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References

  • Anderson JB, Funt J, Thompson DA, Prabhu S, Socha A, Sirjusingh , Dettman JR, Parreiras L, Guttman DS, Regev A et al. 2010. Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Current Biology 20: 13831388.
  • Anderson JB, Korhonen K, Ullrich RC. 1980. Relationships between European and North American biological species of Armillaria mellea. Experimental Mycology 4: 7886.
  • Barton NH, Charlesworth B. 1984. Genetic revolutions, founder effects, and speciation. Annual Review of Ecology and Systematics 15: 133164.
  • Bateson W. 1909. Heredity and variation in modern lights. In: Seward AC, ed. Darwin and modern science. Cambridge, UK: Cambridge University Press, 85101.
  • Brasier CM. 2001. Rapid evolution of introduced plant pathogens via interspecific hybridization. BioScience 51: 123133.
  • Carbone I, Kohn LM. 2001. A microbial population–species interface: nested cladistic and coalescent inference with multilocus data. Molecular Ecology 10: 947964.
  • Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S et al. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5: e1000618.
  • Couch BC, Fudal I, Lebrun M-H, Tharreau D, Valent B, van Kim P, Nottéghem J-L, Kohn LM. 2005. Origins of host-specific populations of the blast pathogen Magnaporthe oryzae in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice. Genetics 170: 613630.
  • Coyne JA, Orr HA. 1998. The evolutionary genetics of speciation. Philosophical Transactions of the Royal Society B: Biological Sciences 353: 287.
  • Craven KD. 2012. Population studies of native grass-endophyte symbioses provide clues for the roles of host jumps and hybridization in driving their evolution. Molecular Ecology 21: 25622564.
  • Croll D, McDonald BA. 2012. The accessory genome as a cradle for adaptive evolution in pathogens. PLoS Pathogens 8: e1002608.
  • Dettman J, Anderson J, Kohn L. 2008. Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora. BMC Evolutionary Biology 8: 35.
  • Dettman JR, Anderson JB, Kohn LM. 2010. Genome-wide investigation of reproductive isolation in experimental lineages and natural species of Neurospora: indetifying candidate regions by microarray-based genotyping and mapping. Evolution 64: 694709.
  • Dettman JR, Jacobson DJ, Turner E, Pringle A, Taylor JW. 2003. Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote. Evolution 57: 27212741.
  • Dettman JR, Sirjusingh C, Kohn LM, Anderson JB. 2007. Incipient speciation by divergent adaptation and antagonistic epistasis in yeast. Nature 447: 585588.
  • Dobzhansky TG, Dobzhansky T. 1937. Genetics and the origin of species. New York, NY, USA: Columbia University Press.
  • Dutheil J, Hobolth A. 2012. Ancestral population genomics. In: Anisimova M, ed. Evolutionary genomics (Methods in molecular biology; vol. 856.). Clifton, NJ, USA: Humana Press, 293313.
  • Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH. 2009. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183: 259274.
  • Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH et al. 2011. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proceedings of the National Academy of Sciences, USA 108: 1873218736.
  • Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484: 186194.
  • Friesen T, Faris J, Solomon PS, Oliver R. 2008. Host-specific toxins: effectors of necrotrophic pathogenicity. Cellular Microbiology 10: 14211428.
  • Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, Faris JD, Rasmussen JB, Solomon PS, McDonald BA, Oliver RP. 2006. Emergence of a new disease as a result of interspecific virulence gene transfer. Nature Genetics 38: 953956.
  • Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology and Evolution 27: 480488.
  • Gavrilets S, Li H, Vose MD. 2000. Patterns of parapatric speciation. Evolution 54: 11261134.
  • Giraud T, Gladieux P, Gavrilets S. 2010. Linking the emergence of fungal plant diseases with ecological speciation. Trends in Ecology and Evolution 25: 387395.
  • Giraud T, Yockteng R, López-Villavicencio M, Refrégier G, Hood ME. 2008. Mating system of the anther smut fungus Microbotryum violaceum: selfing under heterothallism. Eukaryotic Cell 7: 765775.
  • Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A, Giraud T. 2011. Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact. Molecular Biology and Evolution 28: 459471.
  • Glemin S, Bataillon T. 2009. A comparative view of the evolution of grasses under domestication. New Phytologist 183: 273290.
  • Goodwin SB, Ben M'barek S, Dhillon B, Wittenberg AHJ, Crane CF, Hane JK, Foster AJ, Van der Lee TAJ, Grimwood J, Aerts A et al. 2011. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genetics 7: e1002070.
  • Greig D. 2007. A screen for recessive speciation genes expressed in the gametes of F1 hybrid yeast. PLoS Genetics 3: e21.
  • Greig D, Louis EJ, Borts RH, Travisano M. 2002. Hybrid speciation in experimental populations of yeast. Science 298: 17731775.
  • Hane JK, Rouxel T, Howlett BJ, Kema GH, Goodwin SB, Oliver RP. 2011. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biology 12: R45.
  • Hawthorne DJ, Via S. 2001. Genetic linkage of ecological specialization and reproductive isolation in pea aphids. Nature 412: 904907.
  • Hobolth A, Christensen OF, Mailund T, Schierup MH. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics 3: e7.
  • de Jonge R, Bolton MD, Thomma BPHJ. 2011. How filamentous pathogens co-opt plants: the ins and outs of fungal effectors. Current Opinion in Plant Biology 14: 400406.
  • de Jonge R, Van Esse HP, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, Zhang Z, Usami T, Lievens B, Subbarao KV et al. 2012. Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proceedings of the National Academy of Sciences, USA 109: 51105115.
  • Kao KC, Schwartz K, Sherlock G. 2010. A genome-wide analysis reveals no nuclear Dobzhansky-Muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities. PLoS Genetics 6: e1001038.
  • Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BPHJ, Chen Z, Henrissat B, Lee Y-H, Park J et al. 2011. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathogens 7: e1002137.
  • Kohn LM. 2005. Mechanisms of fungal speciation. Annual Review of Phytopathology 43: 279308.
  • Kulathinal RJ, Stevison LS, MaF Noor. 2009. The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS Genetics 5: e1000550.
  • Laurie JD, Ali S, Linning R, Mannhaupt G, Wong P, Güldener U, Münsterkötter M, Moore R, Kahmann R, Bakkeren G et al. 2012. Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. Plant Cell 24: 17331745.
  • Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469: 529533.
  • Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A et al. 2012. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genetics 8: e1003125.
  • Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B et al. 2013. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3: Genes|Genomes|Genetics 3: 4163.
  • McGaugh SE, Noor MA. 2012. Genomic impacts of chromosomal inversions in parapatric Drosophila species. Philosophical Transactions of the Royal Society B: Biological Sciences 367: 422429.
  • Muller H. 1942. Isolating mechanisms, evolution and temperature. Proceedings of the Biological Symposia 6: 71125.
  • Nosil P, Gompert Z, Farkas TE, Comeault AA, Feder JL, Buerkle CA, Parchman TL. 2012. Genomic consequences of multiple speciation processes in a stick insect. Proceedings of the Royal Society B: Biological Sciences 279: 50585065.
  • Nosil P, Harmon LJ, Seehausen O. 2009. Ecological explanations for (incomplete) speciation. Trends in Ecology & Evolution 24: 145156.
  • Oberhofer M, Leuchtman A. 2012. Genetic diversity in epichloid endophytes of Hordelymus europaeus suggests repeated host jumps and interspecific hybridizations. Molecular Ecology 21: 27132726.
  • Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F et al. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens 8: e1003037.
  • Orr MR, Smith TB. 1998. Ecology and speciation. Trends in Ecology & Evolution 13: 502506.
  • Parreiras LS, Kohn LM, Anderson JB. 2011. Cellular effects and epistasis among three determinants of adaptation in experimental populations of Saccharomyces cerevisiae. Eukaryotic Cell 10: 13481356.
  • Presgraves DC, Balagopalan L, Abmayr SM, Orr HA. 2003. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature 423: 715719.
  • Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486: 527538.
  • Raffaele S, Kamoun S. 2012. Genome evolution in filamentous plant pathogens: why bigger can be better. Nature Reviews Microbiology 10: 417430.
  • Rieseberg LH. 2001. Chromosomal rearrangements and speciation. Trends in Ecology & Evolution 16: 351358.
  • Rieseberg LH, Willis JH. 2007. Plant speciation. Science 317: 910914.
  • Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S et al. 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nature Communications 2: 202.
  • Rundle HD, Nosil P. 2005. Ecological speciation. Ecology Letters 8: 336352.
  • Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Gerrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169175.
  • Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DK, Haws DC, Moore N, Oeser B et al. 2013. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genetics 9: e1003323.
  • Servedio MR, Noor MAF. 2003. The role of reinforcement in speciation: theory and data. Annual Review of Ecology, Evolution, and Systematics 34: 339364.
  • Stergiopoulos I, de Wit PJGM. 2009. Fungal effector proteins. Annual Review of Phytopathology 47: 233263.
  • Stukenbrock EH, Banke S, Javan-Nikkhah M, McDonald BA. 2007. Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation. Molecular Biology and Evolution 24: 398411.
  • Stukenbrock EH, Bataillon T, Dutheil JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH. 2011. The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Research 21: 21572166.
  • Stukenbrock EH, Christiansen FB, Hansen TT, Dutheil JY, Schierup MH. 2012. Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proceedings of the National Academy of Sciences, USA 109: 1095410959.
  • Stukenbrock EH, Jorgensen FG, Zala M, Hansen TT, McDonald BA, Schierup MH. 2010. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genetics 6: e1001189.
  • Stukenbrock EH, McDonald BA. 2008. The origins of plant pathogens in agro-ecosystems. Annual review of Phytopathology 46: 75100.
  • Stukenbrock EH, McDonald BA. 2009. Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions. Molecular Plant-Microbe Interactions 22: 371380.
  • Tack AJM, Thrall PH, Barrett LG, Burdon JJ, Laine AL. 2012. Variation in infectivity and aggressiveness in space and time in wild host–pathogen systems: causes and consequences. Journal of Evolutionary Biology 25: 19181936.
  • Tao Y, Zeng ZB, Li J, Hartl DL, Laurie CC. 2003. Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome. Genetics 164: 13991418.
  • Taylor J, Jacobson D, Fisher M. 1999. The evolution of asexual fungi: reproduction, speciation and classification. Annual Review of Phytopathology 37: 197246.
  • Turelli M, Barton NH, Coyne JA. 2001. Theory and speciation. Trends in Ecology & Evolution 16: 330343.
  • Turner E, Jacobson DJ, Taylor JW. 2011. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection. PLoS Genetics 7: e1002204.
  • Via S. 2009. Natural selection in action during speciation. Proceedings of the National Academy of Sciences, USA 106: 99399946.
  • Woolhouse ME, Taylor LH, Haydon DT. 2001. Population biology of multihost pathogens. Science 292: 11091112.
  • Wright KM, Lloyd D, Lowry DB, Macnair MR, Willis JH. 2013. Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus. PLoS Biology 11: e1001497.
  • Xue M, Yang J, Li Z, Hu S, Yao N, Dean RA, Zhao W, Shen M, Zhang H, Li C et al. 2012. Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PLoS Genetics 8: e1002869.