Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades (Q21093400)

5 August 2022

4

Tal Pupko

Tal

Pupko

1 reference

5 August 2022

3

Osnat Penn

Osnat

Penn

1 reference

5 August 2022

Shani Blanga-Kanfi

1

Shani

Blanga-Kanfi

1 reference

1048764548

5 August 2022

Hector Miranda

series ordinal

2

author given names

Hector

author last names

Miranda

1 reference

1048764548

5 August 2022

Ronald W DeBry

series ordinal

5

author given names

Ronald W

author last names

DeBry

1 reference

1048764548

https://scigraph.springernature.com/pub.10.1186/1471-2148-9-71

5 August 2022

language of work or name

English

0 references

publication date

2009

0 references

published in

BMC Evolutionary Biology

0 references

volume

9

0 references

issue

1

0 references

page(s)

71

0 references

exact match

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2148-9-71

cites work

Multiple molecular evidences for a living mammalian fossil

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Retroposed elements as archives for the evolutionary history of placental mammals

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

ProbCons: Probabilistic consistency-based multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

MAFFT version 5: improvement in accuracy of multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Codon-substitution models for heterogeneous selection pressure at amino acid sites

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

ProtTest: selection of best-fit models of protein evolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

MrBayes 3: Bayesian phylogenetic inference under mixed models

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

MODELTEST: testing the model of DNA substitution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Identifying Conflicting Signal in a Multigene Analysis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mammalia)

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae)

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Resolution of the early placental mammal radiation using Bayesian phylogenetics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Molecular phylogenetics and the origins of placental mammals

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

The guinea-pig is not a rodent

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Is the guinea-pig a rodent?

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

CONSEL: for assessing the confidence of phylogenetic tree selection

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

7 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Adaptive evolution of the insulin gene in caviomorph rodents

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

SOAP, cleaning multiple alignments from unstable blocks

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

B1 SINEs in different rodent families.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Automated scanning for phylogenetically informative transposed elements in rodents.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Computing Bayes factors using thermodynamic integration.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Polytomies and Bayesian phylogenetic inference

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Maximum-likelihood phylogenetic analysis under a covarion-like model.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

Rodent monophyly: pitfalls of molecular phylogenies

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674048

29 November 2018

1 reference

12 December 2020

Pervasive adaptive evolution in mammalian fertilization proteins

1 reference

12 December 2020

1 reference

12 December 2020

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

1 reference

12 December 2020

Mammalian phylogeny: Morphology and molecules

1 reference

12 December 2020

Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-9-71

0 references