Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae)

American Journal of Botany

Volumn 100, Issue 12, 2013, Pages 2403-2411

  Escudero, Marcial ^a,b   Hipp, Andrew ^a,b  

^a FIELD MUSEUM OF NATURAL HISTORY   (United States)

^b MORTON ARBORETUM   (United States)

Author keywords

Bounded diversification; Cretaceous; Extinction; Radiation; Speciation; Times of diversification

Indexed keywords

ADAPTIVE RADIATION; CLADISTICS; CRETACEOUS; CRYPSIS; EXTINCTION; HETEROGENEITY; MONOCOTYLEDON; PALEOCENE-EOCENE BOUNDARY; PHYLOGENY; SEDGE; SPECIATION (BIOLOGY); SPECIES DIVERSITY; SPECIES RICHNESS;

ANGIOSPERM; ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; BOUNDED DIVERSIFICATION; CRETACEOUS; CYPERACEAE; EVOLUTION; EXTINCTION; FOSSIL; GENETICS; PHYLOGENY; RADIATION; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; TIMES OF DIVERSIFICATION;

BOUNDED DIVERSIFICATION; CRETACEOUS; EXTINCTION; RADIATION; SPECIATION; TIMES OF DIVERSIFICATION;

ANGIOSPERMS; BIODIVERSITY; BIOLOGICAL EVOLUTION; CYPERACEAE; FOSSILS; GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 84890083054     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1300162     Document Type: Article

References (75)

1. AKAIKE, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723.
2. ALFARO, M. E., F. SANTINI, C. BROCK, H. ALAMILLO, A. DORNBURG, D. L. RABOSKY, G. CARNEVALE, and L. J.H ARMON. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences, USA 106: 13410-13414.
3. ANDERSON, C. L., and T. JANSSEN. 2009. Monocots. In S. B. Hedges and S. Kumar [eds.], The timetree of life, 203-212. Oxford University Press, Oxford, UK.
4. BELL, C. D., D. E.S OLTIS, and P. S.S OLTIS. 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany 97: 1296-1303.
5. BESNARD, G., A. M.M UASYA, F. RUSSIER, E. H. ROALSON, N. SALAMIN, and P.-A. CHRISTIN. 2009. Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): Multiple appearances and genetic convergence. Molecular Biology and Evolution 26: 1909-1919.
6. BREMER, K. 2002. Gondwanan evolution of the grass alliance of families (Poales). Evolution 56: 1374-1387.
7. BRUHL, J. J. 1995. Sedge genera of the world: Relationships and a new classification of the Cyperaceae. Australian Systematic Botany 8: 125-305.
8. BRUHL, J. J., and K. L. WILSON. 2007. Towards a comprehensive survey of C3 and C4 photosynthetic pathways in Cyperaceae. Aliso 23: 99-148.
9. CARDILLO, M., C. D. L. ORME, and I. P. F. OWENS. 2005. Testing for latitudinal bias in diversification rates: An example using new world birds. Ecology 86: 2278-2287.
10. CASTRESANA, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552.
11. CHACÓN, J., S. MADRIÑÁN, M. W. CHASE, and J. J. BRUHL. 2006. Molecular phylogenetics of Oreobolus (Cyperaceae) and the origin and diversification of the American species. Taxon 55: 359-366.
12. CHUNG, K.-S., A. L. HIPP, and E. H. ROALSON. 2012. Chromosome number evolves independently of genome size in a clade with non-localized centromeres (Carex: Cyperaceae). Evolution 66: 2708-2722.
13. COLLINSON, M. E. 1983. Palaeofloristic assemblages and palaeoecology of the Lower Oligocene Bembridge Marls, Hamstead Ledge, Isle of Wight. Botanical Journal of the Linnean Society 86: 177-225.
14. COLLINSON, M. E., and C. J. CLEAL. 2001. Late middle Eocene-early Oligocene (Bartonian-Rupelian) and Miocene palaeobotany of Great Britain. In C. J. Cleal, B. A. Thomas, D. J. Batten, and M. E. Collinson [eds.], Mesozoic and Tertiary palaeobotany of Great Britain, 227-274. Geological Conservation Review Series No. 22, Joint Nature Conservation Committee, Peterborough, UK.
15. DABROS, A., and M. J. WATERWAY. 2008. Segregation of sedge species (Cyperaceae) along environmental gradients in fens of the Schefferville region, northern Quebec. In R. F. C. Naczi and B. A. Ford [eds.], Sedges: Uses, diversity, and systematics of the Cyperaceae, 145-161. Missouri Botanical Garden Press, St. Louis, Missouri, USA.
16. DRUMMOND, A. J., S. Y. W. HO, M. J. PHILLIPS, and A. RAMBAUT. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
17. DRUMMOND, A. J., and A. RAMBAUT. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
18. DRUMMOND, A. J., M. A. SUCHARD, D. XIE, and A. RAMBAUT. 2012a. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
19. DRUMMOND, C. S., R. J. EASTWOOD, S. T. S.M IOTTO, and C. E. HUGHES. 2012b. Multiple continental radiations and correlates of diversification in Lupinus (leguminosae): Testing for key innovation with incomplete taxon sampling. Systematic Biology 61: 443-460.
20. EDGAR, R. C. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
21. EDWARDS, E. J., and C. J.S TILL. 2008. Climate, phylogeny and the ecological distribution of C4 grasses. Ecology Letters 11: 266-276.
22. ESCUDERO, M., A. L. HIPP, T. F. HANSEN, K. L. VOJE, and M. LUCEÑO. 2012b. Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). New Phytologist 195: 237-247.
23. ESCUDERO, M., A. L.H IPP, M. J. WATERWAY, and L. M. VALENTE. 2012a. Diversification rates and chromosome evolution in the most diverse angiosperm genus of the temperate zone (Carex, Cyperaceae). Molecular Phylogenetics and Evolution 63: 650-655.
24. ESCUDERO, M., E. MAGUILLA, and M. LUCEÑO. 2013. Selection by climatic regime and neutral evolutionary processes in holocentric chromosomes (Carex gr. laevigata: Cyperaceae): A microevolutionary approach. Perspectives in Plant Ecology, Evolution and Systematics 15: 118-129.
25. FOREST, F. 2009. Calibrating the tree of life: Fossils, molecules and evolutionary timescales. Annals of Botany 104: 789-794.
26. GIVNISH, T. J., M. AMES, J. R. MCNEAL, M. R. MCKAIN, P. R. STEELE, C. W. DEPAMPHILIS, S. W. GRAHAM, ET AL. 2010. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Garden 97: 584-616.
27. GOETGHEBEUR, P. 1998. Cyperaceae. In K. Kubitzki [ed.], The families and genera of vascular plants vol. 4, 164. Springer, Berlin, Germany.
28. GOVAERTS, R., and D. A. SIMPSON. 2007. World Checklist of Cyperaceae. Royal Botanic Gardens, Kew. http://apps.kew.org/wcsp/
29. GRADSTEIN, F. M., J. G.O GG, M. SCHMITZ, and G. OGG. 2012. The geologic time scale. Elsevier, Oxford, UK.
30. HARMON, L. J., J. T. WEIR, C. D. BROCK, R. E. GLOR, and W. CHALLENGER. 2008. GEIGER: Investigating evolutionary radiations. Bioinformatics (Oxford, England) 24: 129-131.
31. HINCHLIFF, C. E., and E. H. ROALSON. 2013. Using supermatrices for phylogenetic inquiry: an example using the sedges. Systematic Biology 62: 205-219.
32. HIPP, A. L., P. ROTHROCK, and E. ROALSON. 2009. The evolution of chromosome arrangements in Carex (Cyperaceae). Botanical Review 75: 96-109.
33. HIPP, A. L., P. E. ROTHROCK, R. WHITKUS, and J. A. WEBER. 2010. Chromosomes tell half of the story: The correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Molecular Ecology 19: 3124-3138.
34. HO, S. Y. W., and M. J. PHILLIPS. 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58: 367-380.
35. JANSSEN, T., and K. BREMER. 2004. The age of major monocot groups inferred from 800+ rbcL sequences. Botanical Journal of the Linnean Society 146: 385-398.
36. JUNG, J., and H.-K. CHOI. 2013. Recognition of two major clades and early diverged groupswithin the subfamilyCyperoideae (Cyperaceae) including Korean sedges. Journal of Plant Research 126: 335-349.
37. LARRIDON, I., W. HUYGH, M. REYNDERS, A. M. MUASYA, R. GOVAERTS, D. A. SIMPSON, and P. GOETGHEBEUR. 2011a. Nomenclature and typification of names of genera and subdivisions of genera in Cypereae (Cyperaceae): 2. Names of subdivisions of Cyperus. Taxon 60: 868-884
38. LARRIDON, I., M. REYNDERS, W. HUYGH, K. BAUTERS, K. VAN DE PUTTE, A. M. MUASYA, P. BOECKX, ET AL. 2011b. Affinities in C3 Cyperus lineages (Cyperaceae) revealed using molecular phylogenetic data and carbon isotope analysis. Botanical Journal of the Linnean Society 167: 19-46.
39. LARRIDON, I., M. REYNDERS, W. HUYGH, K. BAUTERS, A. VRIJDAGHS, O. LEROUX, A. M. MUASYA, ET AL. 2011c. Taxonomic changes in C3 Cyperus (Cyperaceae) supported by molecular data, morphology, embryography, ontogeny and anatomy. Plant Ecology and Evolution 144: 327-356.
40. LINDER, H. P., and P. J. RUDALL. 2005. Evolutionary history of Poales. Annual Review of Ecology Evolution and Systematics 36: 107-124
41. LIPNEROVÁ, I., P. BUREŠ, L. HOROVÁ, and P. ŠMARDA. 2013. Evolution of genome size in Carex (Cyperaceae) in relation to chromosome number and genomic base composition. Annals of Botany 111: 79-94.
42. MAGALLÓN, S., and A. CASTILLO. 2009. Angiosperm diversification through time. American Journal of Botany 96: 349-365
43. MAGALLÓN, S., and M. J.S ANDERSON. 2001. Absolute diversification rates in angiosperm clades. Evolution 55: 1762-1780.
44. MAI, D. H. 1997. Die oberoligozänen Floren am Nordrand der Sächsischen Lausitz. Palaeontographica B 244: 1124.
45. MAI, D. H. 1999. Die Untermiozänen Floren aus der Spremberger Folge und dem 2 Flözhorizont in der Lausitz. Teil I. Farnpflanzen, Koniferen und Monokotyledonen. Palaeontographica B 250: 176.
46. MAI, D. H. 2000. Die mittelmiozänen und obermiozänen Floren aus der Meuroer und Raunoer Folge in der Lausitz. Teil 1. Farnplflanzen, Koniferen und monocotyledonen. Palaeontographica B 256: 168
47. MANSION, G., F. SELVI, A. GUGGISBERG, and E. CONTI. 2009. Origin of Mediterranean endemics in the Boraginales: Integrative evidence from molecular dating and ancestral area reconstruction. Journal of Biogeography 36: 1282-1296.
48. MUASYA, A. M., D. A. SIMPSON, M. W. CHASE, and A. CULHAM. 2001. A phylogeny of Isolepis (Cyperaceae) inferred using plastid rbcL and trnL-F sequence data. Systematic Botany 26: 342-353.
49. MUASYA, A. M., D. A. SIMPSON, G. A. VERBOOM, P. GOETGHEBEUR, R. F. C. NACZI, M. W. CHASE, and E. SMETS. 2009. Phylogeny of Cyperaceae based on DNA sequence data: Current progress and future prospects. Botanical Review 75: 2-21.
50. ORME, C. D. L., R. P. FRECKLETON, G. H. THOMAS, T. PETZOLDT, S. A. PRITZ, and N.J.B. PISAAC. 2013. Caper version 0.5: Comparative Analyses of Phylogenetics and Evolution in R. http://cran.r-project.org/
51. Pincheira-Donoso, D., A. M. BAUER, S. MEIRI, and P. UETZ. 2013. Global taxonomic diversity of living reptiles. PLoS ONE 8: e59741
52. POSADA, D. 2008. jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
53. R DEVELOPMENT CORE TEAM. 2012. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
54. RABOSKY, D. L. 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60: 1152-1164.
55. RABOSKY, D. L. 2009. Ecological limits on clade diversification in higher taxa. American Naturalist 173: 662-674.
56. RABOSKY, D. L., S. C. DONNELLAN, A. L. TALABA, and I. J. LOVETTE. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proceedings of the Royal Society of London, Series B 274: 2915-2923.
57. RABOSKY, D. L., G. J. SLATER, and M. E. ALFARO. 2012. Clade age and species richness are decoupled across the eukaryotic tree of life. PLoS Biology 10: e1001381.
58. RAMBAUT, A., and A. J. Drummond. 2007. Tracer version 1.4. http://Beast.Bio.Ed.Ac.Uk/Tracer
59. RICKLEFS, R. E. 2006. Global variation in the diversification rate of passerine birds. Ecology 87: 2468-2478.
60. ROALSON, E. H. 2011. Origins and transitions in photosynthetic pathway types in monocots: A review and reanalysis. In A. S. Raghavendra and R. F.Sage [eds.], C4 photosynthesis and related CO2 concentrating mechanisms, 319-338. Springer, Dordrecht, The Netherlands.
61. RONQUIST, F., M. TESLENKO, P. VAN DER MARK, D. L. AYRES, A. DARLING, S. HÖHNA, B. LARGET, ET AL. 2012. Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
62. SAGE, R. F., P.-A. CHRISTIN, and E. J. EDWARDS. 2011. The C4 plant lineages of planet Earth. Journal of Experimental Botany 62: 3155-3169.
63. SANDERSON, M. J. 2003. r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics (Oxford, England) 19: 301-302.
64. SIMPSON, D. A., C. A. FURNESS, T. R. HODKINSON, A. M.M UASYA, and M. W. CHASE. 2003. Phylogenetic relationships in Cyperaceae subfamily Mapanioideae inferred from pollen and plastid DNA sequence data. American Journal of Botany 90: 1071-1086.
65. SIMPSON, D. A., A. M. MUASYA, K. CHAYAMARIT, J. A. N. PARNELL, S. SUDDEE, B. D. E. WILDE, M.B. JONES, et al. 2005. Khaosokia caricoides, a new genus and species of Cyperaceae from Thailand. Botanical Journal of the Linnean Society 149: 357-364.
66. SMITH, S. A., and B. C. O'Meara. 2012. TreePL: Divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics (Oxford, England) 28: 2689-2690.
67. SMITH, S. Y., M. E. COLLINSON, P. J. RUDALL, and D. A. SIMPSON. 2010. The Cretaceous and Paleogene fossil record of Poales: Review and current research. In O. Seberg, G. Petersen, A. Barfod, and J. I. Davis [eds.], Diversity, phylogeny, and evolution in monocotyledons: Proceedings of the Fourth International Conference on the Comparative Biology of the Monocotyledons & the Fifth International Symposium on Grass Systematics and Evolution, 333-356. Aarhus University Press, Aarhus, Germany.
68. STAMATAKIS, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688-2690.
69. TALAVERA, G., and J. CASTRESANA. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564-577.
70. VELLEND, M., M. J. LECHOWICZ, and M. J. WATERWAY. 2000. Environmental distribution of four Carex species (Cyperaceae) in an old-growth forest. American Journal of Botany 87: 1507-1516.
71. VERBOOM, G. A. 2006. A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa. Molecular Phylogenetics and Evolution 38: 79-89.
72. WATERWAY, M. J., T.H OSHINO, and T. MASAKI. 2009. Phylogeny, species richness, and ecological specialization in Cyperaceae tribe Cariceae. Botanical Review 75: 138-159.
73. WIENS, J. J. 2011. The causes of species richness patterns across space, time, and clades and the role of "ecological limits." Quarterly Review of Biology 86: 75-96.
74. ZACHOS, J., H. PAGANI, L. SLOAN, E. THOMAS, and K. BILLUPS. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292: 686-693.
75. ZHANG, X., A. MARCHANT, K. L. WILSON, and J. J. BRUHL. 2004. Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences. Molecular Phylogenetics and Evolution 31: 647-657.