Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes (Q35804034)

From Wikidata

Jump to navigation Jump to search

scientific article published on 12 October 2015

Language	Label	Description	Also known as
English	Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes	scientific article published on 12 October 2015

Statements

scholarly article

1 reference

Europe PubMed Central

10 August 2017

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes (English)

1 reference

Europe PubMed Central

10 August 2017

1 reference

based on heuristic

inferred from title

Emily Moriarty Lemmon

4

object named as

Emily Moriarty Lemmon

1 reference

Europe PubMed Central

10 August 2017

3

object named as

Alan R Lemmon

1 reference

Europe PubMed Central

10 August 2017

Frank T. Burbrink

5

object named as

Frank T Burbrink

1 reference

Europe PubMed Central

10 August 2017

1

object named as

Sara Ruane

1 reference

Europe PubMed Central

10 August 2017

author name string

Christopher J Raxworthy

2

1 reference

Europe PubMed Central

10 August 2017

publication date

12 October 2015

1 reference

Europe PubMed Central

10 August 2017

BMC Evolutionary Biology

1 reference

Europe PubMed Central

10 August 2017

15

1 reference

Europe PubMed Central

10 August 2017

221

1 reference

Europe PubMed Central

10 August 2017

https://scigraph.springernature.com/pub.10.1186/s12862-015-0503-1

0 references

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

The influence of sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

The influence of gene flow on species tree estimation: a simulation study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

STRAW: Species TRee Analysis Web server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Island evolution and systematic revision of Comoran snakes: why and when subspecies still make sense

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

jModelTest 2: more models, new heuristics and parallel computing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Anchored hybrid enrichment for massively high-throughput phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

phangorn: phylogenetic analysis in R

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Illumina sequencing library preparation for highly multiplexed target capture and sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Bayesian inference of species trees from multilocus data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Madagascar as a model region of species diversification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

High-resolution species trees without concatenation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Inferring phylogeny despite incomplete lineage sorting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

27 July 2018

Estimating phylogenetic trees from genome-scale data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Practical performance of tree comparison metrics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

A taxonomic mystery for more than 150 years: Identity, systematic position and Malagasy origin of the snake Elapotinus picteti Jan, 1862, and synonymy of Exallodontophis Cadle, 1999 (Serpentes: Lamprophiidae)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Estimating optimal species trees from incomplete gene trees under deep coalescence.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Bayesian phylogenetics with BEAUti and the BEAST 1.7

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Species trees from highly incongruent gene trees in rice.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Estimating species phylogenies using coalescence times among sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Trees of trees: an approach to comparing multiple alternative phylogenies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Multiple colonization of Madagascar and Socotra by colubrid snakes: evidence from nuclear and mitochondrial gene phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Genome-scale approaches to resolving incongruence in molecular phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4603904

25 September 2018

Genital morphology and systematics of Geodipsas Boulenger, 1896 (Reptilia: Serpentes: Colubridae), with description of a new genus

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

A new black-bellied snake (Pseudoxyrhophiinae: Liophidium) from western Madagascar, with notes on the genus Pararhadinaea

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Molecular phylogeny and systematics of the pseudoxyrhophiine snake genus Liopholidophis (Reptilia, Colubridae): evolution of its exceptional sexual dimorphism and descriptions of new taxa

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Systematics of the snake genera Stenophis and Lycodryas from Madagascar and the Comoros

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Phylogenetic relationships of a new species of pseudoxyrhophiine snake (Reptilia: Lamprophiidae: Thamnosophis) suggest a biogeographical link between western and northern Madagascar

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Error in Phylogenetic Estimation for Bushes in the Tree of Life

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

NEW RECORDS OFLEIOHETERODON MADAGASCARIENSIS(REPTILIA: COLUBRIDAE) FROM THE COMOROS

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene

1 reference

https://api.crossref.org/works/10.1186%2FS12862-015-0503-1

21 January 2018

Identifiers

10.1186/S12862-015-0503-1

1 reference

Europe PubMed Central

10 August 2017

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

10 August 2017

1 reference

Europe PubMed Central

10 August 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q35804034&oldid=2118736691"