Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts

Molecular Phylogenetics and Evolution

Volumn 50, Issue 2, 2009, Pages 326-335

  Fehlberg, Shannon D ^a   Ranker, Tom A ^b  

^a DESERT BOTANICAL GARDEN   (United States)

^b UNIVERSITY OF HAWAII   (United States)

Author keywords

Encelia farinosa; North American Deserts; Phylogeography; Pleistocene glaciation; Population structure; Refugia

Indexed keywords

CHLOROPLAST DNA; SPACER DNA;

ARTICLE; ASTERACEAE; CLASSIFICATION; DESERT CLIMATE; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; NORTH AMERICA; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT;

ASTERACEAE; DESERT CLIMATE; DNA, CHLOROPLAST; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; NORTH AMERICA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ASTERACEAE; ENCELIA; ENCELIA FARINOSA;

EID: 58049152530     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.11.011     Document Type: Article

References (90)

1. Anderson R.S., and Van Devender T.R. Comparison of pollen and macrofossils in packrat (Neotoma) middens: a chronological sequence from the Waterman Mountains of southern Arizona, USA. Rev. Palaeobot. Palynol. 68 (1991) 1-28
2. Aris-Brosou S., and Excoffier L. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13 (1996) 494-504
3. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge
4. Avise J.C., Arnold J., Ball R.M., Bermingham E., Lamb T., Neigel J.E., Reeb C.A., and Saunders N.C. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18 (1987) 489-522
5. Betancourt J.L., Van Devender T.R., and Martin P.S. Packrat Middens: The last 40, 000 Years of Biotic Change (1990), University of Arizona Press, Tucson
6. Bohonak A.J. IBD (isolation by distance): a program for analyses of isolation by distance. J. Hered. 93 (2002) 153-154
7. Brunsfeld S.J., Sullivan J., Soltis D.E., and Soltis P.S. Comparative phylogeography of northwestern North America: a synthesis. In: Silvertown J., and Antonovics J. (Eds). Integrating Ecology and Evolution in a Spatial Context (2001), Blackwell Publishing, Oxford 319-339
8. Castoe T.A., Spencer C.L., and Parkinson C.L. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): a perspective on North American desert biogeography. Mol. Phylogenet. Evol. 42 (2007) 193-212
9. Clark C. Phylogeny and adaptation in the Encelia alliance (Asteraceae: Heliantheae). Aliso 17 (1998) 89-98
10. Clement M., Posada D., and Crandall K. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
11. Cole, K.L., 1981. Late Quaternary Environment in the Eastern Grand Canyon: Vegetational Gradients over the Last 25,000 years. Ph.D. Thesis, University of Arizona.
12. Comes H.P., and Kadereit J.W. The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 3 (1998) 432-438
13. Davis L.G. Gearchaeology and geochronology of Pluvial Lake Chapala, Baja California, Mexico. Geoarchaeology 18 (2003) 205-224
14. Dechaine E.G., and Martin A.P. Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains. Am. J. Bot. 92 (2005) 477-486
15. Dick C.W., Bermingham E., Lemes M.R., and Gribel R. Extreme long distance dispersal of the lowland rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics. Mol. Ecol. 16 (2007) 3039-3049
16. Dobes C.H., Mitchell-Olds T., and Koch M.A. Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. x divaricarpa, and A. holboellii (Brassicaceae). Mol. Ecol. 13 (2004) 349-370
17. Dupanloup I., Schneider S., and Excoffier L. A simulated annealing approach to define the genetic structure of populations. Mol. Ecol. 11 (2002) 2571-2581
18. Fu X.Y. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
19. Gielly L., and Taberlet P. The use of chloroplast DNA to resolve plant phylogenies: non-coding vs rbcL sequences. Mol. Biol. Evol. 11 (1994) 769-777
20. Goldberg D.E., and Turner T.M. Vegetation change and plant demography in permanent plots in the Sonoran Desert. Ecology 67 (1986) 695-712
21. Gómez-Zurita J., and Vogler A.P. Testing introgressive hybridization hypotheses using statistical network analysis of nuclear and cytoplasmic haplotypes in the leaf beetle Timarcha goettingensis species complex. J. Mol. Evol. 62 (2006) 421-433
22. Guerrero B.O., Caballero M., García S.L., Villanueva M., and de la O. Palaeoenvironmental record of the last 70, 000 yr in San Felipe Basin, Sonora Desert, Mexico. Geofis. Int. 38 (1999) 153-163
23. Hamilton M.B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8 (1999) 521-523
24. Hamilton M.B., Braverman J.M., and Soria-Hernanz D.F. Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae. Mol. Biol. Evol. 20 (2003) 1710-1721
25. Hewitt G.M. Some genetic consequences of ice ages, and their role of divergence and speciation. Biol. J. Linn. Soc. 58 (1996) 247-276
26. Hewitt G.M. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. 68 (1999) 87-112
27. Hewitt G.M. The genetic legacy of the Quaternary ice ages. Nature 405 (2000) 907-913
28. Hewitt G.M. Genetic consequences of climatic oscillations in the Quaternary. Phil. Trans. R. Soc. Lond. B Biol. Sci. 359 (2004) 183-195
29. Housman D.C., Price M.V., and Redak R.A. Architecture of coastal and desert Encelia farinosa (Asteraceae): consequences of plastic and heritable variation in leaf characters. Am. J. Bot. 89 (2002) 1303-1310
30. Hunter K.L., Betancourt J.L., Riddle B.R., Van Devender T.R., Cole K.L., and Spaulding W.G. Ploidy race distributions since the last glacial maximum in the North American desert shrub, Larrea tridentata. Global Ecol. Biogeogr. 10 (2001) 521-533
31. Hurtado L.A., Erez T., Castrezana S., and Markow T.A. Contrasting population genetic patterns and evolutionary histories among sympatric Sonoran Desert cactophilic Drosophila. Mol. Ecol. 13 (2004) 1365-1375
32. Jaeger J.R., Riddle B.R., and Bradford D.F. Cryptic neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas. Mol. Ecol. 14 (2005) 3033-3048
33. King J.E., and Van Devender T.R. Pollen analysis of fossil packrat middens from the Sonoran Desert. Quaternary Res. 8 (1977) 191-204
34. Knowles L.L., and Maddison W.P. Statistical phylogeography. Mol. Ecol. 11 (2002) 2623-2635
35. Kress W.J., Wurdack K.J., Zimmer E.A., Weigt L.A., and Janzen D.H. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA 102 (2005) 8369-8374
36. Kyhos D.W. Evidence of different adaptations of flower color variants of Encelia farinosa (Compositae). Madroño 21 (1971) 49-61
37. Lahaye R., van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T.G., and Savolainen V. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA 105 (2008) 2923-2928
38. Leaché A.D., and Mulcahy D.G. Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California. Mol. Ecol. 16 (2007) 5216-5233
39. Liston A., Parker-Defeniks M., Syring J.V., Willyard A., and Cronn R. Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana. Mol. Ecol. 16 (2007) 3926-3937
40. Martin P.S., and Mehringer P.J. Pleistocene pollen analysis and biogeography of the Southwest. In: Wright H.E., and Frey D.G. (Eds). The Quaternary of the United States (1965), Yale University of Press, New Haven 433-451
41. Masta S.E. Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of Sky Island populations?. Evolution 54 (2000) 1699-1711
42. McAuliffe J.R., and Van Devender T.R. A 22,000-year record of vegetation and climate change in the north-central Sonoran Desert. Palaeogeogr. Palaeoclimatol. Palaeoecol. 141 (1998) 253-275
43. Mead J.I., and Phillips III A.M. The late Pleistocene and Holocene fauna and flora of Vulture Cave, Grand Canyon, Arizona. SW Nat. 26 (1981) 257-288
44. Nason J.D., Hamrick J.L., and Fleming T.H. Historical vicariance and post-glacial colonization effects on the evolution of genetic structure in Lophocereus, a Sonoran Desert columnar cactus. Evolution 56 (2002) 2214-2226
45. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York
46. Newton A.C., Allnutt T.R., Gillies A.C.M., Lowe A.J., and Ennos R.A. Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol. Evol. 14 (1999) 140-145
47. Olsen K.M., and Schaal B.A. Evidence on the origin of cassava: phylogeography of Manihot esculenta. Proc. Natl. Acad. Sci. USA 96 (1999) 5586-5591
48. Palmer J.D. Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. Am. Nat. 130 (1987) S6-S29
49. Petit R.J., Pineau E., Demesure B., Bacilieri R., Ducousso A., and Kremer A. Chloroplast DNA footprints of postglacial recolonization by oaks. Proc. Natl. Acad. Sci. USA 94 (1997) 9996-10001
50. Posada D., Crandall K.A., and Templeton A.R. GEODIS: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol. Ecol. 9 (2000) 487-488
51. Räsänen K., and Hendry A.P. Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification. Ecol. Lett. 11 (2008) 624-636
52. Rice W.R. Analyzing tables of statistical tests. Evolution 43 (1989) 223-225
53. Richardson J.E., Pennington R.T., Pennington T.D., and Hollingsworth P.M. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293 (2001) 2242-2245
54. Rogers A.R. Genetic evidence for a Pleistocene population explosion. Evolution 49 (1995) 608-615
55. Rogers A.R., and Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9 (1992) 552-569
56. Rosenberg, M.S., 2001. PASSAGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Ver. 1.1. Department of Biology, Arizona State University.
57. Sandquist D.R., and Ehleringer J.R. Potential adaptability and constraints of response to the changing climates for Encelia farinosa var. phenicondonta from southern Baja California, Mexico. Madroño 43 (1996) 465-478
58. Sandquist D.R., and Ehleringer J.R. Intraspecific variation of drought adaptation in brittlebush: leaf pubescence and timing of leaf loss vary with rainfall. Oecologia 113 (1998) 162-169
59. Sandquist D.R., and Ehleringer J.R. Carbon isotope discrimination differences within and between contrasting populations of Encelia farinosa raised under common-environment conditions. Oecologia 134 (2003) 463-470
60. Sandquist D.R., and Ehleringer J.R. Population- and family-level variation of brittlebush (Encelia farinosa, Asteraceae) pubescence: its relations to drought and implications for selection in variable environments. Am. J. Bot. 90 (2003) 1481-1486
61. Schneider S., and Excoffier L. Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152 (1999) 1079-1089
62. Schneider, S., Roessli, D., Excoffier, L., 2000. ARLEQUIN: A Software for Population Genetics Data Analysis. Ver. 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva.
63. Shaw J., Lickey E.B., Schilling E.E., and Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94 (2007) 275-288
64. Shreve F., and Wiggins I. Vegetation and Flora of the Sonoran Desert (1964), Stanford University Press, Stanford
65. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
66. Smith C.I., and Farrell B.D. Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes. Mol. Ecol. 14 (2005) 1025-1044
67. Soltis D.E., Gitzendanner M.A., Strenge D.D., and Soltis P.S. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst. Evol. 206 (1997) 353-373
68. Soltis D.E., Morris A.B., McLachlan J.S., Manos P.S., and Soltis P.S. Comparative phylogeography of unglaciated eastern North America. Mol. Ecol. 15 (2006) 4261-4293
69. Spaulding W.G. Vegetational and climatic development of the Mojave Desert: the last glacial maximum to the present. In: Betancourt J.L., Van Devender T.R., and Martin P.S. (Eds). Packrat Middens: The last 40, 000 Years of Biotic Change (1990), University of Arizona Press, Tucson 105-133
70. Steele C.A., and Storfer A. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific Giant Salamander (Dicamptodon tenebrosus). Mol. Ecol. 15 (2006) 2477-2487
71. Swofford D.L. PAUP*: Phylogenetic Analysis using Parsimony (* and Other Methods), Version 4.0b10 (2002), Sinauer Associates, Sunderland
72. Taberlet P., Fumagalli L., Wust-Saucy A.-G., and Cosson J.-F. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 7 (1998) 453-464
73. Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics 105 (1983) 437-460
74. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
75. Tajima F. The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics 143 (1996) 1457-1465
76. Templeton A.R. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol. Ecol. 7 (1998) 381-397
77. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-809
78. Templeton A.R., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134 (1993) 659-669
79. Templeton A.R., Boerwinkle E., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117 (1987) 343-351
80. Templeton A.R., Crandall K.A., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132 (1992) 619-633
81. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 241-260
82. Thompson R.S., and Anderson K.H. Biomes of western North America at 18,000, 6000 and 0 14C yr BP reconstructed from pollen and packrat midden data. J. Biogeogr. 27 (2000) 555-584
83. Turner R.M., Bowers J.E., and Burgess T.L. Sonoran Desert Plants (1995), University of Arizona Press, Tucson
84. Van Devender, T.R., 1973. Late Pleistocene Plants and Animals of the Sonoran Desert: A Survey of Ancient Packrat Middens in Southwestern Arizona. Ph.D. Thesis, University of Arizona.
85. Van Devender T.R. Holocene vegetation and climate in the Puerto Blanco Mountains, southwestern Arizona. Quaternary Res. 27 (1987) 51-72
86. Van Devender T.R. Late Quaternary vegetation and climate of the Sonoran Desert, United States and Mexico. In: Betancourt J.L., Van Devender T.R., and Martin P.S. (Eds). Packrat Middens: The last 40,000 Years of Biotic Change (1990), University of Arizona Press, Tucson 134-163
87. Wolfe K.H., Li W.H., and Sharp P.M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNA. Proc. Natl. Acad. Sci. USA 84 (1987) 9054-9058
88. Woodcock D. The late Pleistocene of Death Valley: a climatic reconstruction based on macrofossil data. Palaeogeogr. Palaeoclimatol. Palaeoecol. 57 (1986) 273-283
89. Yuan Q.J., Zhang Z.Y., Peng H., and Ge S. Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam. Mol. Ecol. 17 (2008) 1054-1065
90. Zink R.M., Barrowclough G.G., Atwood J.L., and Blackwell-Rago R.C. Genetics, taxonomy, and conservation of the threatened California Gnatcatcher. Conserv. Biol. 14 (2000) 1394-1405