| [1] | Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, et al. (2012) Population Genomics of Early Events in the Ecological Differentiation of Bacteria. Science 336: 48–51 doi:10.1126/science.1218198.
|
| [2] | Vos M, Didelot X (2009) A comparison of homologous recombination rates in bacteria and archaea. ISME J 3: 199–208 doi:10.1038/ismej.2008.93.
|
| [3] | Kondrashov AS (1983) Multilocus model of sympatric specation I & II. One and Two characters. Theoretical population biology 24: 121–144.
|
| [4] | Kondrashov AS (1986) Multilocus Model of Sympatric Speciation III. Computer Simulations. Theoretical population biology 29: 1–15.
|
| [5] | Kondrashov AS, Kondrashov FA (1999) Interactions among quantitative traits in the course of sympatric speciation. Nature 400: 351–354 doi:10.1038/22514.
|
| [6] | Bush GL (1994) Sympatric speciation in animals: new wine in old bottles. Trends in Ecology and Evolution 9: 285–288 doi:10.1016/0169–5347(94)90031–0.
|
| [7] | Via S (2001) Sympatric speciation in animals: The ugly duckling grows up. Trends in Ecology and Evolution 16: 381–390.
|
| [8] | Kondrashov AS, Mina MV (1986) Sympatric speciation: when is it possible? Biological Journal of the Linnean Society 27: 201–223.
|
| [9] | Mallet J, Meyer A, Nosil P, Feder JL (2009) Space, sympatry and speciation. Journal of Evolutionary Biology 22: 2332–2341 doi:10.1111/j.1420–9101.2009.01816.x.
|
| [10] | Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976–978 doi:10.1126/science.1086909.
|
| [11] | Cohan FM, Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17: R373–R386 doi:10.1016/j.cub.2007.03.032.
|
| [12] | Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315: 476–480.
|
| [13] | Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323: 741–746 doi:10.1126/science.1159388.
|
| [14] | Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiology Reviews 35: 957–976 doi:10.1111/j.1574–6976.2011.00292.x.
|
| [15] | McKinnon J, Rundle H (2002) Speciation in nature: the threespine stickleback model systems. Trends in Ecology and Evolution 17: 480–488.
|
| [16] | Felsenstein J (1981) Skepticism towards Santa Rosalia, or why are there so few kinds of animals? Evolution 35: 124–138.
|
| [17] | Haldane JBS (1932) The Causes of Evolution. London: Longmans, Green & Co.
|
| [18] | Mallet J (2006) What does Drosophila genetics tell us about speciation? Trends in Ecology and Evolution 21: 386–393 doi:10.1016/j.tree.2006.05.004.
|
| [19] | Schluter D (2009) Evidence for ecological speciation and its alternative. Science 323: 737–741 doi:10.1126/science.1160006.
|
| [20] | Cooper TF (2007) Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli. PLOS Biol 5: e225.
|
| [21] | Kondrashov AS (1982) Selection against harmful mutations in large sexual and asexual populations. Genetical Research 40: 325–332.
|
| [22] | Levin BR, Cornejo OE (2009) The Population and Evolutionary Dynamics of Homologous Gene Recombination in Bacterial Populations. PLOS Genet 5: e1000601 doi:10.1371/journal.pgen.1000601.t005.
|
| [23] | Kondrashov FA, Kondrashov AS (2001) Multidimensional epistasis and the disadvantage of sex. Proc Natl Acad Sci USA 98: 12089–12092 doi:10.1073/pnas.211214298.
|
| [24] | Wylie CS, Trout AD, Kessler DA, Levine H (2010) Optimal strategy for competence differentiation in bacteria. PLOS Genet 6. doi:10.1371/journal.pgen.1001108.
|
| [25] | Mayr E (1942) Systematics and the Origin of Species. Cambridge, MA: Harvard University Press.
|
| [26] | Dieckmann U, Doebeli M (1999) On the origin of species by sympatric speciation. Nature 400: 354–357 doi:10.1038/22521.
|
| [27] | Turner T, Hahn M, Nuzhdin S (2005) Genomic islands of speciation in Anopheles gambiae. PLOS Biol 3: 1572–1578 doi:10.1371/journal.pbio.0030285.
|
| [28] | White BJ, Cheng C, Simard F, Costantini C, Besansky NJ (2010) Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae. Mol Ecol 19: 925–939 doi:10.1111/j.1365–294X.2010.04531.x.
|
| [29] | Neafsey DE, Lawniczak MKN, Park DJ, Redmond SN, Coulibaly MB, et al. (2010) SNP genotyping defines complex gene-flow boundaries among african malaria vector mosquitoes. Science 330: 514–517 doi:10.1126/science.1193036.
|
| [30] | Lawniczak MKN, Emrich SJ, Holloway AK, Regier AP, Olson M, et al. (2010) Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences. Science 330: 512–514 doi:10.1126/science.1195755.
|
| [31] | Via S (2012) Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philos Trans R Soc Lond, B, Biol Sci 367: 451–460 doi:10.1098/rstb.2011.0260.
|
| [32] | Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, et al. (2004) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717–723 doi:10.1038/nature02415.
|
| [33] | Colosimo P, Hosemann K, Balabhadra S (2005) Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science. 307: 1928–1933 doi:10.1126/science.1107239.
|
| [34] | Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, et al. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55–61 doi:10.1038/nature10944.
|
| [35] | Cornejo OE, McGee L, Rozen DE (2010) Polymorphic Competence Peptides Do Not Restrict Recombination in Streptococcus pneumoniae. Mol Biol Evol 27: 694–702 doi:10.1093/molbev/msp287.
|
| [36] | Majewski J (2001) Sexual isolation in bacteria. FEMS Microbiol Lett 199: 161–169.
|
| [37] | Falush D, Torpdahl M, Didelot X, Conrad DF, Wilson DJ, et al. (2006) Mismatch induced speciation in Salmonella: model and data. Philos Trans R Soc Lond, B, Biol Sci 361: 2045–2053 doi:10.1098/rstb.2006.1925.
|
| [38] | Eppley JM, Tyson GW, Getz WM, Banfield JF (2007) Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics 177: 407–416 doi:10.1534/genetics.107.072892.
|
| [39] | Denef VJ, Mueller RS, Banfield JF (2010) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4: 599–610 doi:10.1038/ismej.2009.158.
|
| [40] | Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, et al. (2012) Patterns of Gene Flow Define Species of Thermophilic Archaea. PLOS Biol 10: e1001265 doi:10.1371/journal.pbio.1001265.t001.
|
| [41] | Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, et al. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci USA 107: 2383–2390 doi:10.1073/pnas.0907041107.
|
| [42] | Rozen DE, de Visser JAGM, Gerrish PJ (2002) Fitness Effects of Fixed Beneficial Mutations in Microbial Populations. Current Biology 12: 1040–1045 doi:10.1016/S0960–9822(02)00896–5.
|
| [43] | Shapiro BJ, David LA, Friedman J, Alm EJ (2009) Looking for Darwin’s footprints in the microbial world. Trends in Microbiology 17: 196–204 doi:10.1016/j.tim.2009.02.002.
|
| [44] | Vos M (2011) A species concept for bacteria based on adaptive divergence. Trends in Microbiology 19: 1–7 doi:10.1016/j.tim.2010.10.003.
|
| [45] | Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, et al. (2012) Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos Trans R Soc Lond, B, Biol Sci 367: 343–353 doi:10.1098/rstb.2011.0198.
|
| [46] | Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, et al. (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. doi:10.1038/nature11041.
|
| [47] | Lawrence J (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Current opinion in genetics & development 9: 642–648.
|
| [48] | Mandel MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 457: 215–218 doi:10.1038/nature07660.
|
| [49] | Coleman ML, Chisholm SW (2010) Ecosystem-specific selection pressures revealed through comparative population genomics. Proc Natl Acad Sci USA 107: 18634–18639 doi:10.1073/pnas.1009480107.
|
| [50] | Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, et al. (2011) Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environmental Microbiology 13: 265–275 doi:10.1111/j.1462–2920.2010.02328.x.
|
