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The Impact of Missing Data on Species Tree Estimation

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jagm.2000.1133openalex-snapshot

Constructing Optimal Trees from Quartets

inferredcites →https://doi.org/10.1007/978-3-319-08171-7_2openalex-snapshot

Phylogenetic Bias in the Likelihood Method Caused by Missing Data Coupled with Among-Site Rate Variation: An Analytical Approach

inferredcites →https://doi.org/10.1007/s00239-009-9206-9openalex-snapshot

Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum

inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot

Comparison of phylogenetic trees

inferredcites →https://doi.org/10.1016/0169-5347(96)81133-5openalex-snapshot

Combining data in phylogenetic analysis

inferredcites →https://doi.org/10.1016/1055-7903(92)90035-fopenalex-snapshot

Phylogenetic inference based on matrix representation of trees

inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot

Evolution of Protein Molecules

inferredcites →https://doi.org/10.1016/j.aml.2009.08.009openalex-snapshot

Characterizing phylogenetically decisive taxon coverage

inferredcites →https://doi.org/10.1016/j.cub.2013.09.014openalex-snapshot

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

inferredcites →https://doi.org/10.1016/j.tplants.2014.02.011openalex-snapshot

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

inferredcites →https://doi.org/10.1016/j.tplants.2014.02.012openalex-snapshot

Land plant origins and coalescence confusion

inferredcites →https://doi.org/10.1016/j.tree.2006.10.002openalex-snapshot

The supermatrix approach to systematics

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.2006.05.025openalex-snapshot

Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets

inferredcites →https://doi.org/10.1016/j.ympev.2008.05.046openalex-snapshot

The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

inferredcites →https://doi.org/10.1016/j.ympev.2008.08.006openalex-snapshot

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

inferredcites →https://doi.org/10.1016/j.ympev.2009.05.033openalex-snapshot

Coalescent methods for estimating phylogenetic trees

inferredcites →https://doi.org/10.1016/j.ympev.2011.06.012openalex-snapshot

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

inferredcites →https://doi.org/10.1016/j.ympev.2011.10.017openalex-snapshot

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

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.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/10.1038/35106579openalex-snapshot

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot

Broad phylogenomic sampling improves resolution of the animal tree of life

inferredcites →https://doi.org/10.1038/nature12130openalex-snapshot

Inferring ancient divergences requires genes with strong phylogenetic signals

inferredcites →https://doi.org/10.1038/nature12872openalex-snapshot

Three keys to the radiation of angiosperms into freezing environments

inferredcites →https://doi.org/10.1073/pnas.0909672107openalex-snapshot

Phylogenetic analyses reveal the shady history of C 4 grasses

inferredcites →https://doi.org/10.1073/pnas.1205818109openalex-snapshot

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot

Phylotranscriptomic analysis of the origin and early diversification of land plants

inferredcites →https://doi.org/10.1073/pnas.89.22.10648openalex-snapshot

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.

inferredcites →https://doi.org/10.1080/10635150390218330openalex-snapshot

Missing Data, Incomplete Taxa, and Phylogenetic Accuracy

inferredcites →https://doi.org/10.1080/10635150500234583openalex-snapshot

Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?

inferredcites →https://doi.org/10.1080/10635150500354829openalex-snapshot

Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis

inferredcites →https://doi.org/10.1080/10635150600999150openalex-snapshot

Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes

inferredcites →https://doi.org/10.1086/428296openalex-snapshot

Explosive Radiation of Malpighiales Supports a Mid‐Cretaceous Origin of Modern Tropical Rain Forests

inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along 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/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btq062openalex-snapshot

Phybase: an R package for species tree analysis

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/gbe/evr105openalex-snapshot

Systematic Error in Seed Plant Phylogenomics

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/msh182openalex-snapshot

Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments

inferredcites →https://doi.org/10.1093/molbev/msi002openalex-snapshot

Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data

inferredcites →https://doi.org/10.1093/molbev/msn043openalex-snapshot

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot

Bayesian Inference of Species Trees from Multilocus Data

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/msu051openalex-snapshot

Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)

inferredcites →https://doi.org/10.1093/molbev/msu331openalex-snapshot

Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gku1216openalex-snapshot

GenBank

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot

A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

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/sysbio/46.3.523openalex-snapshot

Gene Trees in Species Trees

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/syp075openalex-snapshot

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

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/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/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/syr089openalex-snapshot

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

inferredcites →https://doi.org/10.1093/sysbio/sys070openalex-snapshot

The Evolutionary Root of Flowering Plants

inferredcites →https://doi.org/10.1093/sysbio/syu055openalex-snapshot

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

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/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/10.1098/rspb.2009.0896openalex-snapshot

Assessing the root of bilaterian animals with scalable phylogenomic methods

inferredcites →https://doi.org/10.1099/ijs.0.01472-0openalex-snapshot

Caloramator viterbensis sp. nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy

inferredcites →https://doi.org/10.1099/ijs.0.63090-0openalex-snapshot

Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis

inferredcites →https://doi.org/10.1111/cla.12015openalex-snapshot

Phylogenomics of A nnelida revisited: a cladistic approach using genome‐wide expressed sequence tag data mining and examining the effects of missing data

inferredcites →https://doi.org/10.1111/j.1096-0031.2011.00375.xopenalex-snapshot

Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data

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/j.1558-5646.2011.01476.xopenalex-snapshot

COALESCENT-BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot

Estimating phylogenetic trees from genome‐scale data

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.1206357openalex-snapshot

Terraces in Phylogenetic Tree Space

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/10.1146/annurev-anchem-062012-092628openalex-snapshot

Next-Generation Sequencing Platforms

inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135822openalex-snapshot

High-Throughput Genomic Data in Systematics and Phylogenetics

inferredcites →https://doi.org/10.1146/annurev-genom-082908-150112openalex-snapshot

Methods for Genomic Partitioning

inferredcites →https://doi.org/10.1146/annurev.ento.53.103106.093304openalex-snapshot

Ancient Rapid Radiations of Insects: Challenges for Phylogenetic Analysis

inferredcites →https://doi.org/10.1186/1471-2148-10-155openalex-snapshot

Phylogenomics with incomplete taxon coverage: the limits to inference

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/10.1186/1471-2148-8-95openalex-snapshot

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

inferredcites →https://doi.org/10.1186/1471-2229-7-57openalex-snapshot

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

inferredcites →https://doi.org/10.1186/1741-7007-4-12openalex-snapshot

The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured

inferredcites →https://doi.org/10.1186/1748-7188-5-37openalex-snapshot

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

inferredcites →https://doi.org/10.1186/gb-2012-13-1-r3openalex-snapshot

A genome triplication associated with early diversification of the core eudicots

inferredcites →https://doi.org/10.1371/currents.tol.34260cc27551a527b124ec5f6334b6beopenalex-snapshot

Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated conditions

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.pone.0005764openalex-snapshot

The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

inferredcites →https://doi.org/10.1371/journal.pone.0042925openalex-snapshot

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

inferredcites →https://doi.org/10.1371/journal.pone.0080870openalex-snapshot

Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships

inferredcites →https://doi.org/10.1534/genetics.107.076422openalex-snapshot

Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings

inferredcites →https://doi.org/10.2307/1222480openalex-snapshot

Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees

inferredcites →https://doi.org/10.3724/sp.j.1002.2008.08040openalex-snapshot

Missing data and the accuracy of Bayesian phylogenetics

inferredcites →https://doi.org/10.3732/ajb.1000481openalex-snapshot

Understanding angiosperm diversification using small and large phylogenetic trees

inferredcites →https://doi.org/10.3897/asp.64.e31642openalex-snapshot

A molecular phylogeny of Hexapoda

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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Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

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inferred← citeshttps://doi.org/10.1002/ajb2.1682openalex-snapshot

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

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Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set

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Evidence of introgression amid phylogenetic conflict in Brachyotum , a plant radiation from the Tropical Andes

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Data‐driven guidelines for phylogenomic analyses using SNP data

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Towards optimizing the execution of spark scientific workflows using machine learning‐based parameter tuning

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Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae)

inferred← citeshttps://doi.org/10.1002/ece3.9842openalex-snapshot

2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics

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inferred← citeshttps://doi.org/10.1007/13836_2020_82openalex-snapshot

Population Genomics of Organelle Genomes in Crop Plants

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Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

inferred← citeshttps://doi.org/10.1007/978-3-031-04749-7_10openalex-snapshot

QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data

inferred← citeshttps://doi.org/10.1007/978-3-319-67979-2_15openalex-snapshot

Statistical Consistency of Coalescent-Based Species Tree Methods Under Models of Missing Data

inferred← citeshttps://doi.org/10.1007/s00338-021-02072-3openalex-snapshot

Application of phylogenomic tools to unravel anthozoan evolution

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Molecular and karyological data confirm that the enigmatic genus Platypholis from Bonin-Islands (SE Japan) is phylogenetically nested within Orobanche (Orobanchaceae)

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Inter- and Intraspecific Genetic Variation of Native Hawthorn (Crataegus spp.) Genotypes Grown in the Çoruh Valley in Türkiye

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Nuclear DNA reveals multiple waves of colonisation, reticulate evolution and a large impact of stocking on trout in north-west Africa

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Microbial evolutionary reconstruction in the presence of mosaic sequences

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An alignment-free method for detection of missing regions for phylogenetic analysis

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Origin and diversity of malaria parasites and other Haemosporida

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New Approaches for Inferring Phylogenies in the Presence of Paralogs

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Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

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Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids

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Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

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Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae)

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Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data

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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)

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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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Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships

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A novel reference dated phylogeny for the genus Spodoptera Guenée (Lepidoptera: Noctuidae: Noctuinae): new insights into the evolution of a pest-rich genus

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How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

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Out of chaos: Phylogenomics of Asian Sonerileae

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Next-generation sequencing data show rapid radiation and several long-distance dispersal events in early Costaceae

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The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

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Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

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The legacy of the paleotropical flora belt: extreme continental vicariance and island refugia in Woodwardioid ferns

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Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

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DNA barcoding of medicinal orchids in Asia

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Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics

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Systematics of the genus Halgerda Bergh, 1880 (Heterobranchia : Nudibranchia) of Mozambique with descriptions of six new species

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Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data

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Loss of color terms not demonstrated

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Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses

inferred← citeshttps://doi.org/10.1088/1742-6596/1796/1/012123openalex-snapshot

Alternative ways to handle missing values problem: A case study in earthquake dataset

inferred← citeshttps://doi.org/10.1089/cmb.2022.0212openalex-snapshot

Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data

inferred← citeshttps://doi.org/10.1089/cmb.2022.0357openalex-snapshot

Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data

inferred← citeshttps://doi.org/10.1093/aob/mcad051openalex-snapshot

Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

inferred← citeshttps://doi.org/10.1093/aob/mcae001openalex-snapshot

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

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/btab875openalex-snapshot

Completing gene trees without species trees in sub-quadratic time

inferred← citeshttps://doi.org/10.1093/botlinnean/boag067openalex-snapshot

Applying novel genetic tools to assist in the delimitation of species boundaries within the herbaceous bamboo lineage

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/evab101openalex-snapshot

Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae

inferred← citeshttps://doi.org/10.1093/gbe/evac129openalex-snapshot

A Practical Guide to Design and Assess a Phylogenomic Study

inferred← citeshttps://doi.org/10.1093/molbev/msaa106openalex-snapshot

New Methods to Calculate Concordance Factors for Phylogenomic Datasets

inferred← citeshttps://doi.org/10.1093/molbev/msab365openalex-snapshot

SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss

inferred← citeshttps://doi.org/10.1093/molbev/msad109openalex-snapshot

Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs

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/msx261openalex-snapshot

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

inferred← citeshttps://doi.org/10.1093/molbev/msx268openalex-snapshot

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

inferred← citeshttps://doi.org/10.1093/molbev/msx324openalex-snapshot

Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils

inferred← citeshttps://doi.org/10.1093/molbev/msz014openalex-snapshot

A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies

inferred← citeshttps://doi.org/10.1093/ornithology/ukab025openalex-snapshot

Phylogenomic analyses reveal non-monophyly of the antbird generaHerpsilochmusandSakesphorus(Thamnophilidae), with description of a new genus forHerpsilochmus sellowi

inferred← citeshttps://doi.org/10.1093/ornithology/ukab042openalex-snapshot

Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification

inferred← citeshttps://doi.org/10.1093/sysbio/syaa008openalex-snapshot

The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets

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/syaa097openalex-snapshot

Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees

inferred← citeshttps://doi.org/10.1093/sysbio/syac051openalex-snapshot

Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations

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/syae052openalex-snapshot

Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia

inferred← citeshttps://doi.org/10.1093/sysbio/syae065openalex-snapshot

Robustness of divergence time estimation despite gene tree estimation error: a case study of fireflies (Coleoptera: Lampyridae)

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/syw027openalex-snapshot

Phylogenomics for Systematic Biology

inferred← citeshttps://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

inferred← citeshttps://doi.org/10.1093/sysbio/syx077openalex-snapshot

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

inferred← citeshttps://doi.org/10.1093/sysbio/syz029openalex-snapshot

Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships

inferred← citeshttps://doi.org/10.1093/sysbio/syz066openalex-snapshot

Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses

inferred← citeshttps://doi.org/10.1098/rsbl.2023.0398openalex-snapshot

Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia

inferred← citeshttps://doi.org/10.1098/rspb.2025.3316openalex-snapshot

A true Luciolinae fossil from the mid-Cretaceous Burmese amber provides new insights into the early evolution of fireflies (Coleoptera: Lampyridae)

inferred← citeshttps://doi.org/10.1098/rspb.2026.0100openalex-snapshot

Can ecological interactions drive evolutionary outcomes? Evidence from insect host shifts between parasitic and non-parasitic plants

inferred← citeshttps://doi.org/10.1098/rstb.2015.0335openalex-snapshot

Multilocus inference of species trees and DNA barcoding

inferred← citeshttps://doi.org/10.1101/170696openalex-snapshot

Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships

inferred← citeshttps://doi.org/10.1101/2020.11.09.375196openalex-snapshot

Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

inferred← citeshttps://doi.org/10.1101/2021.10.29.466515openalex-snapshot

A comprehensive evaluation of CRISPR lineage recorders using TraceQC

inferred← citeshttps://doi.org/10.1101/2021.11.18.469131openalex-snapshot

Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict

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/10.1101/2023.09.02.556036openalex-snapshot

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

inferred← citeshttps://doi.org/10.1101/2023.09.20.558635openalex-snapshot

Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models

inferred← citeshttps://doi.org/10.1101/2024.04.03.587887openalex-snapshot

Can ecological interactions drive evolutionary outcomes? Evidence from insect host shifts between parasitic and non-parasitic plants

inferred← citeshttps://doi.org/10.1101/2025.06.02.657453openalex-snapshot

The phylogenetic position of the extinct Hawaiian honeyeaters: Overcoming the limitations of antique DNA

inferred← citeshttps://doi.org/10.1101/2025.08.19.670998openalex-snapshot

Progress in the molecular Phylogeny of Cotesia acuminata and C. melitaearum cryptic species complexes

inferred← citeshttps://doi.org/10.1101/346635openalex-snapshot

A new method for detecting autocorrelation of evolutionary rates in large phylogenies

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/10.1111/1749-4877.12772openalex-snapshot

A molecular phylogeny for all 21 families within Chiroptera (bats)

inferred← citeshttps://doi.org/10.1111/1755-0998.13016openalex-snapshot

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

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/10.1111/1755-0998.14044openalex-snapshot

OGU : A Toolbox for Better Utilising Organelle Genomic Data

inferred← citeshttps://doi.org/10.1111/2041-210x.13790openalex-snapshot

Rapid alignment updating with Extensiphy

inferred← citeshttps://doi.org/10.1111/cla.12170openalex-snapshot

Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia

inferred← citeshttps://doi.org/10.1111/cla.12198openalex-snapshot

Missing data, clade support and “reticulation”: the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re‐examined

inferred← citeshttps://doi.org/10.1111/cla.12409openalex-snapshot

The phylogeny of the Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini)

inferred← citeshttps://doi.org/10.1111/cla.12540openalex-snapshot

Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses

inferred← citeshttps://doi.org/10.1111/eva.13735openalex-snapshot

Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Oncorhynchus clarkii)

inferred← citeshttps://doi.org/10.1111/jfb.13509openalex-snapshot

Multi‐gene phylogeny of jacks and pompanos ( C arangidae), including placement of monotypic vadigo Campogramma glaycos

inferred← citeshttps://doi.org/10.1111/jse.12725openalex-snapshot

Species delimitation of North AmericanNyssaspecies

inferred← citeshttps://doi.org/10.1111/jzs.12262openalex-snapshot

Higher‐level phylogenetic affinities of the Neotropical genusMastigodryasAmaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus forMastigodryas bifossatus

inferred← citeshttps://doi.org/10.1111/nph.70472openalex-snapshot

Whole genome sequencing of historical specimens from the world's largest fungal collection yields high‐quality assemblies

inferred← citeshttps://doi.org/10.1111/syen.12292openalex-snapshot

Molecular phylogeny and temporal diversification of Tanytarsus van der Wulp (Diptera: Chironomidae) support generic synonymies, a new classification and centre of origin

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.12490openalex-snapshot

The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements

inferred← citeshttps://doi.org/10.1111/syen.12569openalex-snapshot

A genome‐wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics

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.12685openalex-snapshot

Whole genome shotgun phylogenomics resolve the diving beetle tree of life

inferred← citeshttps://doi.org/10.1111/syen.70024openalex-snapshot

Over‐reliance on Completeness exposes ultraconserved elements datasets to non‐randomly distributed missing data

inferred← citeshttps://doi.org/10.1111/syen.70041openalex-snapshot

Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)

inferred← citeshttps://doi.org/10.1111/zsc.12210openalex-snapshot

Phylogenomic subsampling: a brief review

inferred← citeshttps://doi.org/10.1111/zsc.12407openalex-snapshot

Phylogeny of the superfamily Gelechioidea (Lepidoptera: Obtectomera), with an exploratory application on geometric morphometrics

inferred← citeshttps://doi.org/10.1111/zsc.70047openalex-snapshot

The Phylogenetic Position of the Extinct Hawaiian Honeyeaters: Overcoming the Limitations of Historical DNA

inferred← citeshttps://doi.org/10.1126/science.aaz6970openalex-snapshot

The evolution of a tropical biodiversity hotspot

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-micro-090817-062436openalex-snapshot

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens

inferred← citeshttps://doi.org/10.1155/jzs/5987677openalex-snapshot

Integrative Approach for the Identification and Delimitation of Orthops Species (Heteroptera, Miridae, and Mirinae) in the Palearctic

inferred← citeshttps://doi.org/10.11606/t.41.2021.tde-05042021-212235openalex-snapshot

Filogenia e tempos de divergência das moscas caliptradas (Diptera: Schizophora: Calyptratae) e classificação da tribo Tachinini (Oestroidea: Tachinidae)

inferred← citeshttps://doi.org/10.1163/1876312x-bja10027openalex-snapshot

The complete mitochondrial genomes of Notiophilus quadripunctatus Dejean, 1826 and Omophron limbatum (Fabricius, 1777): New insights into the mitogenome phylogeny of the Carabidae (Insecta, Coleoptera)

inferred← citeshttps://doi.org/10.1186/s12862-016-0806-xopenalex-snapshot

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

inferred← citeshttps://doi.org/10.1186/s12862-018-1162-9openalex-snapshot

The prevalence of terraced treescapes in analyses of phylogenetic data sets

inferred← citeshttps://doi.org/10.1186/s12862-019-1534-9openalex-snapshot

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal 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/s12864-022-08510-yopenalex-snapshot

Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

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/s13059-020-02000-8openalex-snapshot

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

inferred← citeshttps://doi.org/10.1186/s40168-023-01705-9openalex-snapshot

VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution

inferred← citeshttps://doi.org/10.1186/s43008-019-0002-xopenalex-snapshot

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

inferred← citeshttps://doi.org/10.1371/journal.pone.0348973openalex-snapshot

Progress in the molecular phylogeny of Cotesia acuminata and C. melitaearum cryptic species complexes

inferred← citeshttps://doi.org/10.1534/g3.116.034744openalex-snapshot

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

inferred← citeshttps://doi.org/10.1600/036364420x15862837791221openalex-snapshot

Phylogenomics Resolves the Relationships within Antennaria (Asteraceae, Gnaphalieae) and Yields New Insights into its Morphological Character Evolution and Biogeography

inferred← citeshttps://doi.org/10.1600/036364423x16847773873116openalex-snapshot

Phylogeny of Species, Infraspecific Taxa, and Forms in Iris Subgenus Xiphium (Iridaceae), From the Mediterranean Basin Biodiversity Hotspot

inferred← citeshttps://doi.org/10.1600/036364425x17466502618849openalex-snapshot

Phylogenomic and Ecological Systematics of Melocactus (Cactaceae)

inferred← citeshttps://doi.org/10.17660/actahortic.2024.1414.8openalex-snapshot

Phylogenomics of Orchidaceae: concatenated and coalescent analyses of the plastomes provide different insights into orchid phylogeny

inferred← citeshttps://doi.org/10.21203/rs.2.13279/v1openalex-snapshot

Untangling relationships among terraranan frogs: a phylogenomic approach based on 2,665 loci

inferred← citeshttps://doi.org/10.22541/au.171359897.79634640/v1openalex-snapshot

Organelle Genome Utilities: a toolbox for better utilizing organelle genomic data

inferred← citeshttps://doi.org/10.2994/sajh-d-22-00038.1openalex-snapshot

Treefrog Diversity in the Neotropics: Phylogenetic Relationships of Scinaxini (Anura: Hylidae: Hylinae)

inferred← citeshttps://doi.org/10.3114/sim.2024.109.08openalex-snapshot

Diaporthe species on palms – integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe , with the description of D. pygmaeae sp. nov .

inferred← citeshttps://doi.org/10.3389/fevo.2023.1134764openalex-snapshot

Short branch attraction in phylogenomic inference under the multispecies coalescent

inferred← citeshttps://doi.org/10.3389/fmars.2020.00461openalex-snapshot

The Origin and Correlated Evolution of Symbiosis and Coloniality in Scleractinian Corals

inferred← citeshttps://doi.org/10.3389/fpls.2017.01973openalex-snapshot

Marker Development for Phylogenomics: The Case of Orobanchaceae, a Plant Family with Contrasting Nutritional Modes

inferred← citeshttps://doi.org/10.3389/fpls.2020.00688openalex-snapshot

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

inferred← citeshttps://doi.org/10.3389/fpls.2022.851716openalex-snapshot

New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

inferred← citeshttps://doi.org/10.3389/fpls.2022.868565openalex-snapshot

Cell types as species: Exploring a metaphor

inferred← citeshttps://doi.org/10.3390/microorganisms11112717openalex-snapshot

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex

inferred← citeshttps://doi.org/10.48550/arxiv.1708.02626openalex-snapshot

A combinatorial method for connecting BHV spaces representing different numbers of taxa

inferred← citeshttps://doi.org/10.6084/m9.figshare.19641844openalex-snapshot

Additional file 1 of Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

inferred← citeshttps://doi.org/10.6084/m9.figshare.19641847openalex-snapshot

Additional file 2 of Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

inferred← citeshttps://doi.org/10.6084/m9.figshare.24522604openalex-snapshot

Additional file 1 of VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution

inferred← citeshttps://doi.org/10.6620/zs.2021.60-11openalex-snapshot

Finding Padaeus bovillus (Hemiptera: Pentatomidae): A Phylogenetic Placement and the Description of Its Sister Species.

inferred← citeshttps://doi.org/10.70675/0dd95244z796bz45edz998cz93834a178085openalex-snapshot

Histoire évolutive des remaniements chromosomiques en liaison avec la mobilisation d'éléments transposables chez les téléostéens antarctiques Nototheniidae : la radiation adaptative du groupe " Trematomus "

inferred← citeshttps://doi.org/10.70675/c1c1cf29zfcf5z4b9fza396zc80a51274661openalex-snapshot

Linking microevolutionary and macroevolutionary processes in the diversification of freshwater mollusks from the East African Rift

inferred← citeshttps://doi.org/10.7287/peerj.8976v0.1/reviews/1openalex-snapshot

Peer Review #1 of "Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.8976v0.1/reviews/2openalex-snapshot

Peer Review #2 of "Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis (v0.1)"

inferred← citeshttps://doi.org/10.7717/peerj.8976openalex-snapshot

Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.