How reticulated are species?

BioEssays

Volumn 38, Issue 2, 2016, Pages 140-149

  Mallet, James ^a,b   Besansky, Nora ^c   Hahn, Matthew W ^d  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF NOTRE DAME   (United States)

^d INDIANA UNIVERSITY   (United States)

Author keywords

Admixture; Homoplasy; Introgression; Phylogenetic discordance; Speciation; Species concepts; Tree of life

Indexed keywords

ADAPTIVE RADIATION; ARTICLE; DISEASE CONTROL; EUKARYOTE; EVOLUTION; GENE TRANSFER; GENETIC ANALYSIS; GENOME; GENOMICS; HORIZONTAL GENE TRANSFER; HYBRIDIZATION; INTROGRESSION; NONHUMAN; PHYLOGENY; PROKARYOTE; SPECIES; SPECIES DIFFERENTIATION; TREE OF LIFE; ANIMAL; GENETICS; MOLECULAR EVOLUTION; PLANT; PROCEDURES; TRANSGENIC ORGANISM;

ANIMALS; EUKARYOTA; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENETIC SPECIATION; GENOMICS; ORGANISMS, GENETICALLY MODIFIED; PHYLOGENY; PLANTS;

EID: 84956661631     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201500149     Document Type: Article

References (120)

1. Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-9.
2. Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74: 5088-90.
3. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284: 2124-9.
4. Hilario E, Gogarten JP. 1993. Horizontal transfer of ATPase genes - the tree of life becomes a net of life. BioSyst 31: 111-9.
5. Martin W. 1999. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. BioEssays 21: 99-104.
6. Clark AG, Eisen MB, Smith DR, Bergman CM, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-18.
7. Lindblad-Toh K, Garber M, Zuk O, Lin MF, et al. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-82.
8. Dujon B, Sherman D, Fischer G, Durrens P, et al. 2004. Genome evolution in yeasts. Nature 430: 35-44.
9. Maia VH, Gitzendanner MA, Soltis PS, Wong GK-S, et al. 2014. Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large data set using next-generation sequence data. Int J Plant Sci 175: 613-50.
10. Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, et al. 2011. A functional pylogenomic view of the seed plants. PLoS Genet 7: e1002411.
11. Marcussen T, Sandve SR, Heier L, Spannagl M, et al. 2014. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345: 1250092.
12. Brandvain Y, Kenney AM, Flagel L, Coop G, et al. 2014. Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet 10: e1004410.
13. McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, et al. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res 22: 746-54.
14. Yang Y, Moore MJ, Brockington SF, Soltis DE, et al. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Mol Biol Evol 32: 2001-14.
15. Mayr E. 1963. Animal Species and Evolution. Cambridge, MA: Harvard University Press.
16. Anderson E, Stebbins GL. 1954. Hybridization as an evolutionary stimulus. Evolution 8: 378-88.
17. Heliconius Genome Consortium. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487: 94-8.
18. Fontaine MC, Pease JB, Steele A, Waterhouse RM, et al. 2015. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347: 1258524.
19. Zawadzki P, Roberts MS, Cohan FM. 1995. The log-linear relationship between sexual isolation and sequence divergence in Bacillus is robust. Genetics 140: 917-32.
20. Majewski J, Zawadzki P, Pickerill P, Cohan FM, et al. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J Bacteriol 182: 1016-23.
21. Eppley JM, Tyson GW, Getz WM, Banfield JF. 2007. Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics 177: 407-16.
22. Naor A, Lapierre P, Mevarech M, Papke RT, et al. 2012. Low species barriers in halophilic Archaea and the formation of recombinant hybrids. Curr Biol 22: 1444-8.
23. Gourbière S, Mallet J. 2010. Are species real? The shape of the species boundary with exponential failure, reinforcement, and the "missing snowball". Evolution 64: 1-24.
24. Morales L, Dujon B. 2012. Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev 76: 721-39.
25. Woese CR. 2002. On the evolution of cells. Proc Natl Acad Sci USA 99: 8742-7.
26. Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, et al. 2011. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS ONE 6: e22099.
27. Rivera MC, Lake JA. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431: 152-5.
28. McInerney JO, O'Connell MJ, Pisani D. 2014. The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nat Rev Microbiol 12: 449-55.
29. Puigbò P, Wolf YI, Koonin EV. 2009. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 8: 1-17.
30. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-7.
31. Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8: e62510.
32. Dagan T, Martin W. 2006. The tree of one percent. Genome Biol 7: 118.
33. Lawrence JG, Retchless AC. 2010. The myth of bacterial species and speciation. Biol Philos 25: 569-88.
34. Mindell DP. 2013. The Tree of Life: metaphor, model, and heuristic device. Syst Biol 62: 479-89.
35. Huang J. 2013. Horizontal gene transfer in eukaryotes: the weak-link model. BioEssays 35: 868-75.
36. Keeling PJ, Palmer JD. 2008. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-18.
37. Crisp A, Boschetti C, Perry M, Tunnacliffe A, et al. 2015. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol 16: 50.
38. Gladyshev EA, Meselson M, Arkhipova IR. 2008. Massive horizontal gene transfer in bdelloid rotifers. Science 320: 1210-3.
39. Boschetti C, Carr A, Crisp A, Eyres I, et al. 2012. Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet 8: e1003035.
40. Wu B, Buljic A, Hao W. 2015. Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast. Mol Biol Evol 32: 2559-70.
41. Sela N, Kim E, Ast G. 2010. The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol 11: R59.
42. Kidwell MG. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49-63.
43. Lynch M. 2007. The Origins of Genome Architecture. Sunderland, MA: Sinauer Associates.
44. Lynch M. 2006. The origins of eukaryotic gene structure. Mol Biol Evol 23: 450-68.
45. Rogozin IB, Carmel L, Csuros M, Koonin EV. 2012. Origin and evolution of spliceosomal introns. Biol Direct 7: 11.
46. Schaack S, Gilbert C, Feschotte C. 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol 25: 537-46.
47. Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25: 1979-94.
48. Dutheil JY, Munch K, Nam K, Mailund T, et al. 2015. Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence. PLoS Genet 11: e1005451.
49. Wiuf C, Zhao K, Innan H, Nordborg M. 2004. The probability and chromosomal extent of trans-specific polymorphism. Genetics 168: 2363-72.
50. Teixeira JC, de Filippo C, Weihmann A, Meneu JR, et al. 2015. Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees, and bonobos. Mol Biol Evol 32: 1186-96.
51. Saitou N, Yamamoto F. 1997. Evolution of primate ABO blood group genes and their homologous genes. Mol Biol Evol 14: 399-411.
52. Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet 2: e68.
53. Yang Z. 2014. Molecular Evolution. A Statistical Approach. Oxford: Oxford University Press.
54. Yang Z, Rannala B. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Mol Biol Evol 31: 3125-35.
55. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24: 332-40.
56. Grant PR, Grant BR. 1992. Hybridization of bird species. Science 256: 193-7.
57. Mallet J. 2005. Hybridization as an invasion of the genome. Trends Ecol Evol 20: 229-37.
58. Arnold ML, Sapir Y, Martin NH. 2008. Genetic exchange and the origin of adaptations: prokaryotes to primates. Philos Trans R Soc Lond B Biol Sci 363: 2813-20.
59. Mallet J, Beltrán M, Neukirchen W, Linares M. 2007. Natural hybridization in heliconiine butterflies: the species boundary as a continuum. BMC Evol Biol 7: 28.
60. Bacilieri R, Ducousso A, Petit RJ, Kremer A. 1996. Mating system and asymmetric hybridization in a mixed stand of European oaks. Evolution 50: 900-8.
61. Grant PR. 1993. Hybridization of Darwin's finches on Isla Daphne Major, Galápagos. Philos Trans R Soc Lond B Biol Sci 340: 127-39.
62. Mallet J, McMillan WO, Jiggins CD. 1998. Estimating the mating behavior of a pair of hybridizing Heliconius species in the wild. Evolution 52: 503-10.
63. Lee Y, Marsden CD, Norris LC, Collier TC, et al. 2013. Spatiotemporal dynamics of gene flow and hybrid fitness between the M and S forms of the malaria mosquito, Anopheles gambiae. Proc Natl Acad Sci USA 110: 19854-9.
64. Coyne JA, Orr HA. 1997. " Patterns of speciation in Drosophila" revisited. Evolution 51: 295-303.
65. Price TD, Bouvier MM. 2002. The evolution of F1 postzygotic incompatibilities in birds. Evolution 56: 2083-9.
66. Moyle LC, Nakazato T. 2010. Hybrid incompatibility "snowballs" between Solanum species. Science 329: 1521-3.
67. Moyle LC, Olson MS, Tiffin P, Baum D. 2004. Patterns of reproductive isolation in three angiosperm genera. Evolution 58: 1195-208.
68. Anderson E. 1948. Hybridization of the habitat. Evolution 2: 1-9.
69. Leaché AD, Harris RB, Rannala B, Yang Z. 2013. The influence of gene flow on species tree estimation: a simulation study. Syst Biol 63: 17-30.
70. Coluzzi M, Sabatini A, Petrarca V, Di Deco MA. 1979. Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex. Trans R Soc Trop Med Hyg 73: 483-97.
71. Weetman D, Steen K, Rippon EJ, Mawejje HD, et al. 2014. Contemporary gene flow between wild An. gambiae s.s. and An. arabiensis. Parasites Vectors 7: 345.
72. Mawejje HD, Wilding CS, Rippon EJ, Hughes A, et al. 2013. Insecticide resistance monitoring of field-collected Anopheles gambiae s.l. populations from Jinja, eastern Uganda, identifies high levels of pyrethroid resistance. Med Vet Entomol 27: 276-83.
73. Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, et al. 2013. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Res 23: 1817-28.
74. Lamichhaney S, Berglund J, Almen MS, Maqbool K, et al. 2015. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature 518: 371-5.
75. Brawand D, Wagner CE, Li YI, Malinsky M, et al. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513: 375-81.
76. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, et al. 2014. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci USA 111: 18655-60.
77. Cui R, Schumer M, Kruesi K, Walter R, et al. 2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution 67: 2166-79.
78. Green RE, Krause J, Briggs AW, Maricic T, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-22.
79. Jarvis ED, Mirarab S, Aberer AJ, Li B, et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-31.
80. Suh A, Smeds L, Ellegren H. 2015. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol 13: e1002224.
81. Prum RO, Berv JS, Dornburg A, Field DJ, et al. 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526: 569-73.
82. Whelan NV, Kocot KM, Moroz LL, Halanych KM. 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proc Natl Acad Sci USA 112: 5773-8.
83. Hedrick PW. 2013. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Mol Ecol 22: 4606-18.
84. Mallet J. 2007. Hybrid speciation. Nature 446: 279-83.
85. Rieseberg LH. 1997. Hybrid origins of plant species. Annu Rev Ecol Syst 28: 359-89.
86. Seehausen O. 2004. Hybridization and adaptive radiation. Trends Ecol Evol 19: 198-207.
87. Stankowski S, Streisfeld MA. 2015. Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers. Proc Biol Sci 282: 20151666.
88. Grant PR, Grant BR. 2014. Synergism of natural selection and introgression in the origin of a new species. Am Naturalist 183: 671-81.
89. Mallet J. 2013. Species, concepts of. In Levin SA, ed; Encyclopedia of Biodiversity, Second Edition, Volume 6. Waltham, MA: Academic Press. p. 679-91.
90. Behm JE, Ives AR, Boughman JW. 2010. Breakdown in postmating isolation and the collapse of a species pair through hybridization. Am Naturalist 175: 11-26.
91. Maddison WP. 1997. Gene trees in species trees. Syst Biol 46: 523-36.
92. Liu L, Yu L, Kubatko L, Pearl DK, et al. 2009. Coalescent methods for estimating phylogenetic trees. Mol Phylogen Evol 53: 320-8.
93. Edwards SV. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
94. Orr HA, Turelli M. 2001. The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Evolution 55: 1085-94.
95. Coyne JA, Orr HA. 2004. Speciation. Sunderland, MA: Sinauer Associates.
96. Orr HA, Madden LD, Coyne JA, Goodwin R, et al. 1997. The developmental genetics of hybrid inviability: a mitotic defect in Drosophila hybrids. Genetics 145: 1031-40.
97. Greig D. 2007. A screen for recessive speciation genes expressed in the gametes of F1 hybrid yeast. PLoS Genet 3: 281-6.
98. Greig D. 2008. Reproductive isolation in Saccharomyces. Heredity 102: 39-44.
99. True JR, Weir BS, Laurie CC. 1996. A genome-wide survey of hybrid incompatibility factors by the introgression of marked segments of Drosophila mauritiana chromosomes into Drosophila simulans. Genetics 142: 819-37.
100. Hollocher H, Wu CI. 1996. The genetics of reproductive isolation in the Drosophila simulans clade: X vs. autosomal effects and male vs. female effects. Genetics 143: 1243-55.
101. Masly JP, Presgraves DC. 2007. High-resolution genome-wide dissection of the two rules of speciation in Drosophila. PLoS Biol 5: e243.
102. Wu CI, Palopoli MF, Johnson NA. 1996. Haldane's rule and its legacy: why are there so many sterile males? Trends Ecol Evol 11: 281-4.
103. Chapman T, Partridge L. 1996. Sexual conflict as fuel for evolution. Nature 381: 189-90.
104. Slotman M, della Torre A, Powell JR. 2004. The genetics of inviability and male sterility in hybrids between Anopheles gambiae and An. arabiensis. Genetics 167: 275-87.
105. Maynard Smith J. 1978. The Evolution of Sex. Cambridge: Cambridge University Press.
106. Otto SP. 2009. The evolutionary enigma of sex. Am Naturalist 174: S1-S14.
107. Fisher RA. 1930. The Genetical Theory of Natural Selection. Oxford: Clarendon Press.
108. Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74: 417-33.
109. Finley RL, Collignon P, Larsson DGJ, McEwen SA, et al. 2013. The scourge of antibiotic resistance: the important role of the environment. Clin Infect Dis 57: 704-10.
110. R mutation and of the ace-1 duplication in West African Anopheles gambiae s.s. PLoS ONE 3: e2172.
111. Weill M, Chandre F, Brengues C, Manguin S, et al. 2000. The kdr mutation occurs in the Mopti form of Anopheles gambiae s.s. through introgression. Insect Mol Biol 9: 451-5.
112. Norris LC, Main BJ, Lee Y, Collier TC, et al. 2015. Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets. Proc Natl Acad Sci USA 112: 815-20.
113. Clarkson CS, Weetman D, Essandoh J, Yawson AE, et al. 2014. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation. Nat Commun 5: 4248.
114. Adler PH, Cheke RA, Post RJ. 2010. Evolution, epidemiology, and population genetics of black flies (Diptera: Simuliidae). Infect Genet Evol 10: 846-65.
115. Song Y, Endepols S, Klemann N, Richter D, et al. 2011. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice. Curr Biol 21: 1296-301.
116. Ellstrand NC, Meirmans P, Rong J, Bartsch D, et al. 2013. Introgression of crop alleles into wild or weedy populations. Annu Rev Ecol Evol Syst 44: 325-45.
117. Alphey L. 2014. Genetic control of mosquitoes. Annu Rev Entomol 59: 205-24.
118. Hoffmann AA, Montgomery BL, Popovici J, Iturbe-Ormaetxe I, et al. 2011. Successful establishment of Wolbachia in Aedes populations to suppress dengue transmission. Nature 476: 454-7.
119. Bian G, Joshi D, Dong Y, Lu P, et al. 2013. Wolbachia invades Anopheles stephensi populations and induces refractoriness to Plasmodium infection. Science 340: 748-51.
120. Pike AD, Cirimotich CM, Dimopoulos G. 2013. Impact of transgenic immune deployment on mosquito fitness. In Koenraadt S, Takken W, eds; Ecology and Control of Vector-Borne Diseases, Volume 3, Ecology of Parasite-Vector Interactions. Wageningen: Academic Publishers. p. 19-33.