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To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471650129.dob0522openalex-snapshot
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1007/s00285-010-0355-7openalex-snapshot
Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.jbi.2005.04.001openalex-snapshot
Missing data and the design of phylogenetic analyses
inferredcites →https://doi.org/10.1016/j.jtbi.2008.09.031openalex-snapshot
Sequence length bounds for resolving a deep phylogenetic divergence
inferredcites →https://doi.org/10.1016/j.jtbi.2015.03.006openalex-snapshot
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
inferredcites →https://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1016/j.ympev.2011.06.021openalex-snapshot
Quartet MaxCut: A fast algorithm for amalgamating quartet trees
inferredcites →https://doi.org/10.1016/j.ympev.2013.06.004openalex-snapshot
Effects of missing data on species tree estimation under the coalescent
inferredcites →https://doi.org/10.1016/j.ympev.2013.09.006openalex-snapshot
How low can you go? The effects of mutation rate on the accuracy of species-tree estimation
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.006openalex-snapshot
Should genes with missing data be excluded from phylogenetic analyses?
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.021openalex-snapshot
A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.023openalex-snapshot
Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)
inferredcites →https://doi.org/10.1016/j.ympev.2014.10.022openalex-snapshot
Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies
inferredcites →https://doi.org/10.1016/j.ympev.2015.06.009openalex-snapshot
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
inferredcites →https://doi.org/10.1016/j.ympev.2015.12.013openalex-snapshot
The effects of subsampling gene trees on coalescent methods applied to ancient divergences
inferredcites →https://doi.org/10.1016/j.ympev.2016.04.015openalex-snapshot
Phylogenomic analyses reveal novel relationships among snake families
inferredcites →https://doi.org/10.1016/j.ympev.2016.09.001openalex-snapshot
Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity
inferredcites →https://doi.org/10.1016/j.ympev.2017.02.017openalex-snapshot
New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset
inferredcites →https://doi.org/10.1016/j.ympev.2017.05.002openalex-snapshot
Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
inferredcites →https://doi.org/10.1016/s0022-5193(85)80291-5openalex-snapshot
Cross-species gene transfer; implications for a new theory of evolution
inferredcites →https://doi.org/10.1038/nature12130openalex-snapshot
Inferring ancient divergences requires genes with strong phylogenetic signals
inferredcites →https://doi.org/10.1038/srep22262openalex-snapshot
Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches
inferredcites →https://doi.org/10.1073/pnas.0607004104openalex-snapshot
High-resolution species trees without concatenation
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1089/cmb.2011.0231openalex-snapshot
iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees
inferredcites →https://doi.org/10.1089/cmb.2012.0234openalex-snapshot
Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btn484openalex-snapshot
BEST: Bayesian estimation of species trees under the coalescent model
inferredcites →https://doi.org/10.1093/bioinformatics/btp079openalex-snapshot
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btt394openalex-snapshot
Naive binning improves phylogenomic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btv184openalex-snapshot
ExaML version 3: a tool for phylogenomic analyses on supercomputers
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/gbe/evv026openalex-snapshot
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
inferredcites →https://doi.org/10.1093/genetics/122.4.957openalex-snapshot
Gene genealogy in three related populations: consistency probability between gene and population trees.
inferredcites →https://doi.org/10.1093/genetics/122.4.967openalex-snapshot
Inference from clines stabilized by frequency-dependent selection.
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
inferredcites →https://doi.org/10.1093/molbev/msp250openalex-snapshot
Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/mss086openalex-snapshot
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
inferredcites →https://doi.org/10.1093/molbev/mss208openalex-snapshot
Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
inferredcites →https://doi.org/10.1093/molbev/msu061openalex-snapshot
Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
inferredcites →https://doi.org/10.1093/molbev/msv266openalex-snapshot
The Impact of Missing Data on Species Tree Estimation
inferredcites →https://doi.org/10.1093/molbev/msv347openalex-snapshot
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
inferredcites →https://doi.org/10.1093/molbev/msw079openalex-snapshot
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
inferredcites →https://doi.org/10.1093/molbev/msx126openalex-snapshot
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
inferredcites →https://doi.org/10.1093/oso/9780198566106.001.0001openalex-snapshot
Mathematics of Evolution and Phylogeny
inferredcites →https://doi.org/10.1093/oso/9780198566106.003.0004openalex-snapshot
Statistical Approach to Tests Involving Phylogenies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot
Relationships between gene trees and species trees.
inferredcites →https://doi.org/10.1093/sysbio/syp016openalex-snapshot
Bootstrap Support Is Not First-Order Correct
inferredcites →https://doi.org/10.1093/sysbio/syp017openalex-snapshot
The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
inferredcites →https://doi.org/10.1093/sysbio/syp045openalex-snapshot
Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design
inferredcites →https://doi.org/10.1093/sysbio/syq047openalex-snapshot
Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods
inferredcites →https://doi.org/10.1093/sysbio/syq073openalex-snapshot
The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
inferredcites →https://doi.org/10.1093/sysbio/syq097openalex-snapshot
Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syr025openalex-snapshot
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syr041openalex-snapshot
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
inferredcites →https://doi.org/10.1093/sysbio/syr079openalex-snapshot
Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
inferredcites →https://doi.org/10.1093/sysbio/sys033openalex-snapshot
The Probability of Correctly Resolving a Split as an Experimental Design Criterion in Phylogenetics
inferredcites →https://doi.org/10.1093/sysbio/sys036openalex-snapshot
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syt059openalex-snapshot
Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syt073openalex-snapshot
Conserved Genes, Sampling Error, and Phylogenomic Inference
inferredcites →https://doi.org/10.1093/sysbio/syu046openalex-snapshot
Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferredcites →https://doi.org/10.1093/sysbio/syv058openalex-snapshot
How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syv082openalex-snapshot
SimPhy : Phylogenomic Simulation of Gene, Locus, and Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syw001openalex-snapshot
Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
inferredcites →https://doi.org/10.1093/sysbio/syw014openalex-snapshot
Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods
inferredcites →https://doi.org/10.1093/sysbio/syw027openalex-snapshot
Phylogenomics for Systematic Biology
inferredcites →https://doi.org/10.1093/sysbio/syw030openalex-snapshot
Inconsistency of Species Tree Methods under Gene Flow
inferredcites →https://doi.org/10.1093/sysbio/syw089openalex-snapshot
Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards
inferredcites →https://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
Genome-scale coestimation of species and gene trees
inferredcites →https://doi.org/10.1109/tcbb.2014.2361685openalex-snapshot
Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method
inferredcites →https://doi.org/10.1109/tcbb.2017.2757930openalex-snapshot
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?
inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00420.xopenalex-snapshot
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1111/jse.12160openalex-snapshot
Coalescent methods for estimating species trees from phylogenomic data
inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferredcites →https://doi.org/10.1111/syen.12132openalex-snapshot
The beetle tree of life reveals that C oleoptera survived end‐ P ermian mass extinction to diversify during the C retaceous terrestrial revolution
inferredcites →https://doi.org/10.1126/science.1102036openalex-snapshot
Prospects for Building the Tree of Life from Large Sequence Databases
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1137/s089548010138790xopenalex-snapshot
Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications
inferredcites →https://doi.org/10.1186/1471-2148-10-216openalex-snapshot
Ontogenetic convergence and evolution of foot morphology in European cave salamanders (Family: Plethodontidae)
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2164-15-s1-s11openalex-snapshot
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s11openalex-snapshot
BBCA: Improving the scalability of *BEAST using random binning
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s7openalex-snapshot
Disk covering methods improve phylogenomic analyses
inferredcites →https://doi.org/10.1186/1471-2164-15-s9-s7openalex-snapshot
HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome
inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s1openalex-snapshot
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s2openalex-snapshot
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s3openalex-snapshot
ASTRID: Accurate Species TRees from Internode Distances
inferredcites →https://doi.org/10.1186/1471-2164-16-s6-s2openalex-snapshot
FunPat: function-based pattern analysis on RNA-seq time series data
inferredcites →https://doi.org/10.1186/s12862-014-0169-0openalex-snapshot
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
inferredcites →https://doi.org/10.1214/ss/1063994979openalex-snapshot
Bootstrapping Phylogenetic Trees: Theory and Methods
inferredcites →https://doi.org/10.1371/journal.pcbi.1005932openalex-snapshot
Bayesian inference of phylogenetic networks from bi-allelic genetic markers
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pgen.1005896openalex-snapshot
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pgen.1006006openalex-snapshot
Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0104008openalex-snapshot
Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach
inferredcites →https://doi.org/10.1371/journal.pone.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.4172/2329-9002.1000110openalex-snapshot
Error in Phylogenetic Estimation for Bushes in the Tree of Life
inferredcites →https://doi.org/10.48550/arxiv.1707.04300openalex-snapshot
Coalescent-based species tree estimation: a stochastic Farris transform
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
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Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily
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Towards a species‐level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies
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Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set
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Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants
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Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae)
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Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms ( Ephedra , Gnetales)
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Resolving taxonomic uncertainty and exploring evolutionary relationships in the Cymopterus terebinthinus (Apiaceae) species complex
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Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies
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NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees
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New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation
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Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
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Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model
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Afro-alpine flagships revisited II: elucidating the evolutionary relationships and species boundaries in the giant senecios (Dendrosenecio, Asteraceae)
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Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life
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Volcanic events coincide with plant dispersal across the Northern Andes
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Diversification of Camphorosmeae (Amaranthaceae s.l.) during the Miocene-Pliocene aridification of inland Australia
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New Approaches for Inferring Phylogenies in the Presence of Paralogs
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Inconsistency of parsimony under the multispecies coalescent
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SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko
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Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
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Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
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Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences
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Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)
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Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness
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Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses
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A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107327openalex-snapshot
Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107339openalex-snapshot
Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107342openalex-snapshot
How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107375openalex-snapshot
Phylogenomic analyses of mud dragons (Kinorhyncha)
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107396openalex-snapshot
SNP-based phylogenomic inference in Holarctic ground squirrels (Urocitellus)
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107432openalex-snapshot
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107545openalex-snapshot
A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107550openalex-snapshot
Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107581openalex-snapshot
Out of chaos: Phylogenomics of Asian Sonerileae
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107801openalex-snapshot
Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107864openalex-snapshot
Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107924openalex-snapshot
Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107965openalex-snapshot
Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108064openalex-snapshot
Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108207openalex-snapshot
A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108212openalex-snapshot
Imperiled wanderlust lichens in steppe habitats of western North America comprise geographically structured mycobiont lineages and a reversal to sexual reproduction within this asexual clade
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108326openalex-snapshot
Phylogeny, species delimitation, and biogeographical history of Bredia
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108338openalex-snapshot
Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes – with particular focus on Hymenocoleus Robbr.
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108339openalex-snapshot
Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108457openalex-snapshot
A single widespread species or multiple narrow endemics: a search for boundaries within the Piper amalago complex (Piperaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108648openalex-snapshot
Deciphering reticulation and reproductive trait evolution in a chasmophyte lineage: a phylogenomic approach to the evolutionary patterns within Petrocoptis
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108687openalex-snapshot
Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)
inferred← citeshttps://doi.org/10.1038/s41467-021-25681-6openalex-snapshot
Incipient diploidization of the medicinal plant Perilla within 10,000 years
inferred← citeshttps://doi.org/10.1038/s41576-023-00620-xopenalex-snapshot
Incongruence in the phylogenomics era
inferred← citeshttps://doi.org/10.1038/s41586-019-1693-2openalex-snapshot
One thousand plant transcriptomes and the phylogenomics of green plants
inferred← citeshttps://doi.org/10.1038/s41598-025-16399-2openalex-snapshot
Identifying sets of phylogenetically informative markers for Anastrepha (Diptera: Tephritidae)
inferred← citeshttps://doi.org/10.1071/sb24011openalex-snapshot
Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data
inferred← citeshttps://doi.org/10.1088/1755-1315/1192/1/012004openalex-snapshot
Early growth and genetic performance of Gelam (Melaleuca cajuputi subsp cumingiana) conservation plot: an endemic peatland species in South Sumatera
inferred← citeshttps://doi.org/10.1089/cmb.2020.0424openalex-snapshot
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
inferred← citeshttps://doi.org/10.1089/cmb.2021.0543openalex-snapshot
Scalable Species Tree Inference with External Constraints
inferred← citeshttps://doi.org/10.1089/cmb.2023.0185openalex-snapshot
QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent
inferred← citeshttps://doi.org/10.1093/aob/mcac046openalex-snapshot
Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation
inferred← citeshttps://doi.org/10.1093/aob/mcaf004openalex-snapshot
A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification
inferred← citeshttps://doi.org/10.1093/aob/mcaf289openalex-snapshot
Resolving the tribal affiliation of the East Asia clade: phylogenomic evidence for its inclusion into Komarovieae (Apiaceae: Apioideae)
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa444openalex-snapshot
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab093openalex-snapshot
FASTRAL: improving scalability of phylogenomic analysis
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab875openalex-snapshot
Completing gene trees without species trees in sub-quadratic time
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac265openalex-snapshot
QuCo: quartet-based co-estimation of species trees and gene trees
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz344openalex-snapshot
TreeMerge: a new method for improving the scalability of species tree estimation methods
inferred← citeshttps://doi.org/10.1093/biolinnean/blab095openalex-snapshot
Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery
inferred← citeshttps://doi.org/10.1093/biolinnean/blab139openalex-snapshot
Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus
inferred← citeshttps://doi.org/10.1093/evolinnean/kzaf013openalex-snapshot
On measures of influence and discordance in phylogenomic analyses
inferred← citeshttps://doi.org/10.1093/evolinnean/kzaf018openalex-snapshot
Two-step species tree inference under the multispecies coalescent using full-likelihood
inferred← citeshttps://doi.org/10.1093/g3journal/jkag062openalex-snapshot
Phyling: phylogenetic inference from annotated genomes
inferred← citeshttps://doi.org/10.1093/gbe/evaa113openalex-snapshot
Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets
inferred← citeshttps://doi.org/10.1093/gbe/evad070openalex-snapshot
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
inferred← citeshttps://doi.org/10.1093/gbe/evaf200openalex-snapshot
Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss
inferred← citeshttps://doi.org/10.1093/isd/ixaf019openalex-snapshot
Exploring species delimitation of high-altitude flower bugs (Heteroptera: Anthocoridae) in the presence of complex reticulate evolution: the case of a biodiversity hotspot in the Qinghai–Tibet Plateau and surrounding mountains
inferred← citeshttps://doi.org/10.1093/isd/ixz016openalex-snapshot
Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
inferred← citeshttps://doi.org/10.1093/jhered/esz076openalex-snapshot
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
inferred← citeshttps://doi.org/10.1093/molbev/msaa139openalex-snapshot
ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy
inferred← citeshttps://doi.org/10.1093/molbev/msab151openalex-snapshot
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
inferred← citeshttps://doi.org/10.1093/molbev/msac215openalex-snapshot
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees
inferred← citeshttps://doi.org/10.1093/molbev/msae214openalex-snapshot
The Meaning and Measure of Concordance Factors in Phylogenomics
inferred← citeshttps://doi.org/10.1093/molbev/msae219openalex-snapshot
Gentrius: Generating Trees Compatible With a Set of Unrooted Subtrees and its Application to Phylogenetic Terraces
inferred← citeshttps://doi.org/10.1093/molbev/msaf296openalex-snapshot
Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships
inferred← citeshttps://doi.org/10.1093/nar/gkx1289openalex-snapshot
Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve
inferred← citeshttps://doi.org/10.1093/sysbio/syaa063openalex-snapshot
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction
inferred← citeshttps://doi.org/10.1093/sysbio/syaa064openalex-snapshot
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?
inferred← citeshttps://doi.org/10.1093/sysbio/syaa069openalex-snapshot
A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data
inferred← citeshttps://doi.org/10.1093/sysbio/syaa088openalex-snapshot
The Legacy of Recurrent Introgression during the Radiation of Hares
inferred← citeshttps://doi.org/10.1093/sysbio/syaa097openalex-snapshot
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees
inferred← citeshttps://doi.org/10.1093/sysbio/syab011openalex-snapshot
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
inferred← citeshttps://doi.org/10.1093/sysbio/syab013openalex-snapshot
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)
inferred← citeshttps://doi.org/10.1093/sysbio/syab051openalex-snapshot
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
inferred← citeshttps://doi.org/10.1093/sysbio/syab053openalex-snapshot
Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics
inferred← citeshttps://doi.org/10.1093/sysbio/syab070openalex-snapshot
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition
inferred← citeshttps://doi.org/10.1093/sysbio/syab071openalex-snapshot
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails
inferred← citeshttps://doi.org/10.1093/sysbio/syab075openalex-snapshot
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data
inferred← citeshttps://doi.org/10.1093/sysbio/syab094openalex-snapshot
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution
inferred← citeshttps://doi.org/10.1093/sysbio/syac047openalex-snapshot
Impact of Ghost Introgression on Coalescent-Based Species Tree Inference and Estimation of Divergence Time
inferred← citeshttps://doi.org/10.1093/sysbio/syac055openalex-snapshot
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance
inferred← citeshttps://doi.org/10.1093/sysbio/syac062openalex-snapshot
Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)
inferred← citeshttps://doi.org/10.1093/sysbio/syad038openalex-snapshot
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance
inferred← citeshttps://doi.org/10.1093/sysbio/syad056openalex-snapshot
Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages
inferred← citeshttps://doi.org/10.1093/sysbio/syad065openalex-snapshot
Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses
inferred← citeshttps://doi.org/10.1093/sysbio/syad076openalex-snapshot
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora
inferred← citeshttps://doi.org/10.1093/sysbio/syae017openalex-snapshot
Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic
inferred← citeshttps://doi.org/10.1093/sysbio/syae054openalex-snapshot
Inference of Phylogenetic Networks From Sequence Data Using Composite Likelihood
inferred← citeshttps://doi.org/10.1093/sysbio/syaf009openalex-snapshot
Improved Robustness to Gene Tree Incompleteness, Estimation Errors, and Systematic Homology Errors with Weighted TREE-QMC
inferred← citeshttps://doi.org/10.1093/sysbio/syaf016openalex-snapshot
Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae)
inferred← citeshttps://doi.org/10.1093/sysbio/syaf017openalex-snapshot
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets
inferred← citeshttps://doi.org/10.1093/sysbio/syaf022openalex-snapshot
Phylogenomics Resolve the Systematics and Biogeography of the Ant Tribe Myrmicini and Tribal Relationships within the Hyperdiverse Ant Subfamily Myrmicinae
inferred← citeshttps://doi.org/10.1093/sysbio/syaf044openalex-snapshot
Coping with Ineffective Overlap in Multilocus Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syaf050openalex-snapshot
Practical Guide and Review of Fossil Tip-Dating in Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syaf080openalex-snapshot
Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life
inferred← citeshttps://doi.org/10.1093/sysbio/syaf089openalex-snapshot
Using Gene Trees with Lineage-Specific Duplicates for Phylogenetic Inference Mitigates the Effects of Long-Branch Attraction
inferred← citeshttps://doi.org/10.1093/sysbio/syag060openalex-snapshot
Exploring Incongruence in a Plant Genus with Relatively Recent Polyploidy and Cytoplasmic Discordance
inferred← citeshttps://doi.org/10.1093/sysbio/syy013openalex-snapshot
Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
inferred← citeshttps://doi.org/10.1093/sysbio/syy021openalex-snapshot
Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data
inferred← citeshttps://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferred← citeshttps://doi.org/10.1093/sysbio/syy064openalex-snapshot
Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)
inferred← citeshttps://doi.org/10.1093/sysbio/syy085openalex-snapshot
Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting
inferred← citeshttps://doi.org/10.1093/sysbio/syz044openalex-snapshot
Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents
inferred← citeshttps://doi.org/10.1098/rspb.2018.2776openalex-snapshot
A congruent topology for deep gastropod relationships
inferred← citeshttps://doi.org/10.1098/rspb.2020.2102openalex-snapshot
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)
inferred← citeshttps://doi.org/10.1098/rstb.2021.0244openalex-snapshot
Recent progress on methods for estimating and updating large phylogenies
inferred← citeshttps://doi.org/10.1101/2020.01.28.923805openalex-snapshot
Phylogenetic signal is associated with the degree of variation in root-to-tip distances
inferred← citeshttps://doi.org/10.1101/2020.02.13.947796openalex-snapshot
A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape
inferred← citeshttps://doi.org/10.1101/2020.03.27.012237openalex-snapshot
When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships
inferred← citeshttps://doi.org/10.1101/2021.07.01.450750openalex-snapshot
Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation ( Freziera, Pentaphylacaceae)
inferred← citeshttps://doi.org/10.1101/2021.11.19.469195openalex-snapshot
A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation
inferred← citeshttps://doi.org/10.1101/2022.01.24.474473openalex-snapshot
The evolutionary history of mammoth wasps (Hymenoptera: Scoliidae)
inferred← citeshttps://doi.org/10.1101/2022.05.24.493312openalex-snapshot
Fast and Accurate Species Trees from Weighted Internode Distances
inferred← citeshttps://doi.org/10.1101/2022.06.25.497608openalex-snapshot
TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
inferred← citeshttps://doi.org/10.1101/2022.08.12.503770openalex-snapshot
Resolving marine–freshwater transitions by diatoms through a fog of discordant gene trees
inferred← citeshttps://doi.org/10.1101/2022.11.09.515828openalex-snapshot
Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning
inferred← citeshttps://doi.org/10.1101/2023.01.19.524678openalex-snapshot
Gentrius: identifying equally scoring trees in phylogenomics with incomplete data
inferred← citeshttps://doi.org/10.1101/2023.09.17.558141openalex-snapshot
Mitochondrial genome analyses uncover intriguing population structure across the invasive trajectory of an iconic invader
inferred← citeshttps://doi.org/10.1101/2024.05.06.592828openalex-snapshot
Predicting locus phylogenetic utility using machine learning
inferred← citeshttps://doi.org/10.1101/2024.08.01.605766openalex-snapshot
Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in Section Nintooa ( Lonicera , Caprifoliaceae)
inferred← citeshttps://doi.org/10.1101/2024.08.20.608795openalex-snapshot
Analysis of the effects of mating systems on lineage diversification across multiple genera
inferred← citeshttps://doi.org/10.1101/2024.10.17.618389openalex-snapshot
A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification
inferred← citeshttps://doi.org/10.1101/2024.11.26.625400openalex-snapshot
Systematic exploration of domain assortments in NOD-like receptors uncovers two types of NACHT domains in Sordariales fungi
inferred← citeshttps://doi.org/10.1101/601237openalex-snapshot
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
inferred← citeshttps://doi.org/10.1101/643296openalex-snapshot
Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’
inferred← citeshttps://doi.org/10.1101/668475openalex-snapshot
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
inferred← citeshttps://doi.org/10.1101/765610openalex-snapshot
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )
inferred← citeshttps://doi.org/10.1101/832683openalex-snapshot
Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata )
inferred← citeshttps://doi.org/10.1101/gr.277629.122openalex-snapshot
Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
inferred← citeshttps://doi.org/10.1109/tcbb.2020.2990867openalex-snapshot
Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation
inferred← citeshttps://doi.org/10.1109/tcbbio.2025.3531790openalex-snapshot
Improvement to GLASS/Maximum Tree Method of Species Tree Inference Using Measurement Error Modified Single Linkage Clustering
inferred← citeshttps://doi.org/10.1111/1755-0998.12783openalex-snapshot
HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing
inferred← citeshttps://doi.org/10.1111/1755-0998.12962openalex-snapshot
Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny
inferred← citeshttps://doi.org/10.1111/1755-0998.13350openalex-snapshot
The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles ( Terrapene spp.)
inferred← citeshttps://doi.org/10.1111/1755-0998.13523openalex-snapshot
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations
inferred← citeshttps://doi.org/10.1111/1755-0998.13806openalex-snapshot
Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids
inferred← citeshttps://doi.org/10.1111/2041-210x.13696openalex-snapshot
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution
inferred← citeshttps://doi.org/10.1111/2041-210x.13790openalex-snapshot
Rapid alignment updating with Extensiphy
inferred← citeshttps://doi.org/10.1111/jbi.14352openalex-snapshot
Historical biogeography of a rapid and geographically wide diversification in Neotropical mammals
inferred← citeshttps://doi.org/10.1111/jbi.15161openalex-snapshot
So Young, So Rich: Habitat Shifts Combined With Trait Evolution Promoted Species Radiation in Senecio in the Andes
inferred← citeshttps://doi.org/10.1111/jeb.13355openalex-snapshot
Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda
inferred← citeshttps://doi.org/10.1111/mec.15603openalex-snapshot
Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
inferred← citeshttps://doi.org/10.1111/pce.13847openalex-snapshot
Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation
inferred← citeshttps://doi.org/10.1111/syen.12427openalex-snapshot
Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps
inferred← citeshttps://doi.org/10.1111/syen.12454openalex-snapshot
Assessing support for Blaberoidea phylogeny suggests optimal locus quality
inferred← citeshttps://doi.org/10.1111/syen.12468openalex-snapshot
The limits of Quediini at last (Staphylinidae: Staphylininae): a rove beetle mega‐radiation resolved by comprehensive sampling and anchored phylogenomics
inferred← citeshttps://doi.org/10.1111/syen.12475openalex-snapshot
Reanalysis of the apoid wasp phylogeny with additional taxa and sequence data confirms the placement of Ammoplanidae as sister to bees
inferred← citeshttps://doi.org/10.1111/syen.12582openalex-snapshot
Phylogeny of the flea beetles (Galerucinae: Alticini) and the position of Aulacothorax elucidated through anchored phylogenomics (Coleoptera: Chrysomelidae: Alticini)
inferred← citeshttps://doi.org/10.1111/syen.12592openalex-snapshot
Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius )
inferred← citeshttps://doi.org/10.1111/syen.12685openalex-snapshot
Whole genome shotgun phylogenomics resolve the diving beetle tree of life
inferred← citeshttps://doi.org/10.1111/zsc.12512openalex-snapshot
Gene tree quality affects empirical coalescent branch length estimation
inferred← citeshttps://doi.org/10.1111/zsc.70081openalex-snapshot
Integrating Phylogenomics and Biogeography of Spectracanthicus (Siluriformes: Loricariidae) Reveals Complex Evolutionary History in a Brazilian Shield Endemic Genus
inferred← citeshttps://doi.org/10.1126/science.adk9688openalex-snapshot
CASTER: Direct species tree inference from whole-genome alignments
inferred← citeshttps://doi.org/10.1146/annurev-arplant-042916-041040openalex-snapshot
Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-012121-095340openalex-snapshot
Multispecies Coalescent: Theory and Applications in Phylogenetics
inferred← citeshttps://doi.org/10.1186/s12862-018-1300-4openalex-snapshot
A phylogenomic resolution of the sea urchin tree of life
inferred← citeshttps://doi.org/10.1186/s12864-018-4619-8openalex-snapshot
The performance of coalescent-based species tree estimation methods under models of missing data
inferred← citeshttps://doi.org/10.1186/s12864-018-4621-1openalex-snapshot
SIESTA: enhancing searches for optimal supertrees and species trees
inferred← citeshttps://doi.org/10.1186/s12870-025-06963-3openalex-snapshot
Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae)
inferred← citeshttps://doi.org/10.1186/s12915-020-00944-8openalex-snapshot
Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
inferred← citeshttps://doi.org/10.1186/s13015-017-0120-1openalex-snapshot
Gene tree parsimony for incomplete gene trees: addressing true biological loss
inferred← citeshttps://doi.org/10.1186/s13015-018-0124-5openalex-snapshot
OCTAL: Optimal Completion of gene trees in polynomial time
inferred← citeshttps://doi.org/10.1186/s13015-019-0151-xopenalex-snapshot
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
inferred← citeshttps://doi.org/10.1186/s13015-019-0161-8openalex-snapshot
Non-parametric correction of estimated gene trees using TRACTION
inferred← citeshttps://doi.org/10.1186/s13015-023-00230-6openalex-snapshot
Weighted ASTRID: fast and accurate species trees from weighted internode distances
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1013676openalex-snapshot
T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters
inferred← citeshttps://doi.org/10.1371/journal.pgen.1011739openalex-snapshot
Genomic organization, domain assortments, and nucleotide-binding domain diversity of NLR proteins in Sordariales fungi
inferred← citeshttps://doi.org/10.1371/journal.pone.0309596openalex-snapshot
From museum drawer to tree: Historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections
inferred← citeshttps://doi.org/10.15298/rusjtheriol.20.2.01openalex-snapshot
Chiropteran (Chiroptera; Mammalia) taxonomy in light of modern methods and approaches
inferred← citeshttps://doi.org/10.1600/036364424x17151801116385openalex-snapshot
Phylogenetic Relationships within Monotropoideae (Ericaceae): Implications for Taxonomy and Character Evolution
inferred← citeshttps://doi.org/10.20944/preprints202110.0258.v2openalex-snapshot
Recent Progress on Methods for Estimating and Updating Large Phylogenies
inferred← citeshttps://doi.org/10.2307/j.ctv2wr4wdf.8openalex-snapshot
Large-Scale Species Tree Estimation
inferred← citeshttps://doi.org/10.23860/diss-ada-eren-2023openalex-snapshot
Utilization of Large-Scale Genomic Data and Phylogenetic Methods in Studying Evolutionary Radiations
inferred← citeshttps://doi.org/10.23860/diss-hellwig-martin-2019openalex-snapshot
Computational Gene Association Based on Relative Species Displacement in Gene and Morphology Trees
inferred← citeshttps://doi.org/10.24072/pcjournal.694openalex-snapshot
The effect of gene tree dependence on summary methods for species tree inference
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.5415openalex-snapshot
Quantifying Structure and Variation in Complex Phylogenetic Data
inferred← citeshttps://doi.org/10.32469/10355/69858openalex-snapshot
The evolution of complex calls In meadow Katydids
inferred← citeshttps://doi.org/10.3389/fevo.2024.1243221openalex-snapshot
Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea
inferred← citeshttps://doi.org/10.3389/fpls.2019.01074openalex-snapshot
Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression
inferred← citeshttps://doi.org/10.3389/fpls.2019.01761openalex-snapshot
Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum
inferred← citeshttps://doi.org/10.3389/fpls.2021.765719openalex-snapshot
How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example
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