Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America.

[1]  R. Harrigan,et al.  Evolutionary and ecological drivers of local adaptation and speciation in a North American avian species complex , 2022, Molecular ecology.

[2]  E. Braun,et al.  When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes). , 2021, Gene.

[3]  K. Jønsson,et al.  Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds , 2021, Molecular ecology.

[4]  Taras K. Oleksyk,et al.  The complete genome sequences of 22 parrot species (Psittaciformes, Aves) , 2020 .

[5]  M. Malinsky,et al.  Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files , 2020, Molecular ecology resources.

[6]  Mario Stanke,et al.  BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database , 2020, bioRxiv.

[7]  Sheela P. Turbek,et al.  Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau. , 2019, Ecology letters.

[8]  J. L. Le Roux,et al.  Occurrence and extent of hybridisation between the invasive Mallard Duck and native Yellow-billed Duck in South Africa , 2019, Biological Invasions.

[9]  G. Amato,et al.  Genetic analysis reveals strong phylogeographical divergences within the Scarlet Macaw Ara macao , 2019, Ibis.

[10]  K. McCracken,et al.  Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America , 2019, Ecology and evolution.

[11]  Jia-kuan Chen,et al.  Incomplete lineage sorting and introgression in the diversification of Chinese spot-billed ducks and mallards , 2018, Current zoology.

[12]  J. Flowers,et al.  Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.

[13]  A. von Haeseler,et al.  UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.

[14]  M. Cecchini,et al.  Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease , 2016, Scientific Reports.

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

[16]  M. Jakobsson,et al.  Clumpak: a program for identifying clustering modes and packaging population structure inferences across K , 2015, Molecular ecology resources.

[17]  M. Wink,et al.  Avian genomics: fledging into the wild! , 2015, Journal of Ornithology.

[18]  F. Zou,et al.  Testing hypotheses of mitochondrial gene‐tree paraphyly: unravelling mitochondrial capture of the Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus) , 2014, Molecular ecology.

[19]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[20]  Pall I. Olason,et al.  Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data , 2013, PLoS genetics.

[21]  P. Crochet,et al.  Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact , 2013, Heredity.

[22]  S. Dowd,et al.  A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao) , 2013, PloS one.

[23]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[24]  Frode F. Jacobsen,et al.  Species tree inference in a recent radiation of orioles (Genus Icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group. , 2011, Molecular phylogenetics and evolution.

[25]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[26]  Kenneth Lange,et al.  Enhancements to the ADMIXTURE algorithm for individual ancestry estimation , 2011, BMC Bioinformatics.

[27]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[28]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[29]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[30]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[31]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[32]  Amit R. Indap,et al.  Genes mirror geography within Europe , 2008, Nature.

[33]  P. Andolfatto,et al.  The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis , 2008 .

[34]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[35]  Burkhard Morgenstern,et al.  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.

[36]  Gordon Gremme,et al.  Engineering a software tool for gene structure prediction in higher organisms , 2005, Inf. Softw. Technol..

[37]  G. Luikart,et al.  SNPs in ecology, evolution and conservation , 2004 .

[38]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.