Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Molecular phylogenetic analyses indicate paraphyly of the genus Hybomys (Rodentia: Muridae): Taxonomic implications

(2018) Alain Didier Missoup et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Ethiopian highlands as a cradle of the African fossorial root-rats (genus Tachyoryctes ), the genetic evidence

(2018) Radim Šumbera et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fossils know it best: using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

(2018) Tatiana Aghová et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of the Grey-bellied pygmy mouse group: Highly structured molecular diversity with predictable geographic ranges but morphological crypsis

(2018) Jarmila Krásová et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes)

(2017) Cesar R. L. Amaral et al.   Mitochondrial DNA Part A

Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates

(2017) Scott J. Steppan et al.   PLoS One

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

(2016) Chris A. Hamilton et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary history of the thicket rats (genus Grammomys ) mirrors the evolution of African forests since late Miocene

(2016) Josef Bryja et al.   JOURNAL OF BIOGEOGRAPHY

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)

(2016) Derek B. Tucker et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

(2015) Sara Ruane et al.   BMC EVOLUTIONARY BIOLOGY

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Phylogenetic position of the endemic Mount Oku rat,Lamottemys okuensis(Rodentia: Muridae), based on molecular and morphological data

(2015) Alain Didier Missoup et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents

(2015) Yuri Kimura et al.   Scientific Reports

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular and morphological evidence for a Pleistocene radiation of laminate-toothed rats (Otomys: Rodentia) across a volcanic archipelago in equatorial Africa

(2014) Peter J. Taylor et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa

(2014) Josef Bryja et al.   BMC EVOLUTIONARY BIOLOGY

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

(2014) Luca Pozzi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

African highlands as mammal diversity hotspots: new records ofLamottemys okuensisPetter, 1986 (Rodentia: Muridae) and other endemic rodents from Mt Oku, Cameroon

(2014) Christiane Denys et al.   ZOOSYSTEMA

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hominin evolution in settings of strong environmental variability

(2013) Richard Potts   QUATERNARY SCIENCE REVIEWS

Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents

(2013) John J. Schenk et al.   SYSTEMATIC BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

(2012) Darin R Rokyta et al.   BMC GENOMICS

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Systematics and diversification of Praomys species (Rodentia: Muridae) endemic to the Cameroon Volcanic Line (West Central Africa)

(2012) Alain D. Missoup et al.   ZOOLOGICA SCRIPTA

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

(2011) J. E. McCormack et al.   GENOME RESEARCH

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily

(2008) Emilie Lecompte et al.   BMC EVOLUTIONARY BIOLOGY

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): Multilocus systematics of the old endemic rodents (Muroidea: Murinae)

(2008) Kevin C. Rowe et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY