(Q34354530)

1 August 2017

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals (English)

1 reference

1 August 2017

1 reference

3

1 reference

1 August 2017

5

Emmanuel J P Douzery

1 reference

1 August 2017

2

Vincent Ranwez

1 reference

1 August 2017

Jonathan Romiguier

1

1 reference

PubMed ID

23813978

1 August 2017

Nicolas Galtier

series ordinal

4

1 reference

1 August 2017

29 June 2013

1 reference

Molecular Biology and Evolution

1 August 2017

1 reference

1 August 2017

30

1 reference

1 August 2017

9

1 reference

1 August 2017

2134-2144

1 reference

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

1 August 2017

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Summarizing and correcting the GC content bias in high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The mosaic genome of warm-blooded vertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

21 January 2018

An overview of Ensembl

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Mosaic retroposon insertion patterns in placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Biopython: freely available Python tools for computational molecular biology and bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Discordance of species trees with their most likely gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Tunicates and not cephalochordates are the closest living relatives of vertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Phylogenomics and the reconstruction of the tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Mutation patterns in the human genome: more variable than expected

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The impact of recombination on nucleotide substitutions in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Efficient selection of branch-specific models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Phylogenomics: intersection of evolution and genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The evolution of isochores

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

TimeTree: a public knowledge-base of divergence times among organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Retroposed elements as archives for the evolutionary history of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

High guanine and cytosine content increases mRNA levels in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

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%2FMOLBEV%2FMST116

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Parallel adaptive radiations in two major clades of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Biased gene conversion: implications for genome and sex evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

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%2FMOLBEV%2FMST116

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Recombination explains isochores in mammalian genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Molecular phylogenetics and the origins of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Using genomic data to unravel the root of the placental mammal phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Dynamic evolution of base composition: causes and consequences in avian phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Meiotic recombination favors the spreading of deleterious mutations in human populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Early history of mammals is elucidated with the ENCODE multiple species sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Rooting the eutherian tree: the power and pitfalls of phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The placental mammal ancestor and the post-K-Pg radiation of placentals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

A relationship between GC content and coding-sequence length.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Genetic evidence for complex speciation of humans and chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Genome-scale phylogeny and the detection of systematic biases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The effect of recombination on the accuracy of phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Confirming the phylogeny of mammals by use of large comparative sequence data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Fine-scale recombination patterns differ between chimpanzees and humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

SuperTriplets: a triplet-based supertree approach to phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Genomic evidence for large, long-lived ancestors to placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

The adequacy of morphology for reconstructing the early history of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Placental mammal diversification and the Cretaceous-Tertiary boundary

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Molecules consolidate the placental mammal tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

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%2FMOLBEV%2FMST116

Distribution of DNA methylation, CpGs, and CpG islands in human isochores

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

Genomics, biogeography, and the diversification of placental mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST116

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MST116

1 reference

1 August 2017

1 reference

PubMed ID

23813978