Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin.

[1]  M. Vallinoto,et al.  Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae). , 2018, Molecular phylogenetics and evolution.

[2]  C. Schaefer,et al.  Vegetation cover of Brazil in the last 21 ka: New insights into the Amazonian refugia and Pleistocenic arc hypotheses , 2018 .

[3]  R. T. Brumfield,et al.  Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds , 2017, The American Naturalist.

[4]  F. Rousset,et al.  A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes , 2017, Evolution; international journal of organic evolution.

[5]  J. Reid,et al.  Gene flow and island colonisation of the buff-banded rail (Aves: Rallidae) in Oceania and its implications for insular endemism , 2017 .

[6]  C. C. Ribas,et al.  Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate , 2017 .

[7]  Daniel B. Sloan,et al.  The on‐again, off‐again relationship between mitochondrial genomes and species boundaries , 2017, Molecular ecology.

[8]  G. Hill.  The mitonuclear compatibility species concept , 2017, The Auk.

[9]  S. Barthe,et al.  Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield , 2017, Molecular ecology.

[10]  M. Bush.  Climate science: The resilience of Amazonian forests , 2017, Nature.

[11]  E. Braun,et al.  Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling , 2017 .

[12]  Robert Lanfear,et al.  PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. , 2016, Molecular biology and evolution.

[13]  H. Tuomisto,et al.  Impact of sedimentary processes on white-sand vegetation in an Amazonian megafan , 2016, Journal of Tropical Ecology.

[14]  B. Faircloth,et al.  Tectonic collision and uplift of Wallacea triggered the global songbird radiation , 2016, Nature Communications.

[15]  Huw A. Ogilvie,et al.  StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates , 2016, bioRxiv.

[16]  K. Burns,et al.  Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga). , 2016, Systematic biology.

[17]  A. Meyer,et al.  Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish? , 2016, Ecology and evolution.

[18]  S. Borges,et al.  Bird Communities in Amazonian White‐Sand Vegetation Patches: Effects of Landscape Configuration and Biogeographic Context , 2016 .

[19]  Fernando M. d'Horta,et al.  Comparative Phylogeography of Two Bird Species, Tachyphonus phoenicius (Thraupidae) and Polytmus theresiae (Trochilidae), Specialized in Amazonian White‐sand Vegetation , 2016 .

[20]  A. Vicentini.  The Evolutionary History of Pagamea (Rubiaceae), a White‐sand Specialist Lineage in Tropical South America , 2016 .

[21]  P. Fine,et al.  Habitat Endemism in White‐sand Forests: Insights into the Mechanisms of Lineage Diversification and Community Assembly of the Neotropical Flora , 2016 .

[22]  N. Christensen,et al.  White‐sand Ecosystems in Amazonia , 2016 .

[23]  Travis C Glenn,et al.  Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics. , 2013, Systematic biology.

[24]  Brant C. Faircloth,et al.  PHYLUCE is a software package for the analysis of conserved genomic loci , 2015, bioRxiv.

[25]  J. Townsend,et al.  A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2015, Nature.

[26]  L. Joseph,et al.  Phylogenetic analysis of the Australian rosella parrots (Platycercus) reveals discordance among molecules and plumage. , 2015, Molecular phylogenetics and evolution.

[27]  S. Borges,et al.  What is the avifauna of Amazonian white-sand vegetation? , 2015, Bird Conservation International.

[28]  V. N. Sotnikov,et al.  Effects of Asymmetric Nuclear Introgression, Introgressive Mitochondrial Sweep, and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers , 2015, PloS one.

[29]  A. Aleixo,et al.  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, Molecular phylogenetics and evolution.

[30]  T. Hrbek,et al.  Rivers acting as barriers for bird dispersal in the Amazon , 2014 .

[31]  John Gatesy,et al.  Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. , 2014, Molecular phylogenetics and evolution.

[32]  R. Dobler,et al.  A meta‐analysis of the strength and nature of cytoplasmic genetic effects , 2014, Journal of evolutionary biology.

[33]  Dan G. Bock,et al.  On the adaptive value of cytoplasmic genomes in plants , 2014, Molecular ecology.

[34]  T. O. Laranjeiras,et al.  The avifauna of Viruá National Park, Roraima, reveals megadiversity in northern Amazonia , 2014 .

[35]  R. Dudley,et al.  Molecular Phylogenetics and the Diversification of Hummingbirds , 2014, Current Biology.

[36]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[37]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[38]  A. Llopart,et al.  Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea , 2014, Molecular ecology.

[39]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[40]  B. Faircloth,et al.  Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. , 2013, Systematic biology.

[41]  J. T. Guimarães,et al.  Neogene–Quaternary sedimentary and paleovegetation history of the eastern Solimões Basin, central Amazon region , 2013 .

[42]  J. Metzger,et al.  Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia , 2013 .

[43]  Alexandre M. Fernandes.  Fine-scale endemism of Amazonian birds in a threatened landscape , 2013, Biodiversity and Conservation.

[44]  J. Oliver.  MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES , 2013, Evolution; international journal of organic evolution.

[45]  R. T. Brumfield,et al.  Applications of next-generation sequencing to phylogeography and phylogenetics. , 2013, Molecular phylogenetics and evolution.

[46]  R. Edwards,et al.  Climate change patterns in Amazonia and biodiversity , 2013, Nature Communications.

[47]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[48]  Travis C Glenn,et al.  Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.

[49]  A. Brelsford,et al.  The biogeography of mitochondrial and nuclear discordance in animals , 2012, Molecular ecology.

[50]  Lars Y. Pomara,et al.  Avian Composition Co‐varies with Floristic Composition and Soil Nutrient Concentration in Amazonian Upland Forests , 2012 .

[51]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[52]  B. Hallström,et al.  Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage , 2012, Science.

[53]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[54]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[55]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[56]  A. Yoder,et al.  Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. , 2012, Molecular biology and evolution.

[57]  R. Toonen,et al.  Global Phylogeography with Mixed-Marker Analysis Reveals Male-Mediated Dispersal in the Endangered Scalloped Hammerhead Shark (Sphyrna lewini) , 2012, PloS one.

[58]  J. Cracraft,et al.  A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years , 2012, Proceedings of the Royal Society B: Biological Sciences.

[59]  S. Edwards,et al.  Genetic Introgression: An Integral but Neglected Component of Speciation in Birds , 2011 .

[60]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[61]  T. Stadler,et al.  Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity , 2010, Science.

[62]  N. Pitman,et al.  A Floristic Study of the White-Sand Forests of Peru1 , 2010 .

[63]  N. Espurt,et al.  The Nazca Ridge and uplift of the Fitzcarrald Arch : implications for regional geology in northern South America , 2010 .

[64]  R. Zink,et al.  The causes of mitochondrial DNA gene tree paraphyly in birds. , 2010, Molecular phylogenetics and evolution.

[65]  L. Excoffier,et al.  Genetic Consequences of Range Expansions , 2009 .

[66]  Curtis W. Burney,et al.  Ecology Predicts Levels of Genetic Differentiation in Neotropical Birds , 2009, The American Naturalist.

[67]  J. Avise.  Phylogeography: retrospect and prospect , 2009 .

[68]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[69]  M. Carling,et al.  Haldane's Rule in an Avian System: Using Cline Theory and Divergence Population Genetics to Test for Differential Introgression of Mitochondrial, Autosomal, and Sex-Linked Loci Across the Passerina Bunting Hybrid Zone , 2008, Evolution; international journal of organic evolution.

[70]  J. Norman,et al.  Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes , 2008, BMC Evolutionary Biology.

[71]  R. Zink,et al.  Mitochondrial DNA under siege in avian phylogeography , 2008, Molecular ecology.

[72]  D. Schluter,et al.  Calibrating the avian molecular clock , 2008, Molecular ecology.

[73]  V. Albert,et al.  Amazonian lowland, white sand areas as ancestral regions for South American biodiversity: Biogeographic and phylogenetic patterns in Potalia (Angiospermae: Gentianaceae) , 2008 .

[74]  H. Schubart,et al.  Notes on the vegetation of Amazonia I. A preliminary note on the origin of the open white sand campinas of the lower Rio Negro , 2008, Brittonia.

[75]  Michael Sommer,et al.  Podzol: Soil of the Year 2007. A review on its genesis, occurrence, and functions , 2007 .

[76]  L. Kubatko,et al.  Inconsistency of phylogenetic estimates from concatenated data under coalescence. , 2007, Systematic biology.

[77]  K. Campbell,et al.  The Pan-Amazonian Ucayali Peneplain, late Neogene sedimentation in Amazonia, and the birth of the modern Amazon River system , 2006 .

[78]  B. Whitney,et al.  A NEW SPECIES OF GNATCATCHER FROM WHITE-SAND FORESTS OF NORTHERN AMAZONIAN PERU WITH REVISION OF THE POLIOPTILA GUIANENSIS COMPLEX , 2005 .

[79]  J. Darrozes,et al.  Forebulge dynamics and environmental control in Western Amazonia: The case study of the Arch of Iquitos (Peru) , 2005 .

[80]  G. T. Bueno,et al.  Podzolization as a deferralitization process: a study of an Acrisol–Podzol sequence derived from Palaeozoic sandstones in the northern upper Amazon Basin , 2004 .

[81]  D. Beerling,et al.  Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[82]  C. Witt.  Rates of molecular evolution and their application to neotropical avian biogeography , 2004 .

[83]  S. Borges.  Species poor but distinct: bird assemblages in white sand vegetation in Jaú National Park, Brazilian Amazon , 2003 .

[84]  D. J. Funk,et al.  Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA , 2003 .

[85]  E. Latrubesse.  Evidence of quaternary palaeohydrological changes in middle Amazonia: The Aripuanã-Roosevelt and Jiparaná "fans" , 2002 .

[86]  M. Maslin,et al.  Paleovegetation Simulations of Lowland Amazonia and Implications for Neotropical Allopatry and Speciation , 2001, Quaternary Research.

[87]  B. Whitney,et al.  A NEW ZIMMERIUS TYRANNULET (AVES: TYRANNIDAE) FROM WHITE SAND FORESTS OF NORTHERN AMAZONIAN PERU , 2001 .

[88]  K. Crandall,et al.  TCS: a computer program to estimate gene genealogies , 2000, Molecular ecology.

[89]  D. Mindell,et al.  Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. , 1999, Molecular phylogenetics and evolution.

[90]  B. Whitney,et al.  A new Herpsilochmus antwren (Aves: Thamnophilidae) from northern Amazonian Peru and adjacent ecuador : The role of edaphic heterogeneity of terra firme forest , 1998 .

[91]  H. A. Orr,et al.  Dobzhansky, Bateson, and the genetics of speciation. , 1996, Genetics.

[92]  B. Young,et al.  Neotropical Birds: Ecology and Conservation , 1996 .

[93]  W. Moore.  INFERRING PHYLOGENIES FROM mtDNA VARIATION: MITOCHONDRIAL‐GENE TREES VERSUS NUCLEAR‐GENE TREES , 1995, Evolution; international journal of organic evolution.

[94]  C. Hoorn.  Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: results of a palynostratigraphic study , 1993 .

[95]  D. Levey,et al.  Evolutionary Precursors of Long-Distance Migration: Resource Availability and Movement Patterns in Neotropical Landbirds , 1992, The American Naturalist.

[96]  J. V. Remsen,et al.  FIFTY-TWO AMAZONIAN BIRD SPECIES NEW TO BOLIVIA , 1987 .

[97]  J. Neigel,et al.  Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics , 1987 .

[98]  A. Anderson.  White-Sand Vegetation of Brazilian Amazonia , 1981 .

[99]  W. W. Benson,et al.  Evolution in modern amazonian nonforest islands heliconius hermathena , 1977 .

[100]  B. Monroe,et al.  Avian Speciation in Tropical South America , 1975 .

[101]  J. L. Peters.  Check-List of Birds of the World , 1932, Nature.