Missing data in phylogenetic analysis: reconciling results from simulations and empirical data (Q33857350)

29 July 2017

title

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

1 reference

phylogenetic reconciliation

29 July 2017

1 reference

1 reference

1 reference

1

1 reference

29 July 2017

Matthew C Morrill

2

1 reference

29 July 2017

publication date

28 March 2011

1 reference

29 July 2017

1 reference

29 July 2017

volume

60

1 reference

29 July 2017

issue

5

1 reference

29 July 2017

page(s)

719-731

1 reference

Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence

29 July 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Fossils impact as hard as living taxa in parsimony analyses of morphology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Systematics of Mustelid-Like Carnivores

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Prospects for building the tree of life from large sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

High-resolution species trees without concatenation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

The Amphibian Tree of Life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

MaxAlign: maximizing usable data in an alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

A Revised Phylogeny of Holarctic Treefrogs (Genus Hyla) Based on Nuclear and Mitochondrial DNA Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

MRBAYES: Bayesian inference of phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Can parallel diversification occur in sympatry? Repeated patterns of body-size evolution in coexisting clades of North American salamanders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

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%2FSYR025

Polytomies and Bayesian phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Did egg-laying boas break Dollo's law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Extreme morphological and ecological homoplasy in tropical salamanders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogeny of North American fireflies (Coleoptera: Lampyridae): implications for the evolution of light signals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Missing data, incomplete taxa, and phylogenetic accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Missing data and the design of phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Global patterns of diversification and species richness in amphibians

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Loss and re-evolution of complex life cycles in marsupial frogs: does ancestral trait reconstruction mislead?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Evolutionary and biogeographic origins of high tropical diversity in old world frogs (Ranidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYR025

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYR025

1 reference

29 July 2017

1 reference