Bayesian inference of species trees from multilocus data.

Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol (2012) 32.00

BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol (2014) 6.16

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol (2013) 3.61

Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A (2010) 3.56

Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A (2011) 2.53

Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics (2011) 2.30

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol (2012) 2.20

The Colletotrichum gloeosporioides species complex. Stud Mycol (2012) 2.02

ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics (2014) 1.88

Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82

Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol (2010) 1.74

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc Biol Sci (2010) 1.66

Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun (2014) 1.62

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biol Lett (2012) 1.51

Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst Biol (2011) 1.50

Body Size Adaptations to Altitudinal Climatic Variation in Neotropical Grasshoppers of the Genus Sphenarium (Orthoptera: Pyrgomorphidae). PLoS One (2015) 1.45

Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry. PLoS One (2015) 1.45

Application of the phylogenetic species concept to Wallemia sebi from house dust and indoor air revealed by multi-locus genealogical concordance. PLoS One (2015) 1.43

Alpine endemic spiders shed light on the origin and evolution of subterranean species. PeerJ (2015) 1.42

Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito. Evolution (2013) 1.42

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. PLoS Genet (2016) 1.40

Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol (2012) 1.39

Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits. BMC Evol Biol (2015) 1.39

Species delimitation and global biosecurity. Evol Bioinform Online (2011) 1.36

As Old as the hills: montane scorpions in Southwestern North America reveal ancient associations between biotic diversification and landscape history. PLoS One (2013) 1.36

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genet (2012) 1.35

Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Mol Biol Evol (2010) 1.34

Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea). PLoS One (2014) 1.22

A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum). Proc Natl Acad Sci U S A (2011) 1.21

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics (2015) 1.21

The evolutionary history of Plasmodium vivax as inferred from mitochondrial genomes: parasite genetic diversity in the Americas. Mol Biol Evol (2013) 1.18

Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One (2011) 1.17

Quartet inference from SNP data under the coalescent model. Bioinformatics (2014) 1.15

Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation. BMC Evol Biol (2011) 1.15

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J Math Biol (2010) 1.13

Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders. BMC Evol Biol (2013) 1.13

Homoploid hybrid speciation and genome evolution via chromosome sorting. Proc Biol Sci (2015) 1.12

Bayesian selection of nucleotide substitution models and their site assignments. Mol Biol Evol (2012) 1.12

Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol Biol Evol (2014) 1.10

Computational approaches to species phylogeny inference and gene tree reconciliation. Trends Ecol Evol (2013) 1.10

Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama. Proc Biol Sci (2012) 1.10

Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines. Proc Biol Sci (2012) 1.09

Species delimitation using genome-wide SNP data. Syst Biol (2014) 1.08

Fast and accurate methods for phylogenomic analyses. BMC Bioinformatics (2011) 1.07

STRAW: Species TRee Analysis Web server. Nucleic Acids Res (2013) 1.05

Improved reversible jump algorithms for Bayesian species delimitation. Genetics (2013) 1.05

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proc Biol Sci (2012) 1.04

Integrated Bayesian species delimitation and morphological diagnostics of chorioptic mange mites (Acariformes: Psoroptidae: Chorioptes). Parasitol Res (2014) 1.04

Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host. BMC Evol Biol (2013) 1.02

Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes). PLoS One (2014) 1.01

A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites. BMC Evol Biol (2011) 1.01

Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol (2012) 1.00

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS One (2011) 1.00

Hybridization and long-distance colonization at different time scales: towards resolution of long-term controversies in the sweet vernal grasses (Anthoxanthum). Ann Bot (2013) 1.00

On the need for mechanistic models in computational genomics and metagenomics. Genome Biol Evol (2013) 0.99

Multilocus species trees show the recent adaptive radiation of the mimetic heliconius butterflies. Syst Biol (2015) 0.99

Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata). PLoS One (2013) 0.98

A hairy case: The evolution of filtering carnivorous Drusinae (Limnephilidae, Trichoptera). Mol Phylogenet Evol (2015) 0.97

A novel widespread cryptic species and phylogeographic patterns within several giant clam species (Cardiidae: Tridacna) from the Indo-Pacific Ocean. PLoS One (2013) 0.97

Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions. PLoS One (2011) 0.97

The inference of gene trees with species trees. Syst Biol (2014) 0.97

Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol (2012) 0.96

What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol (2011) 0.96

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol (2011) 0.96

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96

Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China. PLoS One (2012) 0.94

Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Syst Biol (2011) 0.94

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders. BMC Evol Biol (2011) 0.94

Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin. PLoS One (2015) 0.94

Cryptic speciation patterns in Iranian rock lizards uncovered by integrative taxonomy. PLoS One (2013) 0.93

Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives. PLoS One (2012) 0.93

Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Ann Bot (2014) 0.92

A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Mol Phylogenet Evol (2014) 0.92

Lineage-specific late pleistocene expansion of an endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan. BMC Evol Biol (2011) 0.92

Origin and diversification of Lake Ohrid's endemic acroloxid limpets: the role of geography and ecology. BMC Evol Biol (2016) 0.91

Simulating gene trees under the multispecies coalescent and time-dependent migration. BMC Evol Biol (2013) 0.91

Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies. PLoS One (2012) 0.91

Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proc Biol Sci (2014) 0.91

Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions. PLoS Curr (2015) 0.91

The evolutionary host switches of Polychromophilus: a multi-gene phylogeny of the bat malaria genus suggests a second invasion of mammals by a haemosporidian parasite. Malar J (2012) 0.90

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores). Ann Bot (2013) 0.90

Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS One (2012) 0.90

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers. BMC Evol Biol (2011) 0.89

A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Sci Rep (2014) 0.89

Hybrid speciation in a marine mammal: the clymene dolphin (Stenella clymene). PLoS One (2014) 0.89

Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. PLoS One (2012) 0.89

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Mol Ecol (2016) 0.88

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods. Ann Bot (2013) 0.88

Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. BMC Evol Biol (2014) 0.88

Origin and domestication of papaya Yh chromosome. Genome Res (2015) 0.88

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol Biol Evol (2013) 0.88

Flying rocks and flying clocks: disparity in fossil and molecular dates for birds. Proc Biol Sci (2014) 0.88

Molecular evolution and phylogenetics of rodent malaria parasites. BMC Evol Biol (2012) 0.88

Disk covering methods improve phylogenomic analyses. BMC Genomics (2014) 0.87

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa. BMC Evol Biol (2011) 0.87

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea). Ecol Evol (2013) 0.87

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth. Proc Biol Sci (2016) 0.87

Supertrees Based on the Subtree Prune-and-Regraft Distance. Syst Biol (2014) 0.87

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. PLoS One (2015) 0.87

Population structure, mitochondrial polyphyly and the repeated loss of human biting ability in anopheline mosquitoes from the southwest Pacific. Mol Ecol (2012) 0.87

Inference of population structure using multilocus genotype data. Genetics (2000) 147.76

MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (2001) 101.31

BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13

Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56

Evolutionary relationship of DNA sequences in finite populations. Genetics (1983) 40.67

Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68

Sampling theory for neutral alleles in a varying environment. Philos Trans R Soc Lond B Biol Sci (1994) 10.92

Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature (2003) 10.73

Relationships between gene trees and species trees. Mol Biol Evol (1988) 8.63

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79

Genealogical inference from microsatellite data. Genetics (1998) 7.74

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A (2007) 5.64

A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol (1994) 5.26

Consequences of recombination on traditional phylogenetic analysis. Genetics (2000) 5.01

Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol (2009) 4.91

The conditioned reconstructed process. J Theor Biol (2008) 4.69

Inferring phylogeny despite incomplete lineage sorting. Syst Biol (2006) 4.25

Bayesian inference of population size history from multiple loci. BMC Evol Biol (2008) 4.23

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol (2007) 4.13

Discordance of species trees with their most likely gene trees. PLoS Genet (2006) 3.58

Is a new and general theory of molecular systematics emerging? Evolution (2009) 3.44

Inference of population structure under a Dirichlet process model. Genetics (2007) 3.42

Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol (2007) 3.31

STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics (2009) 2.70

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol (2005) 2.64

Optimal sequencing strategies for surveying molecular genetic diversity. Genetics (1996) 2.47

Estimating species phylogenies using coalescence times among sequences. Syst Biol (2009) 2.42

Phylogenetic relationships and evolutionary processes in East African cichlid fishes. Trends Ecol Evol (1993) 2.29

Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol (2009) 2.14

Estimating species trees using multiple-allele DNA sequence data. Evolution (2008) 1.50

Properties of consensus methods for inferring species trees from gene trees. Syst Biol (2009) 1.43

Inferring the population structure and demography of Drosophila ananassae from multilocus data. Genetics (2004) 1.38

Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol (2008) 1.35

Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst Biol (2009) 1.34

Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Syst Biol (2009) 1.31

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles. Proc Biol Sci (2004) 1.26

What is the danger of the anomaly zone for empirical phylogenetics? Syst Biol (2009) 1.15

Phylogenetic analysis in the anomaly zone. Syst Biol (2009) 1.14

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst Biol (2009) 1.05

Bayesian phylogeography finds its roots. PLoS Comput Biol (2009) 10.99

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42

Rise and fall of the Beringian steppe bison. Science (2004) 7.91

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol (2005) 6.77

The molecular population genetics of HIV-1 group O. Genetics (2004) 4.53

Bayesian inference of population size history from multiple loci. BMC Evol Biol (2008) 4.23

Mapping the origins and expansion of the Indo-European language family. Science (2012) 3.76

Accommodating the effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol (2008) 3.07

Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst Biol (2011) 2.94

A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol (2010) 2.73

mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. Mol Biol Evol (2007) 2.67

Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol (2011) 2.37

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol Biol Evol (2007) 2.34

Guided tree topology proposals for Bayesian phylogenetic inference. Syst Biol (2011) 2.32

Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics (2011) 2.30

Evidence for time dependency of molecular rate estimates. Syst Biol (2007) 2.26

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol (2007) 2.25

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol Biol Evol (2005) 2.22

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol (2012) 2.13

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A (2012) 2.07

Estimating the basic reproductive number from viral sequence data. Mol Biol Evol (2011) 1.86

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol Phylogenet Evol (2005) 1.79

A virus reveals population structure and recent demographic history of its carnivore host. Science (2006) 1.78

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. J R Soc Interface (2014) 1.42

Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol (2007) 1.39

Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proc Biol Sci (2009) 1.31

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol Biol (2006) 1.27

Influenza a virus migration and persistence in North American wild birds. PLoS Pathog (2013) 1.19

Bayesian selection of nucleotide substitution models and their site assignments. Mol Biol Evol (2012) 1.12

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. Infect Genet Evol (2011) 1.12

A stochastic simulator of birth-death master equations with application to phylodynamics. Mol Biol Evol (2013) 1.12

How accurate and robust are the phylogenetic estimates of Austronesian language relationships? PLoS One (2010) 1.11

Neotenous origins for pelagic octopuses. Curr Biol (2004) 1.01

Simulating gene trees under the multispecies coalescent and time-dependent migration. BMC Evol Biol (2013) 0.91

Recursive algorithms for phylogenetic tree counting. Algorithms Mol Biol (2013) 0.86

Ancient DNA: would the real Neandertal please stand up? Curr Biol (2004) 0.83

Tree measures and the number of segregating sites in time-structured population samples. BMC Genet (2005) 0.76

Extinction times in autocatalytic systems. J Phys Chem A (2010) 0.75