Miocene Diversification in the Savannahs Precedes Tetraploid Rainforest Radiation in the African Tree Genus Afzelia (Detarioideae, Fabaceae)

Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges

(2020) Armel S. L. Donkpegan et al.   AMERICAN JOURNAL OF BOTANY

The hyperdominant tropical tree Eschweilera coriacea (Lecythidaceae) shows higher genetic heterogeneity than sympatric Eschweilera species in French Guiana

(2020) Myriam Heuertz et al.   Plant Ecology and Evolution

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms

(2019) Cintia G. Freitas et al.   Frontiers in Plant Science

Phylogenetic relationships in two African Cedreloideae tree genera (Meliaceae) reveal multiple rain/dry forest transitions

(2019) Franck K. Monthe et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Multiple shifts to open habitats in Melastomateae (Melastomataceae) congruent with the increase of African Neogene climatic aridity

(2018) Marie Claire Veranso-Libalah et al.   JOURNAL OF BIOGEOGRAPHY

Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology

(2018) Félicien Tosso et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus

(2018) Madlen Stange et al.   SYSTEMATIC BIOLOGY

Taxonomic revision of the African genus Greenwayodendron (Annonaceae)

(2018) Brandet-Junior Lissambou et al.   PhytoKeys

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae)

(2017) Armel S.L. Donkpegan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing

(2017) Mario Fernández-Mazuecos et al.   SYSTEMATIC BIOLOGY

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)

(2017) DAVY U. IKABANGA et al.   Phytotaxa

Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution

(2017) Benjamin M. Anderson et al.   PLoS One

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

(2016) Kasso Daïnou et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS)

(2016) Andrea Ariani et al.   MOLECULAR BREEDING

Population and phylogenomic decomposition via genotyping-by-sequencing in AustralianPelargonium

(2016) Adrienne B. Nicotra et al.   MOLECULAR ECOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability

(2015) R. Toby Pennington et al.   NEW PHYTOLOGIST

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Microsatellite Development and Flow Cytometry in the African Tree Genus Afzelia (Fabaceae, Caesalpinioideae) Reveal a Polyploid Complex

(2015) Armel S. L. Donkpegan et al.   Applications in Plant Sciences

Biome Shifts and Niche Evolution in Plants

(2014) Michael J. Donoghue et al.   Annual Review of Ecology Evolution and Systematics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

(2014) Marcial Escudero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The remarkable congruence of New and Old World savanna origins

(2014) R. Toby Pennington et al.   NEW PHYTOLOGIST

Savanna fire and the origins of the ‘underground forests’ of Africa

(2014) Olivier Maurin et al.   NEW PHYTOLOGIST

Comparative Phylogeography in Rainforest Trees from Lower Guinea, Africa

(2014) Myriam Heuertz et al.   PLoS One

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference

(2014) Joseph Heled et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Leaf venation: structure, function, development, evolution, ecology and applications in the past, present and future

(2013) Lawren Sack et al.   NEW PHYTOLOGIST

Plant Traits Demonstrate That Temperate and Tropical Giant Eucalypt Forests Are Ecologically Convergent with Rainforest Not Savanna

(2013) David Y. P. Tng et al.   PLoS One

Quaternary forest associations in lowland tropical West Africa

(2013) Charlotte S. Miller et al.   QUATERNARY SCIENCE REVIEWS

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets

(2013) Tomochika Fujisawa et al.   SYSTEMATIC BIOLOGY

Extending Coalescent Theory to Autotetraploids

(2012) B. Arnold et al.   GENETICS

Evidence for Adaptation to Fire Regimes in the Tropical Savannas of the Brazilian Cerrado

(2012) Marcelo F. Simon et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats

(2012) J. A. Esselstyn et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia(Cucurbitaceae)

(2011) Norbert Holstein et al.   BMC EVOLUTIONARY BIOLOGY

Testing species delimitation in sympatric species complexes: The case of an African tropical tree, Carapa spp. (Meliaceae)

(2011) Jérôme Duminil et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Detarieae sensu lato (Fabaceae) from the Late Oligocene (27.23 Ma) Guang River flora of north-western Ethiopia

(2010) AARON D. PAN et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Hybridization and introgression across different ploidy levels in the Neotropical orchids Epidendrum fulgens and E. puniceoluteum (Orchidaceae)

(2010) FÁBIO PINHEIRO et al.   MOLECULAR ECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Neogene desertification of Africa

(2009) Brigitte Senut et al.   COMPTES RENDUS GEOSCIENCE

Phylogenetic biome conservatism on a global scale

(2009) Michael D. Crisp et al.   NATURE

Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire

(2009) M. F. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)

(2008) M. L. Ainouche et al.   BIOLOGICAL INVASIONS

Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

(2008) Anne Bruneau et al.   Botany

An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

(2008) James C. Zachos et al.   NATURE