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

[1]  J. Wiens,et al.  Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs , 2023, Molecular biology and evolution.

[2]  W. Duellman,et al.  Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae) , 2023, Genome biology and evolution.

[3]  J. Wiens,et al.  The evolution of reproductive modes and life cycles in amphibians , 2022, Nature Communications.

[4]  A. Allison,et al.  Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs. , 2022, Molecular phylogenetics and evolution.

[5]  Z. Nagy,et al.  Systematic position of the Clicking Frog (Kassinula Laurent, 1940), the problem of chimeric sequences and the revised classification of the family Hyperoliidae. , 2022, Molecular phylogenetics and evolution.

[6]  C. Venditti,et al.  Terrestrial reproduction and parental care drive rapid evolution in the trade-off between offspring size and number across amphibians , 2022, PLoS biology.

[7]  Asif U. Tamuri,et al.  A species-level timeline of mammal evolution integrating phylogenomic data , 2021, Nature.

[8]  Juan M. Guayasamin,et al.  Phylogenetic position of “Cochranella” megista (Anura: Centrolenidae) and first records for Ecuador , 2021, Phyllomedusa: Journal of Herpetology.

[9]  J. Wiens,et al.  Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses , 2021, Systematics and Biodiversity.

[10]  R. Vilà,et al.  DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies , 2021, Systematic biology.

[11]  Daniel M Portik,et al.  Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? , 2020, Systematic biology.

[12]  Jeremy M. Brown,et al.  Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life , 2020, Systematic biology.

[13]  John J. Wiens,et al.  SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets , 2020, Methods in Ecology and Evolution.

[14]  C. Haddad,et al.  The phylogeny of the Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini) , 2020, Cladistics : the international journal of the Willi Hennig Society.

[15]  Jeffrey W. Streicher,et al.  Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs. , 2020, Molecular phylogenetics and evolution.

[16]  W. Jetz,et al.  Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation , 2019, PLoS biology.

[17]  Rafe M. Brown,et al.  FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales , 2019, bioRxiv.

[18]  N. Knowlton,et al.  GenBank is a reliable resource for 21st century biodiversity research , 2019, Proceedings of the National Academy of Sciences.

[19]  A. Furness,et al.  The evolution of parental care diversity in amphibians , 2019, Nature Communications.

[20]  Dan Liang,et al.  A large-scale phylogeny of Microhylidae inferred from a combined dataset of 121 genes and 427 taxa. , 2018, Molecular phylogenetics and evolution.

[21]  V. Ranwez,et al.  MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons , 2018, Molecular biology and evolution.

[22]  Jens,et al.  Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians , 2018, bioRxiv.

[23]  O. Flores-Villela,et al.  Systematics of the frogs allocated to Sarcohyla bistincta sensu lato (Cope, 1877), with description of a new species from Western Mexico. , 2018, Zootaxa.

[24]  W. Jetz,et al.  The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life , 2018, Nature Ecology & Evolution.

[25]  A. J. Crawford,et al.  Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci. , 2018, Molecular phylogenetics and evolution.

[26]  J. Wiens,et al.  Rapid Diversification and Time Explain Amphibian Richness at Different Scales in the Tropical Andes, Earth’s Most Biodiverse Hotspot , 2017, The American Naturalist.

[27]  D. Wake,et al.  Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary , 2017, Proceedings of the National Academy of Sciences.

[28]  W. Wheeler,et al.  Nomenclatural stability does not justify recognition of paraphyletic taxa: A response to Scherz et al. (2016). , 2017, Molecular phylogenetics and evolution.

[29]  Antonis Rokas,et al.  Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets , 2017, bioRxiv.

[30]  J. Wiens,et al.  Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families , 2017, The American Naturalist.

[31]  Robert Lanfear,et al.  PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. , 2016, Molecular biology and evolution.

[32]  K. Beard,et al.  Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status , 2016 .

[33]  K. Bi,et al.  An evaluation of transcriptome‐based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura) , 2016, Molecular ecology resources.

[34]  M. Vences,et al.  Reconciling molecular phylogeny, morphological divergence and classification of Madagascan narrow-mouthed frogs (Amphibia: Microhylidae). , 2016, Molecular phylogenetics and evolution.

[35]  W. Wheeler,et al.  The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae) , 2016, Cladistics : the international journal of the Willi Hennig Society.

[36]  Travis C Glenn,et al.  Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). , 2016, Molecular biology and evolution.

[37]  Liang Liu,et al.  The Impact of Missing Data on Species Tree Estimation. , 2016, Molecular biology and evolution.

[38]  T. Papenfuss,et al.  Historical biogeography resolves the origins of endemic Arabian toad lineages (Anura: Bufonidae): Evidence for ancient vicariance and dispersal events with the Horn of Africa and South Asia , 2015, BMC Evolutionary Biology.

[39]  D. Cannatella,et al.  Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae) , 2015 .

[40]  J. Wiens,et al.  Do missing data influence the accuracy of divergence-time estimation with BEAST? , 2015, Molecular phylogenetics and evolution.

[41]  L. Rowe,et al.  Independent evolution of the sexes promotes amphibian diversification , 2015, Proceedings of the Royal Society B: Biological Sciences.

[42]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[43]  Hong Wang,et al.  Should genes with missing data be excluded from phylogenetic analyses? , 2014, Molecular phylogenetics and evolution.

[44]  A. Pyron,et al.  Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. , 2014, Systematic biology.

[45]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[46]  R. A. Pyron,et al.  Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity , 2013, Proceedings of the Royal Society B: Biological Sciences.

[47]  Dan Liang,et al.  A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata. , 2013, Molecular biology and evolution.

[48]  Juan M. Guayasamin,et al.  Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns. , 2013, Ecology letters.

[49]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[50]  W. Jetz,et al.  The global diversity of birds in space and time , 2012, Nature.

[51]  Brian C. O'Meara,et al.  treePL: divergence time estimation using penalized likelihood for large phylogenies , 2012, Bioinform..

[52]  A. Lemmon,et al.  Anchored hybrid enrichment for massively high-throughput phylogenomics. , 2012, Systematic biology.

[53]  J. Wiens,et al.  Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling , 2012, PloS one.

[54]  A. Pyron,et al.  A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. , 2011, Molecular phylogenetics and evolution.

[55]  J. Wiens,et al.  Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. , 2011, Systematic biology.

[56]  Cynthia Parr,et al.  Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? , 2011, Systematic biology.

[57]  Mike Steel,et al.  Terraces in Phylogenetic Tree Space , 2011, Science.

[58]  Mark A. Miller,et al.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).

[59]  S. Loader,et al.  Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot , 2009, BMC Evolutionary Biology.

[60]  Jeremy M. Brown,et al.  The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference , 2009, Systematic biology.

[61]  S. Hedges,et al.  New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation , 2008 .

[62]  D. Gower,et al.  Global patterns of diversification in the history of modern amphibians , 2007, Proceedings of the National Academy of Sciences.

[63]  R. Henrik Nilsson,et al.  Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective , 2006, PloS one.

[64]  D. Hillis,et al.  Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae. , 2006, Systematic biology.

[65]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[66]  W. Wheeler,et al.  SYSTEMATIC REVIEW OF THE FROG FAMILY HYLIDAE, WITH SPECIAL REFERENCE TO HYLINAE: PHYLOGENETIC ANALYSIS AND TAXONOMIC REVISION , 2005 .

[67]  J. Wiens,et al.  Hylid frog phylogeny and sampling strategies for speciose clades. , 2005, Systematic biology.

[68]  J. Wiens.  Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? , 2005, Systematic biology.

[69]  P. Holland,et al.  Phylogenomics of eukaryotes: impact of missing data on large alignments. , 2004, Molecular biology and evolution.

[70]  J. Wiens.  Missing data, incomplete taxa, and phylogenetic accuracy. , 2003, Systematic biology.

[71]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[72]  K. McGrath,et al.  Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). , 2018, Molecular phylogenetics and evolution.

[73]  R. Murphy,et al.  A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae). , 2017, Molecular phylogenetics and evolution.

[74]  J. Wiens,et al.  How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards. , 2016, Systematic biology.

[75]  J. Wiens,et al.  Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. , 2016, Molecular phylogenetics and evolution.

[76]  K. Schliep.  Bioinformatics Applications Note Phylogenetics Phangorn: Phylogenetic Analysis in R , 2010 .

[77]  Graziano Pesole,et al.  BMC Evolutionary Biology BioMed Central , 2007 .

[78]  P. Moler,et al.  THE AMPHIBIAN TREE OF LIFE , 2006 .

[79]  I. Das,et al.  A new species of kaloula (anura: microhylidae)from north-eastern India , 2004 .

[80]  M. Sanderson.  Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.