Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

PLoS Biology

Volumn 14, Issue 2, 2016, Pages

  Pease, James B ^a   Haak, David C ^a,b   Hahn, Matthew W ^a,c   Moyle, Leonie C ^a  

^a INDIANA UNIVERSITY   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADAPTIVE VARIATION; ALLELE; ARTICLE; CELL LINEAGE; CELL SELECTION; CHROMOSOME; COLOR; CONTROLLED STUDY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC TRAIT; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HETEROCHROMATIN; HETEROZYGOSITY; NONHUMAN; PERUVIANUM; PHYLOGENOMICS; POPULATION STRUCTURE; RADIATION; RED FRUIT COLOR; RNA SEQUENCE; SEASONAL VARIATION; TOMATO; GENETIC POLYMORPHISM; GENETICS; GENOMICS; SPECIES DIFFERENTIATION;

GENETIC SPECIATION; GENOMICS; LYCOPERSICON ESCULENTUM; POLYMORPHISM, GENETIC;

EID: 84955703917     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1002379     Document Type: Article

References (100)

1. Glor RE, Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst. 2010;41(1):251–70. doi: 10.1146/annurev.ecolsys.39.110707.173447
2. Schluter D, The ecology of adaptive radiation. Oxford: Oxford University Press; 2000. 288 p.
3. Gavrilets S, Losos JB, Adaptive radiation: contrasting theory with data. Science. 2009;323(5915):732–7. doi: 10.1126/science.115796619197052
4. Rabosky DL, Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu Rev Ecol Evol Syst. 2013;44(1):481–502. doi: 10.1146/annurev-ecolsys-110512-135800
5. Olson ME, Arroyo-Santos A, Thinking in continua: beyond the “adaptive radiation” metaphor. BioEssays. 2009;31(12):1337–46. doi: 10.1002/bies.20090010219921661
6. Prentis PJ, Wilson JRU, Dormontt EE, Richardson DM, Lowe AJ, Adaptive evolution in invasive species. Trends Plant Sci. 2008;13(6):288–94. doi: 10.1016/j.tplants.2008.03.00418467157
7. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, et al. The genomic substrate for adaptive radiation in African cichlid fish. Nature. 2014;513(7518):375–81. doi: 10.1038/nature1372625186727
8. 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 Res. 2013;23(11):1817–28. doi: 10.1101/gr.159426.11324045163
9. Donoghue MJ, Sanderson MJ, Confluence, synnovation, and depauperons in plant diversification. New Phytol. 2015;207(2):260–74. doi: 10.1111/nph.1336725778694
10. Hudson RR, Testing the constant-rate neutral allele model with protein sequence data. Evolution. 1983;37(1):203–17. doi: 10.2307/2408186
11. Pamilo P, Nei M, Relationships between gene trees and species trees. Mol Biol Evol. 1988;5(5):568–83. 3193878
12. Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark AG, Thornton KR, et al. Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res. 2012;22(8):1499–511. doi: 10.1101/gr.130922.11122534282
13. Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG, Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution. 2013;67(8):2166–79. doi: 10.1111/evo.1209923888843
14. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, et al. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci USA. 2014;111(52):18655–60. doi: 10.1073/pnas.141262711125453089
15. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci USA. 2014;111(45):E4859–E68. doi: 10.1073/pnas.132392611125355905
16. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346(6215):1320–31. doi: 10.1126/science.125345125504713
17. Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, et al. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 2015;347(6217):1258524. doi: 10.1126/science.125852425431491
18. Lamichhaney S, Berglund J, Almen MS, Maqbool K, Grabherr M, Martinez-Barrio A, et al. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature. 2015;518(7539):371–5. doi: 10.1038/nature1418125686609
19. Coyne JA, Orr HA, Speciation. Sunderland, Mass.: Sinauer Associates; 2004. 545 p.
20. Liu L, Yu L, Edwards S, A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 2010;10(1):302. doi: 10.1186/1471-2148-10-302
21. Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T, ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics. 2014;30(17):i541–i8. doi: 10.1093/bioinformatics/btu46225161245
22. Särkinen T, Bohs L, Olmstead R, Knapp S, A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evol Biol. 2013;13(1):214. doi: 10.1186/1471-2148-13-214
23. Szinay D, Wijnker E, van den Berg R, Visser RGF, de Jong H, Bai Y, Chromosome evolution in Solanum traced by cross-species BAC-FISH. New Phytol. 2012;195(3):688–98. doi: 10.1111/j.1469-8137.2012.04195.x22686400
24. Verlaan MG, Szinay D, Hutton SF, de Jong H, Kormelink R, Visser RGF, et al. Chromosomal rearrangements between tomato and Solanum chilense hamper mapping and breeding of the TYLCV resistance gene Ty-1. Plant J. 2011;68(6):1093–103. doi: 10.1111/j.1365-313X.2011.04762.x21883550
25. Anderson LK, Covey PA, Larsen LR, Bedinger P, Stack SM, Structural differences in chromosomes distinguish species in the tomato clade. Cytogenet Genome Res. 2010;129(1–3):24–34. doi: 10.1159/00031385020551606
26. Nakazato T, Warren DL, Moyle LC, Ecological and geographic modes of species divergence in wild tomatoes. Am J Bot. 2010;97(4):680–93. doi: 10.3732/ajb.090021621622430
27. Peralta IE, Spooner DM, Knapp S, Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Syst Bot Monogr. 2008;84:1–186.
28. Grandillo S, Chetelat R, Knapp S, Spooner D, Peralta I, Cammareri M, Kole C, et al. Solanum sect. Lycopersicon. In: Wild Crop Relatives: Genomic and Breeding Resources: SpringerBerlin Heidelberg; 2011. p. 129–215.
29. Moyle LC, Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon). Evolution. 2008;62(12):2995–3013. doi: 10.1111/j.1558-5646.2008.00487.x18752600
30. Baek YS, Covey PA, Petersen JJ, Chetelat RT, McClure B, Bedinger PA, Testing the SI × SC rule: pollen–pistil interactions in interspecific crosses between members of the tomato clade (Solanum section Lycopersicon, Solanaceae). Am J Bot. 2015;102(2):302–11doi: 10.3732/ajb.140048425667082
31. Moyle LC, Nakazato T, Hybrid incompatibility “snowballs” between Solanum species. Science. 2010;329(5998):1521–3. doi: 10.1126/science.119306320847271
32. Igic B, Lande R, Kohn JR, Loss of self‐incompatibility and its evolutionary consequences. Int J Plant Sci. 2008;169(1):93–104. doi: 10.1086/523362
33. Vosters SL, Jewell CP, Sherman NA, Einterz F, Blackman BK, Moyle LC, The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanum sect. Lycopersicon). Mol Ecol. 2014;23(8):1965–78. doi: 10.1111/mec.1270824589309
34. Rick CM, Hawkes JG, Lester RN, Skelding AD, Biosystematic studies in Lycopersicon and closely related species of Solanum. In: The Biology and Taxonomy of Solanaceae. New York: Academic Press; 1979. p. 667–77.
35. McClure B, Cruz-García F, Romero C, Compatibility and incompatibility in S-RNase-based systems. Ann Bot. 2011;108(4):647–58. doi: 10.1093/aob/mcr17921803740
36. Palmer JD, Zamir D, Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci USA. 1982;79(16):5006–10. 16593219
37. Rodriguez F, Wu F, Ané C, Tanksley S, Spooner D, Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?BMC Evol Biol. 2009;9(1):191. doi: 10.1186/1471-2148-9-191
38. Rabosky DL, Glor RE, Equilibrium speciation dynamics in a model adaptive radiation of island lizards. Proc Natl Acad Sci USA. 2010;107(51):22178–83. doi: 10.1073/pnas.100760610721135239
39. Arnold ML, Natural hybridization and evolution. New York: Oxford University Press; 1997. 215 p.
40. The Tomato Genome ConsortiumThe tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485(7400):635–41. doi: 10.1038/nature1111922660326
41. Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, et al. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3. 2014;4(8):1395–405. doi: 10.1534/g3.114.01119724879607
42. Stamatakis A, RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. doi: 10.1093/bioinformatics/btu03324451623
43. Labate JA, Robertson LD, Strickler SR, Mueller LA, Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome. 2014;57(3):169–80. doi: 10.1139/gen-2014-000324884691
44. Salichos L, Rokas A, Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013;497(7449):327–31. doi: 10.1038/nature1213023657258
45. Pease JB, Rosenzweig BK, Encoding data using biological principles: the Multisample Variant Format for phylogenomics and population genomics. Trans Comp Biol Bioinformat. 2015; (In Press).
46. Suh A, Smeds L, Ellegren H, The dynamics of incomplete lineage sorting across the ancient adaptive radiation of Neoavian birds. PLoS Biol. 2015;13(8):e1002224. doi: 10.1371/journal.pbio.100222426284513
47. Carbone L, Alan Harris R, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014;513(7517):195–201. doi: 10.1038/nature1367925209798
48. Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK- S, Carpenter EJ, et al. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Mol Biol Evol. 2015;32(8):2001–14. doi: 10.1093/molbev/msv08125837578
49. The 100 Tomato Genome Sequencing ConsortiumAflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 2014;80(1):136–48. doi: 10.1111/tpj.1261625039268
50. Jimenez-Gomez JM, Maloof JN, Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol. 2009;9(1):85. doi: 10.1186/1471-2229-9-85
51. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A draft sequence of the Neandertal genome. Science. 2010;328(5979):710–22. doi: 10.1126/science.118802120448178
52. Pease JB, Hahn MW, Detection and polarization of introgression in a five-taxon phylogeny. Syst Biol. 2015;64(4):651–62. doi: 10.1101/00468925888025
53. Bai Y, Lindhout P, Domestication and breeding of tomatoes: What have we gained and what can we gain in the future?Ann Bot. 2007;100(5):1085–94. doi: 10.1093/aob/mcm15017717024
54. Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, et al. Genomic analyses provide insights into the history of tomato breeding. Nat Genet. 2014;46(11):1220–6. doi: 10.1038/ng.311725305757
55. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, et al. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE. 2012;7(7):e40563. doi: 10.1371/journal.pone.004056322802968
56. Peralta IE, Spooner DM, Morphological characterization and relationships of wild tomatoes (Solanum L. Sect. Lycopersicon). Syst Bot Monogr. 2005;104:227.
57. Aberer AJ, Krompass D, Stamatakis A, Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Syst Biol. 2013;62(1):162–6. doi: 10.1093/sysbio/sys07822962004
58. Peralta IE, Knapp SK, Spooner DM, New species of wild tomatoes (Solanum section Lycopersicon: Solanaceae) from Northern Peru. Syst Bot. 2005;30(2):424–34. doi: 10.1600/0363644054223657
59. Durand EY, Patterson N, Reich D, Slatkin M, Testing for ancient admixture between closely related populations. Mol Biol Evol. 2011;28(8):2239–52. doi: 10.1093/molbev/msr04821325092
60. Whitney KD, Randell RA, Rieseberg LH, Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus. New Phytol. 2010;187(1):230–9. doi: 10.1111/j.1469-8137.2010.03234.x20345635
61. Arnold ML, Martin NH, Adaptation by introgression. J Biol. 2009;8(9):82. doi: 10.1186/jbiol17619833002
62. Hedrick PW, Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Mol Ecol. 2013;22(18):4606–18. doi: 10.1111/mec.1241523906376
63. Kruijt M, Kip DJ, Joosten MHAJ, Brandwagt BF, de Wit PJGM, The Cf-4 and Cf-9 resistance genes against Cladosporium fulvum are conserved in wild tomato species. Mol Plant Microbe Interact. 2005;18(9):1011–21. doi: 10.1094/MPMI-18-101116167771
64. Rivas S, Thomas CM, Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum. Annu Rev Phytopathol. 2005;43(1):395–436. doi: 10.1146/annurev.phyto.43.040204.140224
65. Mendes FK, Hahn MW, Gene tree discordance causes apparent substitution rate variation. bioRxiv. 2015. doi: 10.1101/029371
66. Fantini E, Falcone G, Frusciante S, Giliberto L, Giuliano G, Dissection of tomato lycopene biosynthesis through virus-induced gene silencing. Plant Physiol. 2013;163(2):986–98. doi: 10.1104/pp.113.22473324014574
67. Giuliano G, Plant carotenoids: genomics meets multi-gene engineering. Curr Opin Plant Biol. 2014;19(0):111–7. doi: 10.1016/j.pbi.2014.05.006
68. The Potato Genome Sequencing ConsortiumGenome sequence and analysis of the tuber crop potato. Nature. 2011;475(7355):189–95. doi: 10.1038/nature1015821743474
69. Yang J-y, Sun Y, Sun A-q, Yi S-y, Qin J, Li M-h, et al. The involvement of chloroplast HSP100/ClpB in the acquired thermotolerance in tomato. Plant Mol Biol. 2006;62(3):385–95. doi: 10.1007/s11103-006-9027-916912911
70. Hiller M, Schaar Bruce T, Indjeian Vahan B, Kingsley David M, Hagey Lee R, Bejerano G, A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep. 2012;2(4):817–23. doi: 10.1016/j.celrep.2012.08.03223022484
71. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G, Dickson M, Grimwood J, et al. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science. 2005;307(5717):1928–33. doi: 10.1126/science.110723915790847
72. Ranc N, Muños S, Xu J, Le Paslier M- C, Chauveau A, Bounon R, et al. Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3. 2012;2(8):853–64. doi: 10.1534/g3.112.00266722908034
73. Xu J, Ranc N, Muños S, Rolland S, Bouchet J- P, Desplat N, et al. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet. 2013;126(3):567–81. doi: 10.1007/s00122-012-2002-823124430
74. Rabosky DL, Slater GJ, Alfaro ME, Clade age and species richness are decoupled across the eukaryotic tree of life. PLoS Biol. 2012;10(8):e1001381. doi: 10.1371/journal.pbio.100138122969411
75. Pfennig DW, McGee M, Resource polyphenism increases species richness: a test of the hypothesis. Philos Trans R Soc Lond B Biol Sci. 2010;365(1540):577–91. doi: 10.1098/rstb.2009.024420083634
76. Wagner CE, Harmon LJ, Seehausen O, Ecological opportunity and sexual selection together predict adaptive radiation. Nature. 2012;487(7407):366–9. doi: 10.1038/nature1114422722840
77. Seehausen O, Hybridization and adaptive radiation. Trends Ecol Evol. 2004;19(4):198–207. doi: 10.1016/j.tree.2004.01.00316701254
78. Seehausen O, Process and pattern in cichlid radiations–inferences for understanding unusually high rates of evolutionary diversification. New Phytol. 2015;207(2):304–12. doi: 10.1111/nph.1345025983053
79. Stankowski S, Streisfeld MA, Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers. Proc Roy Soc B Biol Sci; 2015: The Royal Society.
80. Baute GJ, Kane NC, Grassa CJ, Lai Z, Rieseberg LH, Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytol. 2015;206(2):830–8. doi: 10.1111/nph.1325525641359
81. Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, et al. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science. 2010;330(6006):927–31. doi: 10.1126/science.119458521071659
82. Garzione CN, Hoke GD, Libarkin JC, Withers S, MacFadden B, Eiler J, et al. Rise of the Andes. Science. 2008;320(5881):1304–7. doi: 10.1126/science.114861518535236
83. Garzione CN, Auerbach DJ, Jin-Sook Smith J, Rosario JJ, Passey BH, Jordan TE, et al. Clumped isotope evidence for diachronous surface cooling of the Altiplano and pulsed surface uplift of the Central Andes. Earth Planet Sci Lett. 2014;393(0):173–81. doi: 10.1016/j.epsl.2014.02.029
84. Hartley AJ, Chong G, Houston J, Mather AE, 150 million years of climatic stability: evidence from the Atacama Desert, northern Chile. J Geol Soc London. 2005;162(3):421–4. doi: 10.1144/0016-764904-071
85. Garreaud RD, Molina A, Farias M, Andean uplift, ocean cooling and Atacama hyperaridity: a climate modeling perspective. Earth Planet Sci Lett. 2010;292(1–2):39–50. doi: 10.1016/j.epsl.2010.01.017
86. Luebert F, Weigend M, Phylogenetic insights into Andean plant diversification. Front Ecol Evol. 2014;2:27. doi: 10.3389/fevo.2014.00027
87. Picard D, Sempere T, Plantard O, Direction and timing of uplift propagation in the Peruvian Andes deduced from molecular phylogenetics of highland biotaxa. Earth Planet Sci Lett. 2008;271(1–4):326–36. doi: 10.1016/j.epsl.2008.04.024
88. Doan TM, A south‐to‐north biogeographic hypothesis for Andean speciation: evidence from the lizard genus Proctoporus (Reptilia, Gymnophthalmidae). J Biogeogr. 2003;30(3):361–74. doi: 10.1046/j.1365-2699.2003.00833.x
89. Dillon MO, Tu T, Xie L, Quipuscoa Silvestre V, Wen J, Biogeographic diversification in Nolana (Solanaceae), a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America. J Syst Evol. 2009;47(5):457–76. doi: 10.1111/j.1759-6831.2009.00040.x
90. Weese TL, Bohs L, A three-gene phylogeny of the genus Solanum (Solanaceae). Syst Bot. 2007;32(2):445–63. doi: 10.1600/036364407781179671
91. Solanaceae Source. Solanaceae Source. Available from: http://solanaceaesource.org/.
92. Knapp S, Cronk QCB, Bateman RM, Hawkins JA, Floral diversity and evolution in the Solanaceae. In: Developmental genetics and plant evolution. London; New York: Taylor & Francis; 2002. p. 267–97.
93. Knapp S, Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot. 2002;53(377):2001–22. doi: 10.1093/jxb/erf06812324525
94. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. doi: 10.1093/bioinformatics/bts63523104886
95. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi: 10.1093/bioinformatics/btp35219505943
96. Sanderson MJ, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003;19(2):301–2. doi: 10.1093/bioinformatics/19.2.30112538260
97. Martin SH, Davey JW, Jiggins CD, Evaluating the use of ABBA–BABA statistics to locate introgressed loci. Mol Biol Evol. 2015;32(1):244–57. doi: 10.1093/molbev/msu26925246699
98. Yang Z, PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol. 2007;24(8):1586–91. doi: 10.1093/molbev/msm08817483113
99. Hudson RR, Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337–8. doi: 10.1093/bioinformatics/18.2.33711847089
100. Pease JB, Haak DC, Hahn MW, Moyle LC, Data from: Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation. Dryad Data Repository.