Pleistocene speciation in the genus populus (salicaceae)

Systematic Biology

Volumn 61, Issue 3, 2012, Pages 401-412

  Levsen, Nicholas D ^a   Tiffin, Peter ^b   Olson, Matthew S ^a,c  

^a TEXAS TECH UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

Glaciation; isolation with migration; MIMAR; North America; species distribution model

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; CLIMATE CHANGE; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLANT GENE; POPULUS; SPECIES DIFFERENTIATION;

CLIMATE CHANGE; ECOSYSTEM; GENES, PLANT; GENETIC SPECIATION; GENETIC VARIATION; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULUS;

POPULUS; POPULUS BALSAMIFERA; POPULUS TRICHOCARPA; SALICACEAE;

EID: 84858750604     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr120     Document Type: Article

References (79)

1. Akaike H. 1974. A new look at the statistical identification model. IEEE Trans. Autom. Control. 19:716-723.
2. Axelrod D.I. 1988. An interpretation of high montane conifers in western Tertiary floras. Paleobiology. 14:301-306. (Pubitemid 19309942)
3. Axelrod D.I. 1998. The Oligocene Haynes Creek flora of eastern Idaho. Univ. Calif. Publ. Geol. Sci. 143:1-99.
4. Bennett K.D. 1990. Milankovitch cycles and their effects on species in ecological and evolutionary time. Paleobiology. 16:11-21. (Pubitemid 20416617)
5. Bennett K.D. 2004. Continuing the debate on the role of the Quaternary environmental change for macroevolution. Philos. Trans. R. Soc. B. 359:295-303. (Pubitemid 38231479)
6. Becquet C., Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17:1505-1519. (Pubitemid 47529435)
7. Becquet C., Przeworski M. 2009. Learning about modes of speciation by computational approaches. Evolution. 63:2547-2562.
8. Betts M.G., Diamond A.W., Forbes G.J., Villard M.-A., Gunn J.S. 2006. The importance of spatial autocorrelation, extent and resolution in predicting forest bird occurrence. Ecol. Model. 191:197-224. (Pubitemid 41735463)
9. Brochmann C., Brysting A.K. 2008. The arctic-an evolutionary freezer? Plant Ecol. Divers. 1:181-195.
10. Brunsfeld S.J., Sullivan J., Soltis D.E., Soltis P.S. 2001. Comparative phylogeography of northwestern North America: a synthesis. In: Silvertown J., Antonovicks J., editors. Integrating ecological and evolutionary processes in a spatial context. Oxford: Blackwell Science. p. 319-339.
11. Campana M.G., Hunt H.V., Jones H., White J. 2011. CorrSieve: software for summarizing and evaluating Structure output. Mol. Ecol. Resour. 11:349-352.
12. Cockram J., White J., Leigh F.J., Lea V.J., Chiapparino E., Laurie D.A., Mackay I.J., PowellW., O'Sullivan D.M. 2008. Association mapping of partitioning loci in barley. BMC Genet. 9:16.
13. Collins W.D., Blackmon M., Bitz C., Bonan G., Bretherton C.S., Carton J.A., Chang P., Doney S.C., Hack J.J., Henderson T.B., Kiehl J.T., Large W.G., McKenna D.S., Santer B.D., Smith R.D. 2004. The community climate system model version 3 (CCSM3). J. Climate. 19:2122-2143.
14. Cummings M.P., Neel M.C., Shaw K.L. 2008. A genealogical approach to quantifying lineage divergence. Evolution. 62:2411-2422.
15. Dillen S.Y., Rood S.B., Ceulemans R. 2010. Growth and physiology. In: Jansson S., Bhalerao R.P., Groover A.T., editors. Genetics and genomics of Populus. New York: Springer. p. 39-66.
16. Eckenwalder J.E. 1996. Systematics and evolution of Populus. In: Stettler R.F., Bradshaw H.D. Jr., Heilman P.E., Hinckley T.M., editors. Biology of Populus and its implications for management and conservation. Ottawa (Canada): NRC Research. p. 7-32.
17. Eckenwalder J.E. 2010. Populus. In: Flora of North America Editorial Committee, editors. Flora of North America North of Mexico, 12+ vols. Volume 7. New York: Oxford University Press. p. 5-22.
18. Eldredge N., Thompson J.N., Brakefield P.M., Gavrilets S., Jablonski D., Jackson J.B.C., Lenski R.E., Lieberman B.S., McPeek M.A., Miller W. 3rd 2005. The dynamics of evolutionary stasis. Paleobiology. 31:133-145. (Pubitemid 40906548)
19. Elith J., Kearney M., Phillips S. 2010. The art of modeling rangeshifting species. Methods Ecol. Evol. 1:330-342.
20. Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation studyMol. Ecol. 14:2611-2620. (Pubitemid 40886055)
21. Falush D., Stephens M., Pritchard J.K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164:1567-1587. (Pubitemid 37102217)
22. Futuyma D.J. 2010. Evolutionary constraint and ecological consequences. Evolution. 64:1865-1884.
23. Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695. (Pubitemid 27287289)
24. Gilchrist E.J., Haughn G.W., Ying C.C., Otto S.P., Zhuang J., Cheung D., Hamberger B., Aboutarabi F., Kalynyak T., Johnson L., Johnson L., Bohlmann J., Ellis B.E., Douglas C.J., Cronk Q.C.B. 2006. Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol. Ecol. 15:1367-1378.
25. Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. (Pubitemid 37365050)
26. Hamzeh M., Dayanandan S. 2004. Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast trnT-trnF region and nuclear rDNA. Am. J. Bot. 91:1398-1408. (Pubitemid 43180983)
27. Harrison, R.G. 1998. Linking evolutionary pattern and process: the relevance of species concepts for the study of speciation. In: Howard D.J., Berlocher S.H., editors. Endless forms: species and speciationNew York: Oxford University Press. p. 19-31.
28. Hasumi H., Emori S. 2004. K-1 coupled GCM (MIROC) description-Tokyo (Japan): Center for Climate System Research, University of Tokyo.
29. Hewitt G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58: 247-276. (Pubitemid 26389802)
30. Hey J., Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics. 167:747-760. (Pubitemid 38931862)
31. Hickerson M.J., Carstens B.C., Cavender-Bares J., Crandall K.A., Graham C.H., Johnson J.B., Rissler L., Victoriano P.F., Yoder A.D. 2010. Phylogeographies past, present, and future: 10 years after Avise, 2000. Mol. Phylogenet. Evol. 54:291-301.
32. Hijmans R.J., Cameron S.E., Parra J.L., Jones P.G., Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25:1965-1978. (Pubitemid 43013915)
33. Hosmer D.W., Lemeshow S. 2000. Applied logistic regression. 2nd ed. New York: John Wiley & Sons.
34. Hudson R.R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338. (Pubitemid 34183119)
35. Huntley B. 1991. How plants respond to climate change: migration rates, individualism and the consequences for plant communities. Ann. Bot. 67:15-22.
36. Jakobsson M., Rosenberg N.A. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 23:1801-1806. (Pubitemid 47250313)
37. Kadereit J.W., Griebeler E.M., Comes H.P. 2004. Quaternary diversification in European alpine plants: pattern and process. Philos. Trans. R. Soc. B. 359:265-274. (Pubitemid 38236028)
38. Keller S.R., Olson M.S., Silim S., Schroeder W., Tiffin P. 2010. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar, Populus balsamifera. Mol. Ecol. 19:1212-1226.
39. Kelly J.K. 1997. A test of neutrality based on interlocus associations. Genetics. 146:1197-1206. (Pubitemid 27291000)
40. Kiehl J.T., Gent P.R. 2004. The community climate system model, version 2J. Climate. 17:3666-3682. (Pubitemid 39500320)
41. Knowles L.L. 2000. Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evolution. 54:1337-1348.
42. Knowles L.L., Carstens B.C., Keat M.L. 2007. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Curr. Biol. 17:940-946. (Pubitemid 46839179)
43. Koch M.A., Haubold B., Mitchell-Olds T. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17:1483-1498.
44. Kubatko L.S., Carstens B.C., Knowles L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
45. Landais A., Barnola J.M., Masson-Delmotte V., Jouzel J., Chappellaz J., Caillon N., Huber C., Leuenberger M., Johnsen S.J. 2004. A continuous record of temperature evolution over a sequence of Dansgaard-Oeschger events during Marine Isotopic Stage 4 (76 to 62 kyr BP). Geophys. Res. Lett. 31:L22211.
46. Li N., Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics. 165:2213-2233. (Pubitemid 38040302)
47. Little E.L. 1971. Atlas of the United States trees: volume 1, conifers and important hardwoods. US Department of Agriculture Miscellaneous Publication 1146. Washington (DC): US Department of Agriculture.
48. Martin-Bravo S., Valcrcel V., Vargas P., Luce ño M. 2010. Geographical speciation related to Pleistocene range shifts in the western Mediterranean mountains (Reseda sect. Glaucoreseda, Resedaceae)Taxon. 59:466-482.
49. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
50. Neiman M., Olson M.S., Tiffin P. 2009. Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates. New Phytol. 183:740-750.
51. Olson M.S., Robertson A.L., Takebayashi N., Silim S., Schroeder W.R., Tiffin P. 2010. Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera). New Phytol. 186:526-536.
52. Ossowski S., Schneeberger K., Lucas-Lled J.I., Warthmann N., Clark R.M., Shaw R.G.,Weigel D., Lynch M. 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 327:92-94.
53. Phillips S.J., Anderson R.P., Schapire R.E. 2006. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190:231-259. (Pubitemid 41680650)
54. Phillips S.J., Dud M. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography. 31:161-175. (Pubitemid 351457533)
55. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256. (Pubitemid 351882013)
56. Pritchard J.K., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959. (Pubitemid 30397141)
57. Richards C.L., Carstens B.C., Knowles L.L. 2007. Distribution modeling and statistical phylogeography: an integrative framework for generating and testing alternate biogeographical hypothesesJ. Biogeogr. 32:1833-1845. (Pubitemid 47610616)
58. Richardson J.E., Pennington R.T., Pennington T.D., Hollingsworth P.M. 2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science. 293:2242-2245. (Pubitemid 32900231)
59. Rieseberg L.H., Brouillet L. 1994. Are many species paraphyletic? Taxon. 43:21-32.
60. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497. (Pubitemid 38016658)
61. Schoener T.W. 1968. Anolis lizards of Bimini: resource partitioning in a complex fauna. Ecology. 49:704-726.
62. Smith B.J. 2007. boa: an R package for MCMC output convergence assessment and posterior inferenceJ. Stat. Softw. 21:1-37.
63. Soolanayakanahally R.Y., Guy R.D., Silim S.N., Drewes E.C., Schroeder W.R. 2009. Enhanced assimilation rate and water use efficiency with latitude through photosynthetic capacity and internal conductance in balsam poplar (Populus balsamifera L.). Plant Cell Environ. 32:1821-1832.
64. Stephens M., Scheet P. 2005. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet. 76:449-462. (Pubitemid 40250525)
65. Stephens M., Smith N., Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:978-989. (Pubitemid 32289743)
66. Sterck L., Rombauts S., Jansson S., Sterky F., Rouz P., Van de Peer Y. 2005. EST data suggest that poplar is an ancient polyploidy. New Phytol. 167:165-170. (Pubitemid 40885838)
67. Tajima F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics. 105:437-460. (Pubitemid 14247444)
68. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585-595. (Pubitemid 19274682)
69. Tuskan G.A., DiFazio S.P., Jansson S., Bohlman J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.-L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S, Djardin A., dePamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjrvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Lepl J.-C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouz P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.-J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S., Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y., Rokhsar D. 2006. The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science. 313:1596-1604. (Pubitemid 44414027)
70. Via S. 2009. Natural selection in action during speciation. Proc. Natl. Acad. Sci. U.S.A. 106:9939-9946.
71. Viereck L.A., Foote J.M. 1970. The status of Populus balsamifera and P. trichocarpa in Alaska. Can. Field Nat. 84:169-173.
72. Wakeley J. 2008. Coalescent theory: an introduction. Greenwood Village (CO): Roberts & Company Publishers.
73. Wakeley J., Hey J. 1997. Estimating ancestral population parameters. Genetics. 145:847-855. (Pubitemid 27108038)
74. Waltari E., Hijmans R.J., Peterson A.T., Nyari A.S., Perkins S.L., Guralnick R.P. 2007. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE 2:e563.
75. Warren D.L., Glor R.E., Turelli M. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution. 62:2868-2883.
76. Warren D.L., Seifert S.N. 2011. Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria. Ecol. Appl. 21:335-342.
77. Watterson G.A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
78. Willis K.J., Niklas K.J. 2004. The role of Quaternary environmental change in plant macroevolution: the exception or the rule? Philos. Trans. R. Soc. B. 359:159-172. (Pubitemid 38231469)
79. Zwickl D.J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion [PhD dissertation]. Austin (TX): The University of Texas at Austin.