Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes

PhyloNetworks: A Package for Phylogenetic Networks

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Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

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Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification

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Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

(2017) Mauricio Diazgranados et al.   PeerJ

Biogeography shaped the metabolome of the genus Espeletia: a phytochemical perspective on an Andean adaptive radiation

(2017) Guillermo F. Padilla-González et al.   Scientific Reports

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

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The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

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Inconsistency of Species Tree Methods under Gene Flow

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Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

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Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes

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

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A composite genome approach to identify phylogenetically informative data from next-generation sequencing

(2015) Rachel S. Schwartz et al.   BMC BIOINFORMATICS

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae)

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The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains

(2015) Colin E. Hughes et al.   NEW PHYTOLOGIST

A Phylogenetic Analysis of Lychnophorinae (Asteraceae: Vernonieae) Based on Molecular and Morphological Data

(2015) Benoît Loeuille et al.   SYSTEMATIC BOTANY

Resolving Relationships within Valerianaceae (Dipsacales): New Insights and Hypotheses from Low-Copy Nuclear Regions

(2015) Charles D. Bell et al.   SYSTEMATIC BOTANY

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation and Convergent Evolution within the Jamesonia-Eriosorus Complex in High-Elevation Biodiverse Andean Hotspots

(2014) Patricia Sánchez-Baracaldo et al.   PLoS One

Escape from extreme specialization: passionflowers, bats and the sword-billed hummingbird

(2014) S. Abrahamczyk et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

(2013) Daniel A. Dalquen et al.   PLoS One

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

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

Explosive radiation in high Andean Hypericum—rates of diversification among New World lineages

(2013) Nicolai M. Nürk et al.   Frontiers in Genetics

Páramo is the world's fastest evolving and coolest biodiversity hotspot

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Targeted enrichment strategies for next-generation plant biology

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ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

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Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

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Inferring Phylogenies from RAD Sequence Data

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Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution

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Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

(2012) Christopher S. Drummond et al.   SYSTEMATIC BIOLOGY

Diversitree: comparative phylogenetic analyses of diversification in R

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A nomenclator for the frailejones (Espeletiinae Cuatrec., Asteraceae)

(2012) Mauricio Diazgranados   PhytoKeys

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

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Origins of Biodiversity

(2011) V. Rull   SCIENCE

Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches

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Neotropical biodiversity: timing and potential drivers

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phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

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Giant lobelias exemplify convergent evolution

(2010) Thomas J Givnish   BMC BIOLOGY

An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

(2010) Sven Buerki et al.   JOURNAL OF BIOGEOGRAPHY

Unparalleled rates of species diversification in Europe

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Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

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Spatial and temporal patterns of exhumation across the Venezuelan Andes: Implications for Cenozoic Caribbean geodynamics

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ANDEAN SPECIATION AND VICARIANCE IN NEOTROPICAL MACROCARPAEA (GENTIANACEAE–HELIEAE)1

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

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

Tracing the impact of the Andean uplift on Neotropical plant evolution

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Atmospheric Carbon Dioxide Concentration Across the Mid-Pleistocene Transition

(2009) B. Honisch et al.   SCIENCE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

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Homoploid hybrid speciation in animals

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Origin, adaptive radiation and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae)

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