How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards (Q30991088)

28 June 2017

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards (English)

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28 June 2017

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3

John J Wiens

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28 June 2017

Jeffrey W Streicher

1

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PubMed ID

26330450

28 June 2017

James A Schulte

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2

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28 June 2017

1 September 2015

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28 June 2017

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28 June 2017

65

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28 June 2017

1

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28 June 2017

128-145

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The genome of the green anole lizard and a comparative analysis with birds and mammals

28 June 2017

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RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Ultraconserved Elements in the Human Genome

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Contrasting global-scale evolutionary radiations: phylogeny, diversification, and morphological evolution in the major clades of iguanian lizards

21 January 2018

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Trimmomatic: a flexible trimmer for Illumina sequence data

21 January 2018

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Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

21 January 2018

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Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

21 January 2018

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More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

21 January 2018

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A phylogenomic analysis of turtles

21 January 2018

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Prospects for building the tree of life from large sequence databases

21 January 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

High-resolution species trees without concatenation

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

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A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

21 January 2018

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Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

21 January 2018

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Is it better to add taxa or characters to a difficult phylogenetic problem?

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Bayesian inference of species trees from multilocus data

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Effects of missing data on species tree estimation under the coalescent

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Should genes with missing data be excluded from phylogenetic analyses?

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

21 January 2018

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The accuracy of species tree estimation under simulation: a comparison of methods

21 January 2018

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A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

21 January 2018

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Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Anchored hybrid enrichment for massively high-throughput phylogenomics

21 January 2018

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The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

21 January 2018

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Estimating species trees from unrooted gene trees.

21 January 2018

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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

21 January 2018

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Estimating species phylogenies using coalescence times among sequences.

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Next-generation phylogenetics takes root

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Vicariant origin of malagasy reptiles supports late cretaceous antarctic land bridge

21 January 2018

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APE: Analyses of Phylogenetics and Evolution in R language

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Incomplete taxon sampling is not a problem for phylogenetic inference

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Inferring phylogenies from RAD sequence data

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

STRAW: Species TRee Analysis Web server

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Divergent maximum-likelihood-branch-support values for polytomies

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

21 January 2018

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Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

21 January 2018

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The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach.

21 January 2018

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Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

21 January 2018

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Does adding characters with missing data increase or decrease phylogenetic accuracy?

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Missing data, incomplete taxa, and phylogenetic accuracy

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Missing data in phylogenetic analysis: reconciling results from simulations and empirical data

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

Increased taxon sampling greatly reduces phylogenetic error

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

21 January 2018

Taxon sampling revisited

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV058

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYV058

1 reference

28 June 2017

1 reference

PubMed ID

26330450