How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards
出版年份 2015 全文链接
标题
How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards
作者
关键词
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出版物
SYSTEMATIC BIOLOGY
Volume 65, Issue 1, Pages 128-145
出版商
Oxford University Press (OUP)
发表日期
2015-09-02
DOI
10.1093/sysbio/syv058
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
- (2015) Adam D. Leaché et al. Genome Biology and Evolution
- When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
- (2015) Shea M. Lambert et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- A phylogenomic analysis of turtles
- (2015) Nicholas G. Crawford et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa
- (2015) Tod W. Reeder et al. PLoS One
- ASTRAL: genome-scale coalescent-based species tree estimation
- (2014) S. Mirarab et al. BIOINFORMATICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs
- (2014) Jeffrey W. Streicher et al. MOLECULAR ECOLOGY
- Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
- (2014) Brant C. Faircloth et al. Molecular Ecology Resources
- Should genes with missing data be excluded from phylogenetic analyses?
- (2014) Wei Jiang et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Divergent maximum-likelihood-branch-support values for polytomies
- (2014) Mark P. Simmons et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification
- (2014) Adam D. Leaché et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach
- (2014) K. Sun et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
- (2014) Zhenxiang Xi et al. SYSTEMATIC BIOLOGY
- Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
- (2014) Siavash Mirarab et al. SYSTEMATIC BIOLOGY
- Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
- (2014) Huateng Huang et al. SYSTEMATIC BIOLOGY
- High-Throughput Genomic Data in Systematics and Phylogenetics
- (2013) Emily Moriarty Lemmon et al. Annual Review of Ecology Evolution and Systematics
- A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
- (2013) R Pyron et al. BMC EVOLUTIONARY BIOLOGY
- RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
- (2013) B. Arnold et al. MOLECULAR ECOLOGY
- Effects of missing data on species tree estimation under the coalescent
- (2013) Rasmus Hovmöller et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- STRAW: Species TRee Analysis Web server
- (2013) Timothy I. Shaw et al. NUCLEIC ACIDS RESEARCH
- A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
- (2013) John E. McCormack et al. PLoS One
- Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
- (2013) Brian Tilston Smith et al. SYSTEMATIC BIOLOGY
- Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
- (2013) Marie Cariou et al. Ecology and Evolution
- Contrasting global-scale evolutionary radiations: phylogeny, diversification, and morphological evolution in the major clades of iguanian lizards
- (2012) Thomas Blankers et al. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
- (2012) N. G. Crawford et al. Biology Letters
- Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
- (2012) J. J. Wiens et al. Biology Letters
- Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
- (2012) Lecong Zhou et al. BMC GENOMICS
- Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
- (2012) N. Rohland et al. GENOME RESEARCH
- Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
- (2012) Béatrice Roure et al. MOLECULAR BIOLOGY AND EVOLUTION
- Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
- (2012) David Bryant et al. MOLECULAR BIOLOGY AND EVOLUTION
- Next-generation phylogenetics takes root
- (2012) John E. McCormack et al. MOLECULAR ECOLOGY
- Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
- (2012) Catherine E. Wagner et al. MOLECULAR ECOLOGY
- Inferring Phylogenies from RAD Sequence Data
- (2012) Benjamin E. R. Rubin et al. PLoS One
- Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
- (2012) John J. Wiens et al. PLoS One
- Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
- (2012) Alan R. Lemmon et al. SYSTEMATIC BIOLOGY
- Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
- (2012) Brant C. Faircloth et al. SYSTEMATIC BIOLOGY
- Phylogenetic Insights on Evolutionary Novelties in Lizards and Snakes: Sex, Birth, Bodies, Niches, and Venom
- (2011) Jack W. Sites et al. Annual Review of Ecology Evolution and Systematics
- Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
- (2011) J. E. McCormack et al. GENOME RESEARCH
- Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation
- (2011) Ted M. Townsend et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- The genome of the green anole lizard and a comparative analysis with birds and mammals
- (2011) Jessica Alföldi et al. NATURE
- Estimating Species Trees from Unrooted Gene Trees
- (2011) Liang Liu et al. SYSTEMATIC BIOLOGY
- Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
- (2011) John J. Wiens et al. SYSTEMATIC BIOLOGY
- A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
- (2010) Liang Liu et al. BMC EVOLUTIONARY BIOLOGY
- The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
- (2010) Adam D. Leaché et al. SYSTEMATIC BIOLOGY
- Bayesian Inference of Species Trees from Multilocus Data
- (2009) J. Heled et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
- (2009) Alan R. Lemmon et al. SYSTEMATIC BIOLOGY
- Estimating Species Phylogenies Using Coalescence Times among Sequences
- (2009) Liang Liu et al. SYSTEMATIC BIOLOGY
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
- (2008) T.-K. Seo MOLECULAR BIOLOGY AND EVOLUTION
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