Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Systematic Biology

• Publication date

  2009-10-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/sysbio/syp045PMID 20525604
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mesquite: a modular system for evolutionary analysis. Version 2.6

  2009cited by this paper
• STEM: species tree estimation using maximum likelihood for gene trees under coalescence

  2009cited by this paper
• Gene tree discordance, phylogenetic inference and the multispecies coalescent.

  2009cited by this paper
• What is the danger of the anomaly zone for empirical phylogenetics?

  2009cited by this paper
• Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data.

  2008cited by this paper
• Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies

  2008cited by this paper
• Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae).

  2008cited by this paper
• Resolving Species Phylogenies of Recent Evolutionary Radiations1

  2008cited by this paper
• Estimating Species Trees Using Multiple-Allele DNA Sequence Data

  2008cited by this paper
• Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings

  2008cited by this paper
• Inconsistency of phylogenetic estimates from concatenated data under coalescence.

  2007cited by this paper
• ESTIMATING A GEOGRAPHICALLY EXPLICIT MODEL OF POPULATION DIVERGENCE

  2007cited by this paper
• Mesquite: a modular system for evolutionary analysis. Version 2.01 (Build j28)

  2007cited by this paper
• High-resolution species trees without concatenation

  2007cited by this paper
• Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions.

  2007cited by this paper
• Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

  2007cited by this paper
• Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.

  2007cited by this paper
• Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).

  2006cited by this paper
• Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

  2006cited by this paper
• Inferring phylogeny despite incomplete lineage sorting.

  2006influential reference
• A MULTILOCUS PERSPECTIVE ON REFUGIAL ISOLATION AND DIVERGENCE IN RAINFOREST SKINKS (CARLIA)

  2006cited by this paper
• Discordance of Species Trees with Their Most Likely Gene Trees

  2006cited by this paper
• Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

  2006cited by this paper
• SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES*

  2005cited by this paper
• GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

  2005cited by this paper
• GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

  2005cited by this paper
• PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

  2004cited by this paper
• PHYLIP (Phylogeny Inference Package)

  2004cited by this paper
• Genome-scale approaches to resolving incongruence in molecular phylogenies

  2003cited by this paper
• Generating samples under a Wright-Fisher neutral model of genetic variation

  2002cited by this paper
• PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10

  2002cited by this paper
• TESTS OF PLEISTOCENE SPECIATION IN MONTANE GRASSHOPPERS (GENUS MELANOPLUS) FROM THE SKY ISLANDS OF WESTERN NORTH AMERICA

  2000cited by this paper
• From Gene Trees to Species Trees

  2000cited by this paper
• Phylogeny of Darwin's finches as revealed by mtDNA sequences.

  1999cited by this paper
• How should species phylogenies be inferred from sequence data?

  1999cited by this paper
• PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

  1997cited by this paper
• From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem.

  1997cited by this paper
• Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

  1997cited by this paper
• GENE TREES AND ORGANISMAL HISTORIES: A PHYLOGENETIC APPROACH TO POPULATION BIOLOGY

  1989cited by this paper
• Gene genealogy in three related populations: consistency probability between gene and population trees.

  1989cited by this paper
• Relationships between gene trees and species trees.

  1988cited by this paper
• Gene genealogy and variance of interpopulational nucleotide differences.

  1985cited by this paper
• Evolutionary relationship of DNA sequences in finite populations.

  1983cited by this paper
• Comparison of phylogenetic trees

  1981cited by this paper

• Reference genome choice impacts SNP recovery but not evolutionary inference in young species

  2026cites this paper
• Modern Coral Taxonomy Requires Reproducible Data Alongside Field Observations—Comments on Veron et al. (2025)

  2026cites this paper
• Unraveling the cryptic Bemisia tabaci species complex: Global phylogenomic analysis reveals evolutionary relationships and biogeographic patterns

  2025cites this paper
• Resolving Rapid Radiation of Voles and Lemmings (Arvicolinae: Cricetinae, Rodentia) with QuaddRAD Sequencing and Transcriptome Analysis

  2025cites this paper
• Phylogenomics and comparative genomic perspective on the avian radiation

  2025cites this paper
• Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae).

  2024cites this paper
• Recovery of 1559 metagenome-assembled genomes from the East China Sea’s low-oxygen region

  2024cites this paper
• Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences

  2023cites this paper
• Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

  2023cites this paper
• Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae)

  2023cites this paper
• Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

  2023cites this paper
• Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

  2023cites this paper
• Sampling affects population genetic inference: a case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus).

  2023cites this paper
• Got rhythm? Rhythmicity differences reflect different optimality criteria in feeding and locomotor systems

  2022cites this paper
• Mitochondrial characteristics of Pseudohynobius flavomaculatus a protected salamander in China, and biogeographical implications for the family Hynobiidae (Amphibia, Caudata)

  2022influential citation
• QuCo: quartet-based co-estimation of species trees and gene trees

  2022cites this paper
• Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus.

  2021cites this paper
• Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set

  2021cites this paper
• Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

  2021cites this paper
• Multilocus phylogeny and systematics of Iberian endemic Squalius (Actinopterygii, Leuciscidae)

  2020cites this paper
• One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

  2020cites this paper
• Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

  2020cites this paper
• Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae

  2020cites this paper
• One stop shop II: taxonomic update with molecular phylogeny for important phytopathogenic genera: 26–50 (2019)

  2019cites this paper
• Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta Complex) in the Colorado River

  2019cites this paper
• Taxonomic Uncertainty and Phylogenomics: Rescuing a Contentious Species Complex from the Anomaly Zone

  2019cites this paper
• Applications of the Coalescent for the Evolutionary Analysis of Genetic Data

  2019cites this paper
• Multi-allele species reconstruction using ASTRAL

  2018cites this paper
• Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae).

  2018cites this paper
• A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.

  2018cites this paper
• Assessing the Impacts of Positive Selection on Coalescent‐Based Species Tree Estimation and Species Delimitation

  2018cites this paper
• Adhemarius eurysthenes (Felder, 1874) (Lepidoptera, Sphingidae) in the Atlantic Rain Forest: A phylogeographic perspective

  2018cites this paper
• Chapter 9 Species Delimitation : A Decade After the Renaissance

  2017cites this paper
• To include or not to include: The impact of gene filtering on species tree estimation methods

  2017cites this paper
• Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

  2016influential citation
• Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards

  2016cites this paper
• The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.

  2016cites this paper
• Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses

  2016cites this paper
• Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony.

  2016cites this paper
• Taxonomy and evolution of endemic New Zealand broad-nosed weevils (Coleoptera: Curculionidae: Entiminae)

  2016cites this paper
• Maintenance of species integrity in the context of a recent radiation: the case of Jamesbrittenia (Scrophulariaceae: Limoselleae) in southern Africa

  2016cites this paper
• Notes on currently accepted species of Colletotrichum

  2016cites this paper
• Distribution of coalescent histories under the coalescent model with gene flow.

  2016cites this paper
• Combined next‐generation sequencing and morphology reveal fine‐scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus)

  2015cites this paper
• PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

  2015cites this paper
• The effects of inference method, population sampling, and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps).

  2015influential citation
• Contribuição de marcadores morfológicos e moleculares na elucidação da Sistemática de Ambulycini (Lepidoptera, Sphingidae, Smerinthinae)

  2015cites this paper
• Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies.

  2015cites this paper
• Post-molecular systematics and the future of phylogenetics.

  2015cites this paper
• New species of Ophiocordyceps unilateralis, an ubiquitous pathogen of ants from Thailand.

  2015cites this paper
• The Origin of Land Plants: A Phylogenomic Perspective

  2015cites this paper
• The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews.

  2015cites this paper
• Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

  2015cites this paper
• Estimating phylogenetic trees from genome‐scale data

  2015cites this paper
• Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean

  2015cites this paper
• THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES: POECILE)

  2014cites this paper
• How low can you go? The effects of mutation rate on the accuracy of species-tree estimation.

  2014cites this paper
• Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)

  2014cites this paper
• Systematics and Species Delimitation in New Guinea Skink Species Complexes (Squamata: Scincidae)

  2014influential citation
• Robustness to divergence time underestimation when inferring species trees from estimated gene trees.

  2014influential citation
• Scincidae ) . misleading signal in higher-level skink phylogeny ( Squamata : Detecting the anomaly zone in species trees and evidence for a

  2014cites this paper
• The influence of gene flow on species tree estimation: a simulation study.

  2014cites this paper
• An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

  2014cites this paper
• Species limits, phylogeographic and hybridization patterns in Neotropical leaf frogs (Phyllomedusinae)

  2014cites this paper
• Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers.

  2014cites this paper
• TESTING MITOCHONDRIAL CAPTURE AND DEEP COALESCENCE IN AMAZONIAN CICHLID FISHES (CICHLIDAE: CICHLA)

  2014cites this paper
• Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

  2014cites this paper
• Phylogeography of Heliconius cydno and its closest relatives: disentangling their origin and diversification

  2014cites this paper
• Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations.

  2014cites this paper
• Primate molecular phylogenetics in a genomic era.

  2013cites this paper
• Using biogeographical history to inform conservation: the case of Preble's meadow jumping mouse

  2013cites this paper
• A multilocus phylogenetic analysis of Escallonia (Escalloniaceae): diversification in montane South America.

  2013cites this paper
• Effects of missing data on species tree estimation under the coalescent.

  2013cites this paper
• Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis

  2013cites this paper
• Error in Phylogenetic Estimation for Bushes in the Tree of Life

  2013cites this paper
• Origin of land plants using the multispecies coalescent model.

  2013cites this paper
• Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal.

  2013cites this paper
• Bat Molecular Phylogenetics: Past, Present, and Future Directions

  2013cites this paper
• Exploring signals of historical demography in boreal mammals through integration of statistical conservation phylogenetics, taxonomy, and comparative phylogeography

  2013cites this paper
• Impact of Rates of Gene Duplication and Domain Shuffling on Species Tree Inference with Gene Tree Parsimony

  2013cites this paper
• The Species Problem - Ongoing Issues

  2013cites this paper
• Phylogenetic studies of New World species in the plant genus Psychotria (Rubiaceae)

  2013cites this paper
• Species Delimitation: A Decade After the Renaissance

  2013cites this paper
• Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci.

  2013influential citation
• A Molecular Phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and Its Implications for Classification, Biogeography and the Evolution of Host Plant Use

  2013cites this paper
• A species tree for the Australo-Papuan Fairy-wrens and allies (Aves: Maluridae).

  2012cites this paper
• Recurrent introgression of mitochondrial DNA among hares (Lepus spp.) revealed by species-tree inference and coalescent simulations.

  2012cites this paper
• The effects of sampling on delimiting species from multi-locus sequence data.

  2012cites this paper
• Phylogenetic footprints of an Antarctic radiation: the Trematominae (Notothenioidei, Teleostei).

  2012cites this paper
• Understanding How Stochasticity Impacts Reconstructions of Recent Species Divergent History.

  2012influential citation
• Is recombination a problem for species-tree analyses?

  2012influential citation
• Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae).

  2012influential citation
• Delineating the fishes of the Clinus superciliosus species complex in southern African waters (Blennioidei: Clinidae: Clinini), with the validation of Clinus arborescens Gilchrist & Thompson, 1908 and Clinus ornatus Gilchrist & Thompson, 1908, and with descriptions of two new species

  2012cites this paper
• Eight independent nuclear genes support monophyly of the plovers: the role of mutational variance in gene trees.

  2012cites this paper
• Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy.

  2012influential citation
• WHEN MOLECULES AND MORPHOLOGY CLASH: REVISITING SPECIES TREE RECONSTRUCTION OF AMBYSTOMATID SALAMANDERS USING MULTIPLE NUCLEAR LOCI

  2012cites this paper
• Random roots and lineage sorting.

  2012cites this paper
• A multi-locus phylogeny reveals a complex pattern of diversification related to climate and habitat heterogeneity in southern African white-eyes.

  2012cites this paper
• Coalescent-based species delimitation in an integrative taxonomy.

  2012cites this paper
• Multigene phylogenetic analyses to delimit new species in fungal plant pathogens.

  2012cites this paper