Target journal: Evolution Title: Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Unknown venue

• Publication date

  Unknown publication date

• Fields of study

  Not labeled

• Identifiers

  No identifiers available.

• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders.

  2016influential reference
• Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

  2016cited by this paper
• Phylogeny of the island archipelago frog genus Sanguirana: Another endemic Philippine radiation that diversified 'Out-of-Palawan'.

  2016influential reference
• The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards

  2016cited by this paper
• Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

  2015cited by this paper
• A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)

  2015cited by this paper
• Bayesian long branch attraction bias and corrections.

  2015cited by this paper
• PHYLUCE is a software package for the analysis of conserved genomic loci

  2015cited by this paper
• ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

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

  2015cited by this paper
• Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae).

  2015cited by this paper
• A phylogenomic analysis of turtles.

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

  2015cited by this paper
• Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

  2015cited by this paper
• Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.

  2015cited by this paper
• ASTRID: Accurate Species TRees from Internode Distances

  2015cited by this paper
• Phylogeny of frogs from the genus Physalaemus (Anura, Leptodactylidae) inferred from mitochondrial and nuclear gene sequences.

  2015cited by this paper
• Quartet Inference from SNP Data Under the Coalescent Model

  2014cited by this paper
• The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

  2014cited by this paper
• Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites.

  2014cited by this paper
• Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics

  2014cited by this paper
• The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy.

  2014cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

  2014cited by this paper
• RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

  2014influential reference
• Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

  2014cited by this paper
• BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

  2014influential reference
• From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

  2013influential reference
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

  2013influential reference
• Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales.

  2013cited by this paper
• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

  2013cited by this paper
• AN ADAPTIVE RADIATION OF FROGS IN A SOUTHEAST ASIAN ISLAND ARCHIPELAGO

  2013cited by this paper
• Robust Demographic Inference from Genomic and SNP Data

  2013influential reference
• Evolutionary Processes of Diversification in a Model Island Archipelago

  2013influential reference
• The palaeogeography of Sundaland and Wallacea since the Late Jurassic

  2013influential reference
• More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

  2012cited by this paper
• A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

  2012cited by this paper
• Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model

  2012cited by this paper
• A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

  2012cited by this paper
• Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing

  2012cited by this paper
• Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

  2012influential reference
• Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

  2012influential reference
• Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome.

  2012cited by this paper
• Targeted enrichment strategies for next-generation plant biology.

  2012cited by this paper
• Testing for ancient admixture between closely related populations.

  2011cited by this paper
• Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens.

  2011cited by this paper
• A framework for variation discovery and genotyping using next-generation DNA sequencing data

  2011cited by this paper
• Nuclear-mitochondrial discordance and gene flow in a recent radiation of toads.

  2011cited by this paper
• Adaptive Radiation and Ecological Opportunity in Sulawesi and Philippine Fanged Frog (Limnonectes) Communities

  2011cited by this paper
• New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

  2010influential reference
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010cited by this paper
• Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

  2010cited by this paper
• Phylogenetic Insights on Adaptive Radiation

  2010cited by this paper
• ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

  2010cited by this paper
• Frequent mitochondrial gene introgression among high elevation Tibetan megophryid frogs revealed by conflicting gene genealogies

  2009cited by this paper
• Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory

  2009cited by this paper
• Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings.

  2008cited by this paper
• Calculating bootstrap probabilities of phylogeny using multilocus sequence data.

  2008cited by this paper
• Global patterns of diversification in the history of modern amphibians

  2007cited by this paper
• Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

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

  2007cited by this paper
• Systematics and Zoogeography of Philippine Amphibia

  2007cited by this paper
• Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins.

  2007influential reference
• Inconsistency of phylogenetic estimates from concatenated data under coalescence.

  2007cited by this paper
• Discordance of Species Trees with Their Most Likely Gene Trees

  2006cited by this paper
• Mitogenomic perspectives on the origin and phylogeny of living amphibians.

  2005cited by this paper
• Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations

  2002influential reference
• Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

  2000cited by this paper

• Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification

  2023cites this paper
• Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

  2022cites this paper
• Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches.

  2022cites this paper
• State of the Amphibia 2020: A Review of Five Years of Amphibian Research and Existing Resources

  2022cites this paper
• Phylogenomics reveals the evolution, biogeography, and diversification history of voles in the Hengduan Mountains

  2022cites this paper
• Mitogenomic phylogeny of mud snails of the mostly Atlantic/Mediterranean genus Tritia (Gastropoda: Nassariidae)

  2021cites this paper
• Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

  2021cites this paper
• Pragmatic Assignment of Species Groups Based on Primary Species Hypotheses: The Case of a Dominant Component of the Southern Ocean Benthic Fauna

  2021cites this paper
• Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

  2021cites this paper
• Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene

  2021cites this paper
• Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses

  2021cites this paper
• Counteracting Forces of Introgressive Hybridization and Interspeci c Competition Shape the Morphological Traits of Cryptic Lberian Eptesicus Bats

  2021cites this paper
• DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi

  2021cites this paper
• Impact of the Miocene orogenesis on Kaloula spp. radiation, and implication of local refugia on genetic diversification.

  2021cites this paper
• Evolutionary impacts of introgressive hybridization in a rapidly evolving group of jumping spiders (F. Salticidae, Habronattus americanus group).

  2021cites this paper
• A New, Miniaturized Genus and Species of Snake (Cyclocoridae) from the Philippines

  2020cites this paper
• Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs.

  2020cites this paper
• Multilocus phylogeny of Bornean Bent-Toed Geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns.

  2020cites this paper
• Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana).

  2020cites this paper
• A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

  2020cites this paper
• Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny.

  2020cites this paper
• Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

  2020cites this paper
• FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

  2019cites this paper
• SuperCRUNCH: A toolkit for creating and manipulating supermatrices and other large phylogenetic datasets

  2019cites this paper
• Bridging the Process-Pattern Divide to Understand the Origins and Early Stages of Adaptive Radiation: A Review of Approaches With Insights From Studies of Anolis Lizards.

  2019cites this paper
• Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana)

  2019cites this paper
• Untangling relationships among terraranan frogs: a phylogenomic approach based on 2,665 loci

  2019cites this paper
• Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements.

  2019cites this paper
• Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization

  2019cites this paper
• SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space.

  2018cites this paper
• Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing

  2018cites this paper
• Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

  2018cites this paper
• The first complete genomes of Metalmarks and the classification of butterfly families.

  2017cites this paper
• Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

  2017cites this paper