Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
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[1] Maite G. Barrón,et al. Population genomics of transposable elements in Drosophila. , 2014, Annual review of genetics.
[2] Young Bun Kim,et al. Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel , 2014, Proceedings of the National Academy of Sciences.
[3] H. Ellegren,et al. Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data , 2015, Systematic biology.
[4] Thomas M. Keane,et al. RetroSeq: transposable element discovery from next-generation sequencing data , 2013, Bioinform..
[5] Robert P. Davey,et al. Population genomics of domestic and wild yeasts , 2008, Nature.
[6] H. Ellegren,et al. Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. , 2006, Molecular biology and evolution.
[7] Pall I. Olason,et al. Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data , 2013, PLoS genetics.
[8] J. Jurka,et al. A universal classification of eukaryotic transposable elements implemented in Repbase , 2008, Nature Reviews Genetics.
[9] Md. Shamsuzzoha Bayzid,et al. Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.
[10] H. Ellegren. Evolutionary stasis: the stable chromosomes of birds. , 2010, Trends in ecology & evolution.
[11] H. Kazazian. Mobile Elements: Drivers of Genome Evolution , 2004, Science.
[12] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[13] E. Galun. Transposable Elements , 2003, Springer Netherlands.
[14] Maite G. Barrón,et al. The transposable element Bari‐Jheh mediates oxidative stress response in Drosophila , 2014, Molecular ecology.
[15] Albert J. Vilella,et al. The genome of a songbird , 2010, Nature.
[16] Josefa González,et al. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila , 2014, PLoS genetics.
[17] E. Jarvis,et al. Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles , 2016, Genome biology and evolution.
[18] J. Brosius,et al. A universal method for the study of CR1 retroposons in nonmodel bird genomes. , 2012, Molecular biology and evolution.
[19] J. Bennetzen,et al. A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.
[20] G. Mayhew,et al. The Arabidopsis thaliana mobilome and its impact at the species level , 2016, eLife.
[21] A. Vinogradov. NUCLEOTYPIC EFFECT IN HOMEOTHERMS: BODY‐MASS INDEPENDENT RESTING METABOLIC RATE OF PASSERINE BIRDS IS RELATED TO GENOME SIZE , 1997, Evolution; international journal of organic evolution.
[22] C. Witt,et al. Metabolic ‘engines’ of flight drive genome size reduction in birds , 2014, Proceedings of the Royal Society B: Biological Sciences.
[23] Juan Moreno,et al. Evolutionary analysis of the female-specific avian W chromosome , 2015, Nature Communications.
[24] Aurélie Kapusta,et al. Evolution of bird genomes—a transposon's‐eye view , 2017, Annals of the New York Academy of Sciences.
[25] M. Quail,et al. The industrial melanism mutation in British peppered moths is a transposable element , 2016, Nature.
[26] D. Ray,et al. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera , 2013, Mobile DNA.
[27] Michael D. Wilson,et al. Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages , 2012, Cell.
[28] L. Zhivotovsky. Estimating population structure in diploids with multilocus dominant DNA markers , 1999, Molecular ecology.
[29] Leanne S. Whitmore,et al. Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites , 2015, Genome research.
[30] H. Ellegren,et al. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. , 2017, Molecular ecology resources.
[31] Kyudong Han,et al. Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome , 2017, Mobile DNA.
[32] John D McPherson,et al. Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites. , 2014, Molecular biology and evolution.
[33] C. Feschotte,et al. Dynamics of genome size evolution in birds and mammals , 2017, Proceedings of the National Academy of Sciences.
[34] B. Laenen,et al. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora , 2016, Proceedings of the National Academy of Sciences.
[35] H. Ellegren,et al. The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds , 2015, PLoS biology.
[36] Kazutaka Katoh,et al. Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..
[37] Floriane Plard,et al. Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates , 2015, Genome biology and evolution.
[38] M. Kiefmann,et al. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds , 2011, Nature communications.
[39] M. Fujita,et al. Genome evolution in Reptilia, the sister group of mammals. , 2010, Annual review of genomics and human genetics.
[40] Miriam K. Konkel,et al. A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. , 2010, Seminars in cancer biology.
[41] Elizabeth Hénaff,et al. Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution , 2015, BMC Genomics.
[42] Yuliya V. Karpievitch,et al. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation , 2016, bioRxiv.
[43] H. Ellegren,et al. PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers , 2016, Molecular ecology.
[44] L. Excoffier,et al. Computer programs for population genetics data analysis: a survival guide , 2006, Nature Reviews Genetics.
[45] D. Ray,et al. Evolution and Diversity of Transposable Elements in Vertebrate Genomes , 2017, Genome biology and evolution.
[46] Jianrong Wang,et al. MIR retrotransposon sequences provide insulators to the human genome , 2015, Proceedings of the National Academy of Sciences.
[47] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[48] H. Ellegren,et al. High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree , 2016, PLoS genetics.
[49] Thomas M. Keane,et al. The genomic landscape shaped by selection on transposable elements across 18 mouse strains , 2012, Genome Biology.
[50] Andreas R. Pfenning,et al. Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.
[51] Pall I. Olason,et al. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers , 2015, Genome research.
[52] Pall I. Olason,et al. The genomic landscape of species divergence in Ficedula flycatchers , 2012, Nature.
[53] E. Danchin,et al. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. , 2016, Trends in ecology & evolution.
[54] J. Brosius,et al. De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds , 2016, bioRxiv.
[55] D. C. Hancks,et al. Active human retrotransposons: variation and disease. , 2012, Current opinion in genetics & development.
[56] Mark A. Miller,et al. Creating the CIPRES Science Gateway for inference of large phylogenetic trees , 2010, 2010 Gateway Computing Environments Workshop (GCE).
[57] David Haussler,et al. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes , 2007, Proceedings of the National Academy of Sciences.
[58] Meganathan P. Ramakodi,et al. Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes , 2014, Genome biology and evolution.
[59] O. Kohany,et al. Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.
[60] M. G. Kidwell,et al. CHAPTER 3 – Transposable Elements , 2005 .
[61] I. K. Jordan,et al. Transposable element polymorphisms recapitulate human evolution , 2015, Mobile DNA.
[62] Pall I. Olason,et al. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution , 2014, Molecular ecology.
[63] H. Ellegren,et al. Direct estimate of the rate of germline mutation in a bird , 2016, Genome research.
[64] T. J. Robinson,et al. Molecular cytogenetic and genomic insights into chromosomal evolution , 2011, Heredity.
[65] A. Hughes,et al. Small genomes for better flyers , 1995, Nature.
[66] Leonardo Mariño-Ramírez,et al. Benchmarking computational tools for polymorphic transposable element detection , 2016, Briefings Bioinform..
[67] R. Martienssen,et al. Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.
[68] D. Kordis. Transposable Elements in Reptilian and Avian (Sauropsida) Genomes , 2010, Cytogenetic and Genome Research.
[69] B. Faircloth,et al. Tectonic collision and uplift of Wallacea triggered the global songbird radiation , 2016, Nature Communications.
[70] Alexander Suh,et al. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex , 2016, Nature Communications.
[71] Stuart R. Dennis,et al. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species , 2015, Molecular ecology.
[72] J. McGuire,et al. The smallest avian genomes are found in hummingbirds , 2009, Proceedings of the Royal Society B: Biological Sciences.
[73] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[74] S. Edwards,et al. The Evolution of Intron Size in Amniotes: A Role for Powered Flight? , 2012, Genome biology and evolution.
[75] Jun S. Liu,et al. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome , 2007, Proceedings of the National Academy of Sciences.
[76] A. Shedlock. Phylogenomic investigation of CR1 LINE diversity in reptiles. , 2006, Systematic biology.
[77] Colin N. Dewey,et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004, Nature.
[78] I. Roldán‐Ruiz,et al. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size , 2002, Molecular ecology.
[79] A. Janke,et al. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes , 2017, bioRxiv.
[80] Tyler A. Elliott,et al. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.
[81] R. Gregory. The evolution of the genome , 2005 .
[82] Gabor T. Marth,et al. An integrated map of structural variation in 2,504 human genomes , 2015, Nature.
[83] J. Rougemont,et al. A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.
[84] Ryan E. Mills,et al. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology , 2017, Genome research.
[85] Brendan D. O'Fallon,et al. The genomic and phenotypic diversity of Schizosaccharomyces pombe , 2015, Nature Genetics.
[86] Andrew W Jones,et al. Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. , 2015, Molecular phylogenetics and evolution.
[87] Kai Ye,et al. Mobster: accurate detection of mobile element insertions in next generation sequencing data , 2014, Genome Biology.
[88] Daniel H. Huson,et al. SplitsTree: analyzing and visualizing evolutionary data , 1998, Bioinform..