Quaternary climate changes as speciation drivers in the Amazon floodplains

Chronology of Terra Firme formation in Amazonian lowlands reveals a dynamic Quaternary landscape

(2019) F.N. Pupim et al.   QUATERNARY SCIENCE REVIEWS

A dynamic continental moisture gradient drove Amazonian bird diversification

(2019) Sofia Marques Silva et al.   Science Advances

Modern and late Pleistocene particulate organic carbon transport by the Amazon River: Insights from long-chain alkyl diols

(2019) Christoph Häggi et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

A field study of the confluence between Negro and Solimões Rivers. Part 1: Hydrodynamics and sediment transport

(2018) Carlo Gualtieri et al.   COMPTES RENDUS GEOSCIENCE

Primary productivity in the western tropical Atlantic follows Neogene Amazon River evolution

(2018) E.I. Lammertsma et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

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

The Amazon at sea: Onset and stages of the Amazon River from a marine record, with special reference to Neogene plant turnover in the drainage basin

(2017) Carina Hoorn et al.   GLOBAL AND PLANETARY CHANGE

Phylogeography and population dynamics of Antbirds (Thamnophilidae) from Amazonian fluvial islands

(2017) Érik L. Choueri et al.   JOURNAL OF BIOGEOGRAPHY

multi-dice : r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes

(2017) Alexander T. Xue et al.   Molecular Ecology Resources

Hydroclimate changes across the Amazon lowlands over the past 45,000 years

(2017) Xianfeng Wang et al.   NATURE

Damming the rivers of the Amazon basin

(2017) Edgardo M. Latrubesse et al.   NATURE

The architecture of river networks can drive the evolutionary dynamics of aquatic populations

(2016) Andréa T. Thomaz et al.   EVOLUTION

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

(2016) Michael G. Harvey et al.   SYSTEMATIC BIOLOGY

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Cryptic speciation in the white-shouldered antshrike (Thamnophilus aethiops, Aves – Thamnophilidae): The tale of a transcontinental radiation across rivers in lowland Amazonia and the northeastern Atlantic Forest

(2015) Gregory Thom et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Visualizing spatial population structure with estimated effective migration surfaces

(2015) Desislava Petkova et al.   NATURE GENETICS

Mid-Late Pleistocene OSL chronology in western Amazonia and implications for the transcontinental Amazon pathway

(2015) Dilce F. Rossetti et al.   SEDIMENTARY GEOLOGY

Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia

(2015) Luciano B. Beheregaray et al.   Frontiers in Genetics

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

Climate change patterns in Amazonia and biodiversity

(2013) Hai Cheng et al.   Nature Communications

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Climatic oscillations shape the phylogeographical structure of Atlantic Forest fire-eye antbirds (Aves: Thamnophilidae)

(2012) MARCOS MALDONADO-COELHO   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

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

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

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Tree species compositional change and conservation implications in the white-water flooded forests of the Brazilian Amazon

(2011) Ana Luisa Albernaz et al.   JOURNAL OF BIOGEOGRAPHY

No population genetic structure in a widespread aquatic songbird from the Neotropics

(2011) Carlos Daniel Cadena et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

The impact of Quaternary sea level changes on the evolution of the Amazonian lowland

(2009) Georg Irion et al.   HYDROLOGICAL PROCESSES

Suspended sediment yields in the Amazon basin: an assessment using the Brazilian national data set

(2009) Naziano Filizola et al.   HYDROLOGICAL PROCESSES

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics