Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera

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

(2021) Ondřej Mikula et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Rufous Sengi is not Elephantulus —Multilocus reconstruction of evolutionary history of sengis from the subfamily Macroscelidinae

(2021) Jarmila Krásová et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent

(2020) Ondřej Mikula et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Systematics, Ecology, and Host Switching: Attributes Affecting Emergence of the Lassa Virus in Rodents across Western Africa

(2020) Ayodeji Olayemi et al.   Viruses-Basel

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

(2020) Thomas L.P. Couvreur et al.   BIOLOGICAL REVIEWS

Rapid peripatric speciation linked with drainage evolution in a rare African rodent, Mastomys shortridgei (Rodentia: Muridae)

(2020) Seth J. Eiseb et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Allopatric Speciation in Asia Contributed to the Diversity Anomaly between Eastern Asia and Eastern North America: Evidence from Anchored Phylogenomics of Stewartia (Theaceae)

(2019) Jian-Hua Li et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae)

(2019) Sara Martín-Hernanz et al.   Frontiers in Plant Science

The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity

(2019) Violaine Nicolas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

(2019) Nathan S. Upham et al.   PLOS BIOLOGY

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

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Biogeographic implications of small mammals from Northern Highlands in Tanzania with first data from the volcanic Mount Kitumbeine

(2018) Christopher Sabuni et al.   MAMMALIA

Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient

(2018) Josef Bryja 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

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes

(2017) Xin Chen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Hantavirus Strains in East Africa Related to Western African Hantaviruses

(2017) Jana Těšíková et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

When Viruses Don’t Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses

(2017) Sophie Gryseels et al.   PLoS Pathogens

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

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Late Miocene global cooling and the rise of modern ecosystems

(2016) Timothy D. Herbert et al.   Nature Geoscience

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

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

New Hosts of The Lassa Virus

(2016) Ayodeji Olayemi et al.   Scientific Reports

Suwa, G., Beyene, Y., Nakaya, H., Bernor, R.L., Boisserie, J.-R., Bibi, F., Ambrose, S.H., Sano, K., Katoh, S., and Asfaw, B. (2015) Newly discovered cercopithecid, equid and other mammalian fossils from the Chorora Formation, Ethiopia. Anthropological Science, 123(1): 19–39.

(2015)   ANTHROPOLOGICAL SCIENCE

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

(2015) Richard O. Prum et al.   NATURE

Gairo virus, a novel arenavirus of the widespread Mastomys natalensis : Genetically divergent, but ecologically similar to Lassa and Morogoro viruses

(2015) Sophie Gryseels et al.   VIROLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

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

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A mitochondrial phylogeographic scenario for the most widespread African rodent,Mastomys natalensis

(2013) Paolo Colangelo et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The role of dispersal and vicariance in the Pleistocene history of an East African mountain rodent,Praomys delectorum

(2013) Josef Bryja et al.   JOURNAL OF BIOGEOGRAPHY

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

(2012) Darin R Rokyta et al.   BMC GENOMICS

40Ar/39Ar dating of Bed I, Olduvai Gorge, Tanzania, and the chronology of early Pleistocene climate change

(2012) Alan L. Deino   JOURNAL OF HUMAN EVOLUTION

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

(2012) Julien Soubrier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessment of Three Mitochondrial Genes (16S, Cytb, CO1) for Identifying Species in the Praomyini Tribe (Rodentia: Muridae)

(2012) Violaine Nicolas et al.   PLoS One

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

Species limits within the Praomys delectorum group (Rodentia: Muridae: Murinae) of East Africa: a morphometric reassessment and biogeographical implications

(2012) MICHAEL D. CARLETON et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Novel Arenavirus Sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from Côte d'Ivoire: Implications for Evolution of Arenaviruses in Africa

(2011) David Coulibaly-N'Golo et al.   PLoS One

The impact of the Congo River and its tributaries on the rodent genus Praomys: speciation origin or range expansion limit?

(2011) JAN KENNIS et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Terrestrial Small Mammals as Reservoirs of Mycobacterium ulcerans in Benin

(2010) L. Durnez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

(2010) V. Nicolas et al.   JOURNAL OF BIOGEOGRAPHY

Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay

(2010) J. BRYJA et al.   MOLECULAR ECOLOGY

Presence of Mopeia Virus, an African Arenavirus, Related to Biotope and Individual Rodent Host Characteristics: Implications for Virus Transmission

(2010) Benny Borremans et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

(2009) Carine Brouat et al.   JOURNAL OF BIOGEOGRAPHY

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

(2009) Thomas Briese et al.   PLoS Pathogens

Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees

(2008) Thomas LP Couvreur et al.   BMC BIOLOGY

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

Potential mammalian reservoirs in a bubonic plague outbreak focus in Mbulu District, northern Tanzania, in 2007

(2008) Rhodes H. Makundi et al.   MAMMALIA

Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratusandP. tullbergi) in West Africa: different reactions to past forest fragmentation

(2008) V. NICOLAS et al.   MOLECULAR ECOLOGY

Phylogeography of a Sahelian rodent species Mastomys huberti: a Plio-Pleistocene story of emergence and colonization of humid habitats

(2008) KARINE MOULINE et al.   MOLECULAR ECOLOGY

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY