The Mimulus moschatus alliance (Phrymaceae): Molecular and morphological phylogenetics and their conservation implications

Systematic Botany

Volumn 31, Issue 2, 2006, Pages 380-397

  Whittall, Justen B ^a,d   Carlson, Matthew L ^b   Beardsley, Paul M ^c   Meinke, Robert J ^a   Liston, Aaron ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b Environment and Natural Resources Institute   (United States)

^c Nucl Eng Idaho State University   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Autogamy; ETS; Homoplasy; ITS; rpl16; trnL F

Indexed keywords

MIMULUS (ANGIOSPERM); MIMULUS AMPLIATUS; MIMULUS DUDLEYI; MIMULUS FLORIBUNDUS; MIMULUS HYMENOPHYLLUS; MIMULUS JUNGERMANNIOIDES; MIMULUS MOSCHATUS; MIMULUS NORRISII; MIMULUS PATULUS; MIMULUS WASHINGTONENSIS; PHRYMACEAE;

EID: 33745501987     PISSN: 03636445     EISSN: 03636445     Source Type: Journal    
DOI: 10.1600/036364406777585810     Document Type: Article

References (72)

1. ALFARO, M. E., S. ZOLLER, and F. M. LUTZONI. 2003. Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20: 255-266.
2. ARGUE, C. L. 1980. Pollen morphology in the genus Mimulus (Scrophulariaceae) and its taxonomic significance. American Journal of Botany 67: 68-87.
3. _. 1986. Some taxonomic implications of pollen and seed morphology in Mimulus hymenophyllus and M. jungermannioides and comparisons with other putative members of the M. moschatus alliance (Scrophulariaceae). Canadian Journal of Botany 64: 1331-1337.
4. BEARDSLEY, P. M., S. E. SHOENIG, J. B. WHITTALL, and R. G. OLMSTEAD. 2004. Patterns of evolution in western North American Mimulus (Phrymaceae). American Journal of Botany 91: 474-489.
5. BERNHARDT, P. 2000. Convergent evolution and adaptive radiation of beetle-pollinated angiosperms. Plant Systematics and Evolution 222: 293-320.
6. BLACKLEDGE, T. A. and R. G. GILLESPIE. 2004. Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders. Proceeding of the National Academy of Sciences USA 101: 16228-16233.
7. BONFIELD, J. K., K. F. SMITH, and R. A. STADEN. 1995. A new DNA sequence assembly program. Nucleic Acids Research 24: 4992-4999.
8. BRADSHAW, H. D., K. G. OTTO, B. E. FREWEN, J. K. MCKAY, and D. W. SCHEMSKE. 1998. Quantitative trait loci affecting differences in floral morphology between two species of monkeyflower (Mimulus). Genetics 149: 367-382.
9. _ and D. W. SCHEMSKE. 2003. Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature 426: 176-178.
10. BROWER, A. V. Z. 1994. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proceedings of the National Academy of Sciences of the United States of America 91: 6491-6495.
11. BUCKLEY, T. R. 2002. Model misspecification and probabilitstic tests of topology: evidence from empirical data sets. Systematic Biology 51: 509-523.
12. CABRERO-SAÑUDO, F.-J. and R. ZARDOYA. 2004. Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data. Molecular Phylogenetics and Evolution 31: 1084-1100.
13. CALIFORNIA NATURAL DIVERSITY DATABASE. 2004. State and federally listed endangered, threatened, and rare plants of California. Department of Fish and Game. Sacramento, California.
14. CARLSON, M. L. 2002. Evolution of mating system and inbreeding depression in the Mimulus moschatus alliance. Ph.D. Thesis. University of Alaska Fairbanks, Fairbanks, Alaska.
15. _ and R. J. MEINKE. 1994. Status report for Mimulus patulus. U.S. Fish and Wildlife Service, Region 1, Boise, Idaho, and Oregon Natural Heritage Data Base, Portland, Oregon.
16. DE QUEIROZ, A., M. J. DONOGHUE, and J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657-681.
17. DOUADY, C., F. DELSUC, Y. BOUCHER, W. DOOLITTLE, and E. DOUZERY. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution 20: 248-254.
18. FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417-419.
19. FENSTER, C. B. and K. RITLAND. 1994. The quantitative genetics of mating system divergence in the yellow monkeyflower species complex. Heredity 73: 422-435.
20. FISHMAN, L., A. J. KELLY, E. MORGAN, and J. H. WILLIS. 2001. A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 159: 1701-1716.
21. _, and J. H. WILLIS. 2002. Minor quantitative trait loci underlie floral traits associated with mating system divergence in Mimulus. Evolution 56: 2138-2155.
22. FUNK, D. J., D. J. FUTUYMA, G. ORTI, and A. MEYER. 1995. Mitochondrial DNA sequences and multiple data sets: a phylogenetic study of phytophagous beetles (Chrysomelidae: Ophraella). Molecular Biology and Evolution 12: 627-640.
23. GENETICS COMPUTER GROUP. 1999. Wisconsin Package 10.0. Madison: Wisconsin.
24. GOODWILLIE, C. and J. W. STILLER. 2001. Evidence for polyphyly in a species of Linanthus (Polemoniaceae): convergent evolution of self-fertilizing taxa. Systematic Botany 26: 273-282.
25. GRANT, A. L. 1924. A monograph of the genus Mimulus. Annals of the Missouri Botanical Garden 11: 99-388.
26. GRANT, V. 1954. Genetic and taxonomic studies in Gilia. IV. Gilia achilleaefolia. Aliso 3: 1-18.
27. HECKARD, L. R. and J. R. SHEVOCK. 1985. Mimulus norrisii (Scrophulariaceae), a new species from the southern Sierra Nevada. Madroño 32: 179-185.
28. HILLIS, D. M. and J. J. WIENS. 2000. Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. Pp. 1-20 in Phylogenetic analysis of morphological data, ed. J. Weins. Washington D.C.: Smithsonian Institution Press.
29. HITCHCOCK, C. L. and A. CRONQUIST. 1969. Mimulus. Pp. 337-350 in Vascular plants of the Pacific Northwest, eds. C. L. Hitchcock and A. Cronquist. Seattle: University of Washington Press.
30. HU, F. Y., D. Y. TAO, E. SACKS, B. Y. FU, P. XU, J. LI, Y. YANG, K. MCNALLY, G. S. KHUSH, A. H. PATERSON, and Z. K. LI. 2005. Convergent evolution of perenniality in rice and sorghum. Proceeding of the National Academy of Sciences of the United States of America 100: 4050-4054.
31. HUELSENBECK, J. P. and B. RANNALA. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53: 904-913.
32. IDAHO CONSERVATION DATA CENTER. 2003. Idaho special status of vascular plants. Boise: Idaho Fish and Game Department.
33. IVEY, C. T., D. E. CARR, and M. D. EUBANKS. 2004. Effects of inbreeding in Mimulus guttatus on tolerance to herbivory in natural environments. Ecology 85: 567-574.
34. JORDAN, W. C., M. W. COURTNEY, and J. E. NEIGEL. 1996. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). American Journal of Botany 83: 430-439.
35. KALLERSJO, M., V. A. ALBERT, and J. S. FARRIS. 1999. Homoplasy increases phylogenetic structure. Cladistics 15: 91-93.
36. KARRON, J. D., R. J. MITCHELL, K. G. HOLMQUIST, J. M. BELL, and B. FUNK. 2004. The influence of floral display size on selfing rates in Mimulus ringens. Heredity 92: 2242-248.
37. KELCHNER, S. A. and L. G. CLARK. 1997. Molecular evolution and phylogenetic utility of the chloroplast intron in Chusquea and the Bambusideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397.
38. LEWIS, H. 1973. The origin of diploid neospecies. American Naturalist 107: 161-170.
39. LEWIS, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.
40. _, M. T. HOLDER, and K. E. HOLSINGER. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54: 241-253.
41. MCCRACKEN, K. G., J. HARSHMAN, D. A. MCCLELLAN, and A. D. AFTON. 1999. Data set incongruence and correlated character evolution: an example of functional convergence in the hindlimbs of stifftail diving ducks. Systematic Biology 48: 683-714.
42. MEINKE, R. J. 1983. Mimulus hymenophyllus (Scrophulariaceae): a new species from the Snake River Canyon area of eastern Oregon. Madroño 30: 147-152.
43. _. 1992. Systematic and reproductive studies of Mimulus (Scrophulariaceae) in the Pacific Northwest: implications for conservation biology. Ph.D. Thesis. Oregon State University, Corvallis, Oregon.
44. _. 1995. Mimulus evanescens (Scrophulariaceae): a new annual species from the northern Great Basin. Great Basin Naturalist 55: 249-257.
45. MONTANA NATURAL HERITAGE PROGRAM. 2004. Plant species of concern. Helena, Montana.
46. NYLANDER, J. A. A., F. RONQUIST, J. P. HUELSENBECK, and J. L. NIEVES-ALDREY. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67.
47. OREGON NATURAL HERITAGE INFORMATION CENTER. 2004. Rare, threatened and endangered species of Oregon. Portland, Oregon.
48. PENNELL, F. W. 1951. Scrophulariaceae. Pp. 686-859 in An illustrated flora of the Pacific states, ed. L. Abrams. Palo Alto: Stanford University Press.
49. PICKETT, K. M. and C. P. RANDLE. 2005. Strange Bayes indeed: uniform topological priors imply non-uniform clade priors. Molecular Phylogenetics and Evolution 34: 203-211.
50. POSADA, D. and K. A. CRANDALL. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
51. PRATHER, L. A. 1999. The relative lability of floral vs. non-floral characters and a morphological phylogenetic analysis of Cobaea (Polemoniaceae). Botanical Journal of the Linnean Society 131: 433-450.
52. RAMSEY, J., H. D. BRADSHAW, and D. W. SCHEMSKE. 2003. Components of reproductive isolation between themonkeyflowers Mimulus lewisii and M. cardinalis (Phrymaceae). Evolution 57: 1520-1534.
53. RANDLE, C. P., M. E. MORT, and D. J. CRAWFORD. 2005. Bayesian inference of phylogenetics revisited: developments and concerns. Taxon 54: 9-15.
54. RANNALA, B. and Z. YANG. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
55. RONQUIST, F. and J. P. HUELSENBECK. 2003. MrBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
56. SANDERSON, M. J. and M. J. DONOGHUE. 1989. Patterns of variation in levels of homoplasy. Evolution 43: 1781-1795.
57. SCHEMSKE, D. W. and H. D. BRADSHAW. 1999. Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proceedings of the National Academy of Sciences USA 96: 11910-11915.
58. SCOTLAND, R. W., R. G. OLMSTEAD, and J. R. BENNETT. 2003. Phylogeny reconstruction: the role of morphology. Systematic Biology 52: 539-548.
59. SIMMONS, M. P. and H. OCHOTERENA. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
60. SMALL, R. L., J. A. RYBURN, R. C. CRONN, T. S. SEELANAN, and J. F. WENDEL. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
61. SMITH, N. D. and A. H. TURNER. 2005. Morphology's role in phylogeny reconstruction: perspectives from paleontology. Systematic Biology 54: 166-173.
62. SUZUKI, Y., G. GLAZKO, and M. NEI. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceeding of the National Academy of Sciences USA 99: 16138-16143.
63. SWIGONOVA, Z. and K. M. KJER. 2004. Phylogeny and host-plant association in the leaf beetle genus Trirhabda LeConte (Coleoptera: Chrysomelidae). Molecular Phylogenetics and Evolution 32: 358-374.
64. SWOFFORD, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony (*and other methods). 4.0b10. Sunderland: Sinauer Associates.
65. THOMPSON, D. 1992. Mimulus. Pp. 1037-1046 in The Jepson manual of higher plants of California, eds. J. Hickman. Berkeley: University of California Press.
66. WASHINGTON NATURAL HERTIAGE PROGRAM. 2004. Endangered, threatened, and sensitive plants of Washington. Washington State Department of Natural Resources. Olympia, Washington.
67. WHITTALL, J. B. 1999. A molecular phylogeny for the Mimulus moschatus alliance (Scrophulariaceae) and its conservation implications. M. S. Thesis. Oregon State University, Corvallis, Oregon.
68. _, A. LISTON, S. GISLER, and R. J. MEINKE. 2000. Detecting nucleotide additivity from direct sequences is a SNAP: an example from Sidalcea (Malvaceae). Plant Biology 2: 211-217.
69. WIENS, J. J. 2004. The role of morphological data in phylogeny reconstruction. Systematic Biology 53: 653-661.
70. _, P. T. CHIPPINDALE, and D. HILLIS. 2003. When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders. Systematic Biology 52: 501-514.
71. WILCOX, T. P., D. J. ZWICKL, T. A. HEATH, and D. HILLIS. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25: 361-371.
72. WYATT, R., E. A. EVANS, and J. C. SORENSON. 1992. The evolution of self-pollination in granite outcrop species of Arenaria (Caryophyllaceae). VI. Electrophoretically detectable genetic variation. Systematic Botany 17: 201-209.