Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary

Generation lengths of the world's birds and their implications for extinction risk

(2020) Jeremy P. Bird et al.   CONSERVATION BIOLOGY

Extending phylogeography to account for lineage fusion

(2019) Ryan C. Garrick et al.   JOURNAL OF BIOGEOGRAPHY

Beyond Reproductive Isolation: Demographic Controls on the Speciation Process

(2019) Michael G. Harvey et al.   Annual Review of Ecology Evolution and Systematics

Multispecies hybridization in birds

(2019) Jente Ottenburghs   Avian Research

A dynamic continental moisture gradient drove Amazonian bird diversification

(2019) Sofia Marques Silva et al.   Science Advances

Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America

(2019) Jason T. Weir et al.   PLOS BIOLOGY

Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation

(2019) Paola Pulido‐Santacruz et al.   EVOLUTION

Taxonomy as tyranny

(2018) Nigel J. Collar   IBIS

Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection

(2018) Richard H. Ree et al.   JOURNAL OF BIOGEOGRAPHY

Mammals and meaningful taxonomic units: the debate about species concepts and conservation

(2018) Frank E. Zachos   MAMMAL REVIEW

Cryptic species as a window into the paradigm shift of the species concept

(2018) Cene Fišer et al.   MOLECULAR ECOLOGY

Molecular systematics and biogeography of lowland antpittas (Aves, Grallariidae): The role of vicariance and dispersal in the diversification of a widespread Neotropical lineage

(2018) Lincoln Carneiro et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

(2018) Paola Pulido-Santacruz et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species

(2018) Gregory Thom et al.   SYSTEMATIC BIOLOGY

The dual role of Amazonian rivers in the generation and maintenance of avian diversity

(2018) Luciano N. Naka et al.   Science Advances

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird

(2017) Alfredo O. Barrera-Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glacial Amazonia at the canopy-scale: Using a biophysical model to understand forest robustness

(2017) Hiromitsu Sato et al.   QUATERNARY SCIENCE REVIEWS

Avian introgression in the genomic era

(2017) Jente Ottenburghs et al.   Avian Research

Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate

(2016) Mateus Ferreira et al.   JOURNAL OF BIOGEOGRAPHY

Body mass-corrected molecular rate for bird mitochondrial DNA

(2016) Benoit Nabholz et al.   MOLECULAR ECOLOGY

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

(2016) Arnald Marcer et al.   Ecology and Evolution

Late quaternary dynamics in the Madeira river basin, southern Amazonia (Brazil), as revealed by paleomorphological analysis

(2015) Ericson H. Hayakawa et al.   ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS

Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds

(2015) Jason T. Weir et al.   EVOLUTION

The Complete Chloroplast Genome of Guadua angustifolia and Comparative Analyses of Neotropical-Paleotropical Bamboos

(2015) Miaoli Wu et al.   PLoS One

Multiple speciation across the Andes and throughout Amazonia: the case of the spot-backed antbird species complex (Hylophylax naevius/Hylophylax naevioides)

(2014) Alexandre M. Fernandes et al.   JOURNAL OF BIOGEOGRAPHY

Bamboo-dominated forests and pre-Columbian earthwork formations in south-western Amazonia

(2014) Crystal H. McMichael et al.   JOURNAL OF BIOGEOGRAPHY

Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects

(2014) Ivan C. Phillipsen et al.   MOLECULAR ECOLOGY

The drivers of tropical speciation

(2014) Brian Tilston Smith et al.   NATURE

Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations

(2014) N. Alcala et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

On the nonidentifiability of migration time estimates in isolation with migration models

(2011) VITOR C. SOUSA et al.   MOLECULAR ECOLOGY

A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years

(2011) C. C. Ribas et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

OSL age determinations of Pleistocene fluvial deposits in Central Amazonia

(2010) Emílio A.A. Soares et al.   ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

(2010) Ryan C Garrick et al.   BMC EVOLUTIONARY BIOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Ecology Predicts Levels of Genetic Differentiation in Neotropical Birds

(2009) Curtis W. Burney et al.   AMERICAN NATURALIST

BIOMOD - a platform for ensemble forecasting of species distributions

(2009) Wilfried Thuiller et al.   ECOGRAPHY

How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

(2009) J. L. Strasburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments

(2009) J-F. FLOT   Molecular Ecology Resources

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

(2009) José S.L. Patané et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Experimental evidence for extreme dispersal limitation in tropical forest birds

(2008) R. P. Moore et al.   ECOLOGY LETTERS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Calibrating the avian molecular clock

(2008) J. T. WEIR et al.   MOLECULAR ECOLOGY

First macrofossil evidence of a pre-Holocene thorny bamboo cf. Guadua (Poaceae: Bambusoideae: Bambuseae: Guaduinae) in south-western Amazonia (Madre de Dios — Peru)

(2008) Jean Olivier et al.   REVIEW OF PALAEOBOTANY AND PALYNOLOGY