(Q30991088)

28 June 2017

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

1 reference

28 June 2017

1 reference

1 reference

3

John J Wiens

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28 June 2017

1

Jeffrey W Streicher

1 reference

28 June 2017

James A Schulte

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

1 reference

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

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

21 January 2018

1 reference

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

Ultraconserved Elements in the Human Genome

21 January 2018

1 reference

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

1 reference

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

Trimmomatic: a flexible trimmer for Illumina sequence data

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

A phylogenomic analysis of turtles

21 January 2018

1 reference

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

Prospects for building the tree of life from large sequence databases

21 January 2018

1 reference

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

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

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

High-resolution species trees without concatenation

21 January 2018

1 reference

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

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

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

Effects of missing data on species tree estimation under the coalescent

21 January 2018

1 reference

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

1 reference

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

Should genes with missing data be excluded from phylogenetic analyses?

21 January 2018

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

Anchored hybrid enrichment for massively high-throughput phylogenomics

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

Estimating species trees from unrooted gene trees.

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

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

Next-generation phylogenetics takes root

21 January 2018

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

1 reference

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

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

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

Vicariant origin of malagasy reptiles supports late cretaceous antarctic land bridge

21 January 2018

1 reference

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

APE: Analyses of Phylogenetics and Evolution in R language

21 January 2018

1 reference

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

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

1 reference

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

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

Incomplete taxon sampling is not a problem for phylogenetic inference

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

Inferring phylogenies from RAD sequence data

21 January 2018

1 reference

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

1 reference

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

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

21 January 2018

1 reference

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

STRAW: Species TRee Analysis Web server

21 January 2018

1 reference

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

Divergent maximum-likelihood-branch-support values for polytomies

21 January 2018

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

Missing data, incomplete taxa, and phylogenetic accuracy

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

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

21 January 2018

1 reference

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

1 reference

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

1 reference

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

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

21 January 2018

1 reference

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

1 reference

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

Increased taxon sampling greatly reduces phylogenetic error

21 January 2018

1 reference

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

21 January 2018

Taxon sampling revisited

1 reference

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