided insufficient granularity to resolve subfamilies compared to non-coding terminal repeats
RECOMBINATION-MEDIATED REGULATORY EVOLUTION OF HUMAN ENDOGENOUS RETROVIRUS HERVH · Cornell · PhD
Tried and failed
phylogenetic inference from single anatomical partition applied to morphological evolutionary tree reconstruction. Outcome: worse than baseline. Reason: isolated postcranial characters lacked sufficient phylogenetic signal and introduced severe homoplasy-driven misplacements
Effects of Additional Postcranial Data on the Topologies of Early Eocene Primate Phylogenies · UT Austin
Tried and failed
concatenating top marker genes for phylogenetic distance applied to microbial eukaryotic genome taxonomic classification. Reason: diminishing returns with plateauing resolution unable to match whole-genome sequence resolution
Expanding The Bioinformatics Toolbox for Diversity and Taxonomic Studies of Microbial Eukaryotic Pathogens · Georgia Tech · PhD
Considered and rejected
Considered and rejected: Rejected using mitochondrial genomes for deep heterobranch phylogenetic nodes because they perform poorly compared to transcriptomic datasets.
Considered and rejected
Considered and rejected: Rejected classifying higher bacterial ranks and lineage divergences using 16S rRNA gene fragments alone due to insufficient phylogenetic resolution and primer bias, opting instead for genome-wide relative evolutionary divergence (RED).
Tried and failed
phylogenetic classification using single isolated morphological markers applied to dialect subgrouping and classification. Reason: progressive aspect markers were conflated with indicative markers, leading to erroneous lineage groupings
A Diachronic Analysis of Western Armenian Verbal Morphology · Penn · PhD
Distance sketching heuristics and embedding approximations distort tree topology and relationships
Approximate distance metrics from k-mer sketching, MinHash sketches, and hyperbolic embeddings generate inconsistent distances that misplace parent-child relationships and distort hierarchical topologies. These heuristic approximations frequently underperform exact sequence alignments or reference-constrained placement methods when reconstructing phylogenetic trees.
Tried and failed
averaging latent feature vectors for consensus structure applied to phylogenetic species tree construction. Reason: mean latent feature vector did not correspond to a valid representative tree structure
Scalable and extensible data Structures and methods for big data in phylogenomics and phylogenetics · Iowa State · PhD
Tried and failed
approximate sequence distance via k-mer sketching applied to phylogenetic graph edge construction. Outcome: worse than baseline. Reason: Inconsistent distance estimations produced incorrect parent-child relationships compared to exact edit distance
Graph-Based Computational Approaches for Modeling Viral Evolution · Virginia Tech · Doctorate
Lost to a baseline
hydraPlus beat BHMDS on phylogenetic tree distortion (0.1206 vs 0.1214).
Estimation and Inference for Network Data · University of Washington · PhD
Lost to a baseline
Simpler systems like LDN (GQD 0.0458) and CCM (0.0854) outperformed the more complex SVM (0.0989) on Austronesian phylogenetic tree reconstruction.
Algorithmic advancements in Computational Historical Linguistics · Tübingen · PhD
Tried and failed
MinHash sketching distance estimation applied to closely related fungal phylogenetic reconstruction. Outcome: worse than baseline. Reason: Default sketch size caused excessive intra-clade variation and misplaced phylogenetic topology compared to alignment methods
Computational Genomics to Characterize the Distribution, Diversity and Drug Resistance of Fungal Pathogens · Georgia Tech · PhD
Tried and failed
unsupervised metric learning for tree reconstruction applied to single-cell phenotypic lineage reconstruction. Outcome: did not generalise. Reason: simulated data properties did not translate to complex biological noise in real single-cell datasets
Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning · Penn · PhD
Aggressive taxon pruning and strict matrix filtering destabilize consensus topologies
Filtering out suspected homoplasy, missing data, or rare features reduces informative character counts and degrades branch support across trees. Similarly, pruning unstable taxa or low-frequency features can collapse internal clades and reduce overall tree resolution rather than improving consensus stability.
Tried and failed
maximum parsimony phylogenetic consensus analysis applied to morphological character matrix with missing data. Outcome: unstable. Reason: fragmentary and unstable rogue taxa collapsed resolution across all internal clades in the consensus tree
A NEW PHYLOGENETIC ANALYSIS AND CHARACTER MATRIX REASSESSMENT FOR THE COELACANTHS (SARCOPTERYGII: COELACANTHIFORMES) · Cornell · PhD
Tried and failed
aggressive taxon pruning to resolve consensus polytomies applied to morphological maximum parsimony phylogenetic analysis. Outcome: unstable. Reason: removes highly complete, informative taxa and causes severe tree consensus instability
A NEW PHYLOGENETIC ANALYSIS AND CHARACTER MATRIX REASSESSMENT FOR THE COELACANTHS (SARCOPTERYGII: COELACANTHIFORMES) · Cornell · PhD
Tried and failed
maximum parsimony phylogenetic reconstruction across morphological partitions applied to fossil primate morphological dataset. Outcome: worse than baseline. Reason: produced a less resolved consensus tree and misclassified target taxon compared to baseline PAUP implementation
Effects of Additional Postcranial Data on the Topologies of Early Eocene Primate Phylogenies · UT Austin
Tried and failed
filtering noisy features prior to parsimony inference applied to phylogenetic matrix resolution across diverse taxa. Outcome: data insufficient. Reason: removing suspected homoplastic characters severely reduced information content, preventing relationship resolution among taxa
A NEW PHYLOGENETIC ANALYSIS AND CHARACTER MATRIX REASSESSMENT FOR THE COELACANTHS (SARCOPTERYGII: COELACANTHIFORMES) · Cornell · PhD
Tried and failed
strict missing data filtering of loci applied to phylogenetic alignment matrix. Outcome: worse than baseline. Reason: filtering reduced total informative sites, decreasing branch support and creating topological conflict
The evolutionary history and diversity of the Mickey Mouse Plants (the genus Ochna) · Imperial · PhD
Fast approximate methods and parsimony produce inferior likelihoods or unstable taxon placements
Fast heuristic tree builders like FastTree2 yielded substantially poorer likelihood scores than rigorous maximum likelihood and Bayesian frameworks. Furthermore, parsimony and unconstrained heuristic placements resulted in unstable positioning of divergent taxa and biased trees compared to fully probabilistic models.
Considered and rejected
Considered and rejected: FastTree2 was rejected for comprehensive phylogenetic inference and cross-comparisons because its likelihood scores were substantially worse than IQ-TREE 2, RAxML, and MrBayes.
Discovery and characterization of diverse microbial RNA-guided systems · MIT · PhD
Considered and rejected
Considered and rejected: Rejected FastTree2 for comprehensive phylogenetic cross-comparisons due to substantially worse likelihood scores than IQ-TREE 2, RAxML, or MrBayes.
Data Driven Discovery of Modular Biological Systems · MIT · PhD
Considered and rejected
Considered and rejected: Excluded Poxviridae from definitive replisome/transcription phylogenies due to unstable phylogenetic placement across diagnostic trees
Comparative and Evolutionary genomics of Nucleocytoviricota · Virginia Tech · Doctorate
Considered and rejected
Considered and rejected: Rejected parsimony in favor of maximum likelihood for phylogenetic reconstruction because ML provides a probabilistic model rather than minimal change steps.
Quantitatively Investigating the Genetic Response of the Euryhaline Sailfin Molly (Poecilia latipinna) to Manipulations of Environmental and Dietary Magnesium · York University · Master's
Considered and rejected
Considered and rejected: Single-reference mapping and SNP extraction for ancient microbial phylogeny was rejected due to substantial phylogenetic reconstruction bias and unreliability.
Evolutionary analysis of the human microbiome using ancient metagenomic samples · University of Trento · PhD
Outgroup rooting and molecular clocks degrade under long branch attraction and rate heterogeneity
Divergent outgroups and long branches cause long-branch attraction artifacts, misplacing root positions across gene trees and bacterial lineages. In addition, relaxed molecular clocks fail when rate variation across lineages becomes excessively high, and heuristic divergence dating struggles on short branches.
Tried and failed
outgroup rooting for phylogenetic tree reconstruction applied to divergent homologous gene families. Reason: long-branch attraction artifacts caused inconsistent and unresolved root placements across gene trees
Global distribution and ancient evolution of far-red photosynthesis · Imperial · PhD
Tried and failed
outgroup rooting with distant lineages applied to bacterial phylogenetic tree inference. Outcome: unstable. Reason: recombination events on long branches distorted phylogenetic signals and root placement
Genomic insights into the host range and interspecies transmission dynamics of Staphylococcus aureus · Cambridge · PhD
Tried and failed
RelTime heuristic divergence dating applied to phylogenetic tree with short branches. Outcome: worse than baseline. Reason: produced broader confidence intervals and divergent node ages, struggling on short branches compared to Bayesian methods
The evolution of anthraquinones as an adaptive trait in lichen-forming fungi · Imperial · PhD
Considered and rejected
Considered and rejected: Rejected minimal ancestor deviation (MAD) and midpoint rooting for the global MMP tree because wide differences in branch lengths between metazoan and prokaryotic lineages systematically biased roots toward prokaryotes
Bridging the gap between microbial and metazoan evolutionary history · MIT · PhD
Tried and failed
relaxed lognormal molecular clock Bayesian phylogenetic inference applied to global viral genetic sequences. Reason: mutation rate standard deviation was too high (>1), indicating excessive rate heterogeneity across lineages
GENES IN SPACE! AN EXPLORATION OF POPULATION GENETICS AND STRUCTURE AT MULTIPLE SPATIAL SCALES · Cornell · PhD
Network models and comparative trait analyses become intractable or biased under lineage discordance
Fitting trait evolution models or network methods across reticulating clades becomes mathematically intractable when multiple introgression events create shared edges between hybrid nodes. Under incomplete lineage sorting and gene tree discordance, network trait models also produce severely biased evolutionary rate estimates compared to simpler baseline trees.
Tried and failed
Species-level trait evolution models applied to phylogenetic networks with incomplete lineage sorting. Reason: High effective population size caused severe overestimation of evolutionary rate when traits evolved along discordant gene trees.
Modeling the diverse suite of gene flow processes on phylogenetic networks and its implications for macroevolutionary patterns · Iowa State · PhD
Lost to a baseline
Major displayed tree model produced less biased evolutionary rate sigma^2 estimates than lineage-sorting models on H1 and H2 networks when traits were simulated under the network model.
Modeling the diverse suite of gene flow processes on phylogenetic networks and its implications for macroevolutionary patterns · Iowa State · PhD
Considered and rejected
Considered and rejected: Decided against fitting Pagel's lambda and Ornstein-Uhlenbeck models for the 61-species bird phylogenetic analysis due to poor performance/failure on trees under 200 species.
The Evolutionary Ecology of Flash Displays and Other Transiently Visible Anti-predation Signals · Carleton University · PhD
Considered and rejected
Considered and rejected: Rejected phylogenetic network analysis methods (e.g., Solís-Lemus et al. 2016) because multiple introgression events caused shared edges between hybrid nodes, making network models mathematically intractable.
Introgression, Population Structure, and Systematics of the Sphagnum capillifolium complex · Duke · PhD
Left open by the authors
Problems the authors named and did not get to.
Left open
Evaluate MSA Transformer representations against phylogenetic trees and patristic distances rather than simple Hamming distances across protein sequences. Blocker: None
Revealing and exploiting coevolution through protein language models · EPFL · PhD
Left open
Investigate phylogenetic relationships among Ambystoma species to clarify morphological evolution patterns. Blocker: Lacks specific target dataset, genetic/morphological markers, or concrete phylogenetic methodology
Changes in central Texas herpetofauna during the late Quaternary : an examination of lizards and salamanders from Hall’s Cave · UT Austin · PhD
Left open
Perform a comprehensive co-evolutionary analysis of host-parasite phylogenies across all bee host families using resolved host trees. Blocker: Detailed host phylogenetic trees across all bee host families were not yet available
THE EVOLUTION OF BROOD PARASITISM IN BEES AND OTHER ANIMALS · Cornell · PhD
Left open
Develop cytonuclear coevolution detection methods that account for incomplete lineage sorting, hybridization, and gene duplication in phylogenomics. Blocker: No concrete mathematical or algorithmic formulation specified for incorporating ILS/hybridization into ERC frameworks
Cytonuclear coevolution investigations in papilionoid legumes and medicago (fabaceae) · UT Austin · PhD
Left open
Gather phylogenetic and evolutionary evidence on the original selective pressures and timeline of pain origination. Blocker: Task is an open-ended biological/evolutionary research direction lacking concrete methodology or clear data scope
Foundations of pain · UT Austin · PhD
Left open
Compare phylogenetic or fossil occurrence patterns with reconstructed river capture landscapes to empirically test geomorphic controls on speciation rates. Blocker: Lacks specific target taxa, geographic locations, and concrete datasets to compare against landscape models.
Dynamic river networks drive landscape change and biological evolution · MIT · PhD
Left open
Cluster bacterial host source classes using phylogenetic trees to reduce classification output space complexity. Blocker: None
Applications of Machine Learning in Source Attribution and Gene Function Prediction · Virginia Tech · Master's
Left open
Develop robust machine learning algorithms for graphical models such as Ising models or phylogenetic trees with malicious nodes. Blocker: Task is framed as a broad research direction without specific algorithms, performance targets, or detailed formulations
Statistical Inference in the Differential Privacy Model · Cornell · PhD
Left open
Extend the PhyNE MCMC framework to jointly estimate niche model parameters and phylogenetic tree topology and branch lengths. Blocker: None
Phylogenetic Niche Modeling · Virginia Tech · Master's
Left open
Implement hierarchical or multi-scale flow matching architectures in PhylaFlow to scale phylogenetic tree inference to datasets beyond 50 leaves. Blocker: None
Foundation Model Guided Flow Matching on Tree Manifold for Differentiable Phylogenetics · Harvard · Master's
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Ethan France · Cornell · PhD · 2023
A NEW PHYLOGENETIC ANALYSIS AND CHARACTER MATRIX REASSESSMENT FOR THE COELACANTHS (SARCOPTERYGII: COELACANTHIFORMES) - George Balabanian · Penn · PhD · 2024
A Diachronic Analysis of Western Armenian Verbal Morphology - Joshua Alexander Justison · Iowa State · PhD · 2024
Modeling the diverse suite of gene flow processes on phylogenetic networks and its implications for macroevolutionary patterns - Jiabo Cui · Harvard · Master's · 2026
Foundation Model Guided Flow Matching on Tree Manifold for Differentiable Phylogenetics - Joanna R. Bateman · Texas Tech · PhD · 2026
Exome analyses and species delimitations of the Heteromys pictus-spectabilis species complex - Badhan Das · Virginia Tech · Doctorate · 2026
Graph-Based Computational Approaches for Modeling Viral Evolution - CHRISTOPHER J GRASSA · Harvard · PhD · 2025
Establishing a Genetic System for Studying Cannabis Domestication - Christopher Ross Doering · MIT · PhD · 2025
Anti-phage defense as a driver of molecular innovation - Undine Sophie Mies · University of Marburg · PhD · 2025
Phylogeny and metabolism ofEndomicrobiaceae and ElusimicrobiaceaeExploring reductive genome evolution in two hostassociated lineages of Elusimicrobiota Phylogenie und Stoffwechsel von Endomicrobiaceae - Da Kuang · Penn · PhD · 2025
Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning - Damiano Sgarbossa · EPFL · PhD · 2025
Revealing and exploiting coevolution through protein language models - Jonas Max Hermann · Harvard · PhD · 2024
Das Buch von geistlicher Armut: Überlieferung, Armutskonzept, Rezeption
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