TY - STD TI - Mayr E: Animal species and evolution. Animal species and their evolution 1963. ID - ref1 ER - TY - JOUR AU - Mallet, J. PY - 1995 DA - 1995// TI - A species definition for the modern synthesis JO - Trends Ecol Evol VL - 10 UR - https://doi.org/10.1016/0169-5347(95)90031-4 DO - 10.1016/0169-5347(95)90031-4 ID - Mallet1995 ER - TY - BOOK AU - Coyne, J. A. AU - Orr, H. A. PY - 2004 DA - 2004// TI - Speciation PB - Sinauer Associates Sunderland CY - MA ID - Coyne2004 ER - TY - JOUR AU - Bolnick, D. I. AU - Fitzpatrick, B. M. PY - 2007 DA - 2007// TI - Sympatric Speciation: Models and Empirical Evidence JO - Annu Rev Ecol Evol Syst VL - 38 UR - https://doi.org/10.1146/annurev.ecolsys.38.091206.095804 DO - 10.1146/annurev.ecolsys.38.091206.095804 ID - Bolnick2007 ER - TY - JOUR AU - Fitzpatrick, B. M. AU - Fordyce, J. A. AU - Gavrilets, S. PY - 2008 DA - 2008// TI - What, if anything, is sympatric speciation? JO - J Evol Biol VL - 21 UR - https://doi.org/10.1111/j.1420-9101.2008.01611.x DO - 10.1111/j.1420-9101.2008.01611.x ID - Fitzpatrick2008 ER - TY - JOUR AU - Niemiller, M. L. AU - Fitzpatrick, B. M. AU - Miller, B. T. PY - 2008 DA - 2008// TI - Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies JO - Mol Ecol VL - 17 UR - https://doi.org/10.1111/j.1365-294X.2008.03750.x DO - 10.1111/j.1365-294X.2008.03750.x ID - Niemiller2008 ER - TY - JOUR AU - Terai, Y. AU - Seehausen, O. AU - Sasaki, T. AU - Takahashi, K. AU - Mizoiri, S. AU - Sugawara, T. PY - 2006 DA - 2006// TI - Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040433 DO - 10.1371/journal.pbio.0040433 ID - Terai2006 ER - TY - JOUR AU - Ellegren, H. AU - Smeds, L. AU - Burri, R. AU - Olason, P. I. AU - Backstrom, N. AU - Kawakami, T. PY - 2012 DA - 2012// TI - The genomic landscape of species divergence in Ficedula flycatchers JO - Nature VL - 491 ID - Ellegren2012 ER - TY - STD TI - Hearn J, Stone GN, Bunnefeld L, Nicholls JA, Barton NH, Lohse K: Likelihood-based inference of population history from low coverage de novo genome assemblies. Mol Ecol 2013:n/a–n/a. ID - ref9 ER - TY - STD TI - Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, et. al: Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research 2013. ID - ref10 ER - TY - STD TI - Lohse K, Frantz LAF: Neandertal Admixture in Eurasia Confirmed by Maximum Likelihood Analysis of Three Genomes. Genetics 2014. ID - ref11 ER - TY - JOUR AU - Green, R. E. AU - Krause, J. AU - Briggs, A. W. AU - Maricic, T. AU - Stenzel, U. AU - Kircher, M. PY - 2010 DA - 2010// TI - A Draft Sequence of the Neandertal Genome JO - Science VL - 328 UR - https://doi.org/10.1126/science.1188021 DO - 10.1126/science.1188021 ID - Green2010 ER - TY - JOUR AU - Reich, D. AU - Green, R. E. AU - Kircher, M. AU - Krause, J. AU - Patterson, N. AU - Durand, E. Y. PY - 2010 DA - 2010// TI - Genetic history of an archaic hominin group from Denisova Cave in Siberia JO - Nature VL - 468 UR - https://doi.org/10.1038/nature09710 DO - 10.1038/nature09710 ID - Reich2010 ER - TY - JOUR AU - Mitsui, Y. AU - Setoguchi, H. PY - 2012 DA - 2012// TI - Demographic histories of adaptively diverged riparian and non-riparian species of Ainsliaea (Asteraceae) inferred from coalescent analyses using multiple nuclear loci JO - BMC Evol Biol VL - 12 UR - https://doi.org/10.1186/1471-2148-12-254 DO - 10.1186/1471-2148-12-254 ID - Mitsui2012 ER - TY - JOUR AU - Mihola, O. AU - Trachtulec, Z. AU - Vlcek, C. AU - Schimenti, J. C. AU - Forejt, J. PY - 2009 DA - 2009// TI - A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase JO - Science VL - 323 UR - https://doi.org/10.1126/science.1163601 DO - 10.1126/science.1163601 ID - Mihola2009 ER - TY - JOUR AU - Perez, D. E. AU - Wu, C. I. PY - 1995 DA - 1995// TI - Further characterization of the Odysseus locus of hybrid sterility in Drosophila: one gene is not enough JO - Genetics VL - 140 ID - Perez1995 ER - TY - JOUR AU - Masly, J. P. AU - Jones, C. D. AU - Noor, M. A. F. AU - Locke, J. AU - Orr, H. A. PY - 2006 DA - 2006// TI - Gene Transposition as a Cause of Hybrid Sterility in Drosophila JO - Science VL - 313 UR - https://doi.org/10.1126/science.1128721 DO - 10.1126/science.1128721 ID - Masly2006 ER - TY - JOUR AU - Phadnis, N. AU - Orr, H. A. PY - 2009 DA - 2009// TI - A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids JO - Science VL - 323 UR - https://doi.org/10.1126/science.1163934 DO - 10.1126/science.1163934 ID - Phadnis2009 ER - TY - JOUR AU - Turner, T. L. AU - Hahn, M. W. AU - Nuzhdin, S. V. PY - 2005 DA - 2005// TI - Genomic Islands of Speciation in Anopheles gambiae JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030285 DO - 10.1371/journal.pbio.0030285 ID - Turner2005 ER - TY - JOUR AU - Noor, M. A. F. AU - Bennett, S. M. PY - 2009 DA - 2009// TI - Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species JO - Heredity VL - 103 UR - https://doi.org/10.1038/hdy.2009.151 DO - 10.1038/hdy.2009.151 ID - Noor2009 ER - TY - JOUR AU - Michel, A. P. AU - Sim, S. AU - Powell, T. H. Q. AU - Taylor, M. S. AU - Nosil, P. AU - Feder, J. L. PY - 2010 DA - 2010// TI - Widespread genomic divergence during sympatric speciation JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.1000939107 DO - 10.1073/pnas.1000939107 ID - Michel2010 ER - TY - JOUR AU - Vicoso, B. AU - Bachtrog, D. PY - 2013 DA - 2013// TI - Reversal of an ancient sex chromosome to an autosome in Drosophila JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12235 DO - 10.1038/nature12235 ID - Vicoso2013 ER - TY - JOUR AU - Newman, T. L. AU - Tuzun, E. AU - Morrison, V. A. AU - Hayden, K. E. AU - Ventura, M. AU - McGrath, S. D. PY - 2005 DA - 2005// TI - A genome-wide survey of structural variation between human and chimpanzee JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.4338005 DO - 10.1101/gr.4338005 ID - Newman2005 ER - TY - JOUR AU - Popesco, M. C. AU - MacLaren, E. J. AU - Hopkins, J. AU - Dumas, L. AU - Cox, M. AU - Meltesen, L. PY - 2006 DA - 2006// TI - Human Lineage–Specific Amplification, Selection, and Neuronal Expression of DUF1220 Domains JO - Science VL - 313 UR - https://doi.org/10.1126/science.1127980 DO - 10.1126/science.1127980 ID - Popesco2006 ER - TY - JOUR AU - Dumas, L. AU - Kim, Y. H. AU - Karimpour-Fard, A. AU - Cox, M. AU - Hopkins, J. AU - Pollack, J. R. PY - 2007 DA - 2007// TI - Gene copy number variation spanning 60 million years of human and primate evolution JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6557307 DO - 10.1101/gr.6557307 ID - Dumas2007 ER - TY - JOUR AU - Perry, G. H. AU - Yang, F. AU - Marques-Bonet, T. AU - Murphy, C. AU - Fitzgerald, T. AU - Lee, A. S. PY - 2008 DA - 2008// TI - Copy number variation and evolution in humans and chimpanzees JO - Genome Res VL - 39 UR - https://doi.org/10.1101/gr.082016.108 DO - 10.1101/gr.082016.108 ID - Perry2008 ER - TY - JOUR AU - Dennis, M. Y. AU - Nuttle, X. AU - Sudmant, P. H. AU - Antonacci, F. AU - Graves, T. A. AU - Nefedov, M. PY - 2012 DA - 2012// TI - Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication JO - Cell VL - 149 UR - https://doi.org/10.1016/j.cell.2012.03.033 DO - 10.1016/j.cell.2012.03.033 ID - Dennis2012 ER - TY - JOUR AU - Perry, G. H. AU - Dominy, N. J. AU - Claw, K. G. AU - Lee, A. S. AU - Fiegler, H. AU - Redon, R. PY - 2007 DA - 2007// TI - Diet and the evolution of human amylase gene copy number variation JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng2123 DO - 10.1038/ng2123 ID - Perry2007 ER - TY - JOUR AU - Nguyen, D. -. Q. AU - Webber, C. AU - Hehir-Kwa, J. AU - Pfundt, R. AU - Veltman, J. AU - Ponting, C. P. PY - 2008 DA - 2008// TI - Reduced purifying selection prevails over positive selection in human copy number variant evolution JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.077289.108 DO - 10.1101/gr.077289.108 ID - Nguyen2008 ER - TY - JOUR AU - Guerrier, S. AU - Coutinho-Budd, J. AU - Sassa, T. AU - Gresset, A. AU - Jordan, N. V. AU - Chen, K. PY - 2009 DA - 2009// TI - The F-BAR Domain of srGAP2 Induces Membrane Protrusions Required for Neuronal Migration and Morphogenesis JO - Cell VL - 138 UR - https://doi.org/10.1016/j.cell.2009.06.047 DO - 10.1016/j.cell.2009.06.047 ID - Guerrier2009 ER - TY - JOUR AU - Frantz, L. AU - Schraiber, J. AU - Madsen, O. AU - Megens, H. -. J. AU - Bosse, M. AU - Paudel, Y. PY - 2013 DA - 2013// TI - Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-9-r107 DO - 10.1186/gb-2013-14-9-r107 ID - Frantz2013 ER - TY - JOUR AU - Myers, N. AU - Mittermeier, R. A. AU - Mittermeier, C. G. AU - Fonseca, G. A. B. AU - Kent, J. PY - 2000 DA - 2000// TI - Biodiversity hotspots for conservation priorities JO - Nature VL - 403 UR - https://doi.org/10.1038/35002501 DO - 10.1038/35002501 ID - Myers2000 ER - TY - JOUR AU - Blouch, R. A. AU - Groves, C. P. PY - 1990 DA - 1990// TI - Naturally occurring suid hybrid in Java JO - Zeitschrift für Säugetierkunde VL - 55 ID - Blouch1990 ER - TY - STD TI - Oliver W: The IUCN Red List of Threatened Species. Volume 2014.2; 2008. ID - ref34 ER - TY - JOUR AU - Sudmant, P. H. AU - Kitzman, J. O. AU - Antonacci, F. AU - Alkan, C. AU - Malig, M. AU - Tsalenko, A. PY - 2010 DA - 2010// TI - Project 1000 Genomes, Eichler EE: Diversity of human copy number variation and multicopy genes JO - Science VL - 39 UR - https://doi.org/10.1126/science.1197005 DO - 10.1126/science.1197005 ID - Sudmant2010 ER - TY - JOUR AU - Bickhart, D. M. AU - Hou, Y. AU - Schroeder, S. G. AU - Alkan, C. AU - Cardone, M. F. AU - Matukumalli, L. K. PY - 2012 DA - 2012// TI - Copy number variation of individual cattle genomes using next-generation sequencing JO - Genome res VL - 22 UR - https://doi.org/10.1101/gr.133967.111 DO - 10.1101/gr.133967.111 ID - Bickhart2012 ER - TY - JOUR AU - Esteve-Codina, A. AU - Paudel, Y. AU - Ferretti, L. AU - Raineri, E. AU - Megens, H. -. J. AU - Silio, L. PY - 2013 DA - 2013// TI - Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-148 DO - 10.1186/1471-2164-14-148 ID - Esteve-Codina2013 ER - TY - JOUR AU - Paudel, Y. AU - Madsen, O. AU - Megens, H. -. J. AU - Frantz, L. AU - Bosse, M. AU - Bastiaansen, J. PY - 2013 DA - 2013// TI - Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-449 DO - 10.1186/1471-2164-14-449 ID - Paudel2013 ER - TY - JOUR AU - Groenen, M. A. M. AU - Archibald, A. L. AU - Uenishi, H. AU - Tuggle, C. K. AU - Takeuchi, Y. AU - Rothschild, M. F. PY - 2012 DA - 2012// TI - Analyses of pig genomes provide insight into porcine demography and evolution JO - Nature VL - 491 UR - https://doi.org/10.1038/nature11622 DO - 10.1038/nature11622 ID - Groenen2012 ER - TY - JOUR AU - Flicek, P. AU - Amode, M. R. AU - Barrell, D. AU - Beal, K. AU - Brent, S. AU - Carvalho-Silva, D. PY - 2012 DA - 2012// TI - Ensembl 2012 JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr991 DO - 10.1093/nar/gkr991 ID - Flicek2012 ER - TY - STD TI - Felsenstein J: PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164–166. ID - ref41 ER - TY - JOUR AU - Lewis, P. O. PY - 2001 DA - 2001// TI - A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data JO - Systematic Biology VL - 50 UR - https://doi.org/10.1080/106351501753462876 DO - 10.1080/106351501753462876 ID - Lewis2001 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogenetic trees JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.754 DO - 10.1093/bioinformatics/17.8.754 ID - Huelsenbeck2001 ER - TY - JOUR AU - Henrichsen, C. N. AU - Chaignat, E. AU - Reymond, A. PY - 2009 DA - 2009// TI - Copy number variants, diseases and gene expression JO - Human Molecular Genetics VL - 18 UR - https://doi.org/10.1093/hmg/ddp011 DO - 10.1093/hmg/ddp011 ID - Henrichsen2009 ER - TY - JOUR AU - Zhang, F. AU - Gu, W. AU - Hurles, M. E. AU - Lupski, J. R. PY - 2009 DA - 2009// TI - Copy Number Variation in Human Health, Disease, and Evolution JO - Annual Review of Genomics and Human Genetics VL - 10 UR - https://doi.org/10.1146/annurev.genom.9.081307.164217 DO - 10.1146/annurev.genom.9.081307.164217 ID - Zhang2009 ER - TY - JOUR AU - Sudmant, P. H. AU - Huddleston, J. AU - Catacchio, C. R. AU - Malig, M. AU - Hillier, L. W. AU - Baker, C. PY - 2013 DA - 2013// TI - Great Ape Genome Project, Marques-Bonet T, Eichler EE: Evolution and diversity of copy number variation in the great ape lineage JO - Genome Research VL - 23 UR - https://doi.org/10.1101/gr.158543.113 DO - 10.1101/gr.158543.113 ID - Sudmant2013 ER - TY - JOUR AU - Liu, G. E. AU - Hou, Y. AU - Zhu, B. AU - Cardone, M. F. AU - Jiang, L. AU - Cellamare, A. PY - 2010 DA - 2010// TI - Analysis of copy number variations among diverse cattle breeds JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.105403.110 DO - 10.1101/gr.105403.110 ID - Liu2010 ER - TY - JOUR AU - Alkan, C. AU - Kidd, J. M. AU - Marques-Bonet, T. AU - Aksay, G. AU - Antonacci, F. AU - Hormozdiari, F. PY - 2009 DA - 2009// TI - Personalized copy number and segmental duplication maps using next-generation sequencing JO - Nat Genet VL - 41 UR - https://doi.org/10.1038/ng.437 DO - 10.1038/ng.437 ID - Alkan2009 ER - TY - JOUR AU - Hach, F. AU - Hormozdiari, F. AU - Alkan, C. AU - Hormozdiari, F. AU - Birol, I. AU - Eichler, E. E. PY - 2010 DA - 2010// TI - Sahinalp SC: mrsFAST: a cache-oblivious algorithm for short-read mapping JO - Nat Meth VL - 7 UR - https://doi.org/10.1038/nmeth0810-576 DO - 10.1038/nmeth0810-576 ID - Hach2010 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Högstrand, K. AU - Böhme, J. PY - 1999 DA - 1999// TI - Gene conversion of major histocompatibility complex genes is associated with CpG-rich regions JO - Immunogenetics VL - 49 UR - https://doi.org/10.1007/s002510050518 DO - 10.1007/s002510050518 ID - Högstrand1999 ER - TY - JOUR AU - Galtier, N. AU - Piganeau, G. AU - Mouchiroud, D. AU - Duret, L. PY - 2001 DA - 2001// TI - GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis JO - Genetics VL - 159 ID - Galtier2001 ER - TY - JOUR AU - Bentley, D. R. AU - Balasubramanian, S. AU - Swerdlow, H. P. AU - Smith, G. P. AU - Milton, J. AU - Brown, C. G. PY - 2008 DA - 2008// TI - Accurate whole human genome sequencing using reversible terminator chemistry JO - Nature VL - 456 UR - https://doi.org/10.1038/nature07517 DO - 10.1038/nature07517 ID - Bentley2008 ER - TY - STD TI - Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research. 2008;36:e105–5. ID - ref54 ER - TY - JOUR AU - Aird, D. AU - Ross, M. AU - Chen, W. -. S. AU - Danielsson, M. AU - Fennell, T. AU - Russ, C. PY - 2011 DA - 2011// TI - Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries JO - Genome Biology VL - 12 UR - https://doi.org/10.1186/gb-2011-12-2-r18 DO - 10.1186/gb-2011-12-2-r18 ID - Aird2011 ER - TY - STD TI - Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Research. 2012;40:e72–2. ID - ref56 ER - TY - JOUR AU - Oyola, S. AU - Otto, T. AU - Gu, Y. AU - Maslen, G. AU - Manske, M. AU - Campino, S. PY - 2012 DA - 2012// TI - Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-1 DO - 10.1186/1471-2164-13-1 ID - Oyola2012 ER - TY - JOUR AU - Quail, M. AU - Smith, M. AU - Coupland, P. AU - Otto, T. AU - Harris, S. AU - Connor, T. PY - 2012 DA - 2012// TI - A tale of three next generation sequencing platforms: comparison of Ion Torrent Pacific Biosciences and Illumina MiSeq sequencers JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-341 DO - 10.1186/1471-2164-13-341 ID - Quail2012 ER - TY - JOUR AU - Haider, S. AU - Ballester, B. AU - Smedley, D. AU - Zhang, J. AU - Rice, P. AU - Kasprzyk, A. PY - 2009 DA - 2009// TI - BioMart Central Portal—unified access to biological data JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp265 DO - 10.1093/nar/gkp265 ID - Haider2009 ER - TY - JOUR AU - Maere, S. AU - Heymans, K. AU - Kuiper, M. PY - 2005 DA - 2005// TI - BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti551 DO - 10.1093/bioinformatics/bti551 ID - Maere2005 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. PY - 2003 DA - 2003// TI - Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks JO - Genome Research VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - JOUR AU - Fan, Y. AU - Wu, R. AU - Chen, M. -. H. AU - Kuo, L. AU - Lewis, P. O. PY - 2011 DA - 2011// TI - Choosing among Partition Models in Bayesian Phylogenetics JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msq224 DO - 10.1093/molbev/msq224 ID - Fan2011 ER - TY - JOUR AU - Xie, W. AU - Lewis, P. O. AU - Fan, Y. AU - Kuo, L. AU - Chen, M. -. H. PY - 2011 DA - 2011// TI - Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection JO - Systematic Biology VL - 60 UR - https://doi.org/10.1093/sysbio/syq085 DO - 10.1093/sysbio/syq085 ID - Xie2011 ER -