Range persistence during the last glacial maximum: Carex macrocephala was not restricted to glacial refugia

Molecular Ecology

Volumn 18, Issue 20, 2009, Pages 4256-4269

  King, Matthew G ^a   Horning, Matthew E ^b   Roalson, Eric H ^c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b PACIFIC NORTHWEST RESEARCH STATION   (United States)

^c WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Coastal refuge; Cyperaceae; Pleistocene glaciation; Population genetics

Indexed keywords

MICROSATELLITE DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; CYPERACEAE; DNA SEQUENCE; GENE FLOW; GENETIC VARIABILITY; GENETICS; INBREEDING; MOLECULAR EVOLUTION; NORTH AMERICA; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS;

CAREX PLANT; DNA, PLANT; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; INBREEDING; MICROSATELLITE REPEATS; NORTH AMERICA; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

CAREX MACROCEPHALA; CYPERACEAE;

EID: 70349850540     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04280.x     Document Type: Article

References (82)

1. Abbott RJ, Brochmann C (2003) History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology, 12, 299 313.
2. Abbott R, Smith LC, Milne RL, Crawford RM, Wolff K, Balfour J (2000) Molecular analysis of plant migration and refugia in the Arctic. Science, 289, 1343 1346.
3. Anderson LL, Hu FS, Nelson DM, Petit RJ, Paige KN (2006) Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proceedings of the National Academy of Sciences, USA, 103, 12447 12450.
4. Arafeh R, Kadereit JW (2006) Long-distance seed dispersal, clone longevity and lack of phylogeographical structure in the European distributional range of the coastal Calystegia soldanella (L.) R.Br. (Convolvulaceae). Journal of Biogeography, 33, 1461 1469.
5. Arnaud-Haond S, Belkhir K (2007) Genclone: a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization. Molecular Ecology, 7, 15 17.
6. Arnaud-Haond S, Duarte CM, Alberto F, Serräo EA (2007) Standardizing methods to address clonality in population studies. Molecular Ecology, 16, 5115 5139.
7. Balloux F, Amos W, Coulson T (2004) Does heterozygosity estimate inbreeding in real populations? Molecular Ecology, 13, 3021 3031.
8. Barendregt RW, Duk-Rodkin A (2004) Chronology and extent of Late Cenozoic ice sheets in North America: a magnetostratigraphic assessment. In : Quaternary Glaciations - Extent and Chronology; Part II: North America (eds Ehlers J, Gibbard PL pp. 1 8. Elsevier, Amsterdam.
9. Barrie JV, Conway KW (1999) Late Quaternary glaciation and postglacial stratigraphy of the northern Pacific margin of Canada. Quaternary Research, 51, 113 123.
10. Bockelmann AC, Reusch TBH, Bijlsma R, Bakker JP (2003) Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes. Molecular Ecology, 12, 505 515.
11. Bonin A, Bellemain E, Bronken Eidesen P et al. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261 3273.
12. Brunsfeld SJ, Sullivan J (2006) A multi-compartmented glacial refugium in the northern Rocky Mountains: evidence from the phylogeography of Cardamine constancei (Brassicaceae). Conservation Genetics, 6, 895 904.
13. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative phylogeography of northwestern North America: a synthesis. In : Integrating Ecological and Evolutionary Processes in a Spatial Context (eds Silvertown J, Antonovics J pp. 319 339. Blackwell Science, Oxford.
14. Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2004) Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology, 53, 781 792.
15. Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J (2005) Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modeling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14, 255 265.
16. Charlesworth D (2003) Effects of inbreeding on the genetic diversity of populations. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 358, 1051 1070.
17. DeChaine EG, Martin AP (2004) Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA. Evolution, 58, 113 127.
18. Demboski JR, Cook JA (2001) Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America. Molecular Ecology, 10, 1227 1240.
19. Demboski JR, Sullivan J (2003) Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America. Molecular Phylogenetics and Evolution, 26, 389 408.
20. Demboski JR, Stone KD, Cook JA (1999) Further perspectives on the Haida Gwaii glacial refugium. Evolution, 53, 2008 2012.
21. Dorken ME, Barrett SCH (2004) Chloroplast haplotype variation among monoecious and dioecious populations of Sagittaria latifolia (Alismataceae) in eastern North America. Molecular Ecology, 13, 2699 2707.
22. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571 2581.
23. Edh K, Widen B, Ceplitis ALF (2007) Nuclear and chloroplast microsatellites reveal extreme population differentiation and limited gene flow in the Aegean endemic Brassica cretica (Brassicaceae). Molecular Ecology, 16, 4972 4983.
24. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479 491.
25. Excoffier L, Laval G, Schneider S (2005) arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
26. Fenster CB, Vekemans X, Hardy OJ (2003) Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae). Evolution, 57, 995 1007.
27. Fleming MA, Cook JA (2002) Phylogeography of endemic ermine (Mustela erminea) in southeast Alaska. Molecular Ecology, 11, 795 807.
28. Fulton RJ, Ryder JM, Tsang S (2004) The Quaternary glacial record of British Columbia, Canada. In : Quaternary Glaciations - Extent and Chronology; Part II: North America (eds Ehlers J, Gibbard PL pp. 39 50. Elsevier, Amsterdam.
29. Galtier N, Depaulis F, Barton NH (2000) Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics, 155, 981 987.
30. Gao X, Starmer J (2007) Human population structure detection via multilocus genotype clustering. BMC Genetics, 8, 34.
31. Glémin S, Bazin E, Charlesworth D (2006) Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proceedings of the Royal Society of London, Series B: Biological Sciences, 273, 3011 3019.
32. Good JM, Demboski JR, Nagorsen DW, Sullivan J (2003) Phylogeography and introgressive hybridization: Chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution, 57, 1900 1916.
33. Goudet J (1995) fstat (version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485 486.
34. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633 1638.
35. Hetherington R, Barrie JV, Reid RGB et al. (2003) Late Pleistocene coastal paleogeography of the Queen Charlotte Islands, British Columbia, Canada, and its implications for terrestrial biogeography and early postglacial human occupation. Canadian Journal of Earth Sciences, 40, 1755 1766.
36. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247 276.
37. Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions: Biological Sciences, 359, 183 195.
38. Hodgins KA, Barrett SCH (2007) Population structure and genetic diversity in tristylous Narcissus triandrus: insights from microsatellite and chloroplast DNA variation. Molecular Ecology, 16, 2317 2332.
39. Ingvarsson PK (2002) A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution, 56, 2368 2373.
40. Ishikawa S-I, Furukawa A, Okuda T, Oikawa T (1993) Germination requirements in Carex kobomugi (Sea Isle). Journal of Plant Research, 106, 245 248.
41. Kaufman DS, Manley WF (2004) Pleistocene maximum and Late Wisconsinan glacier extents across Alaska, U.S.A. In : Quaternary Glaciations - Extent and Chronology; Part II: North America (eds Ehlers J, Gibbard PL pp. 9 28. Elsevier, Amsterdam.
42. King MG, Roalson EH (2009a) Discordance between phylogenetics and coalescent-based divergence modelling: exploring phylogeographic patterns of speciation in the Carex macrocephala species complex. Molecular Ecology, 18, 468 482.
43. King MG, Roalson EH (2009b) Isolation and characterization of 11 microsatellite loci from Carex macrocephala (Cyperaceae). Conservation Genetics, 10, 531 533. DOI :.
44. Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers. Molecular Ecology, 10, 691 701.
45. Magri D, Fineschi S, Bellarosa R et al. (2003) The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean. Molecular Ecology, 12, 1 13.
46. Masta SE (2000) Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations? Evolution, 54, 1699 1711.
47. Mastrogiuseppe J (2002) Flora of North America: north of Mexico. In : Volume 23 Magnoliophyta: Commelinidae (in part): Cyperaceae (ed. Flora of North America Editorial Committee). pp. 307 309. Oxford University Press, New York.
48. Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution, 60, 2399 2402.
49. Michalski SG, Durka W (2007) High selfing and high inbreeding depression in peripheral populations of Juncus atratus. Molecular Ecology, 16, 4715 4727.
50. Naciri Y, Gaudeul M (2007) Phylogeography of the endangered Eryngium alpinum L. (Apiaceae) in the European Alps. Molecular Ecology, 16, 2721 2733.
51. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA, 70, 3321 3323.
52. Nettel A, Dodd RS (2007) Drifting propagules and receding swamps: genetic footprints of mangrove recolonization and dispersal along tropical coasts. Evolution, 61, 958 971.
53. Nielson M, Lohman K, Sullivan J (2001) Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest. Evolution, 55, 147 160.
54. Nordborg M (2000) Linkage disequilibrium, genetrees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics, 154, 923 929.
55. O'Connell LM, Ritland K, Thompson SL (2008) Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers. Botany, 86, 194 203.
56. Olsen JL, Stam WT, Coyer JA et al. (2004) North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Molecular Ecology, 13, 1923 1941.
57. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535 538.
58. Pannell JR, Verdú M (2006) The evolution of gender specialization from dimorphic hermaphroditism: paths from heterodichogamy to gynodioecy and androdioecy. Evolution, 60, 660 673.
59. Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
60. Petit RJ, Aguinagalde I, de Beaulieu J-L et al. (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563 1565.
61. Pollak E (1987) On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics, 117, 353 360.
62. Porter SC (2004) Glaciation of western Washington, U.S.A. In : Quaternary Glaciations - Extent and Chronology; Part II: North America (eds Ehlers J, Gibbard PL pp. 289 294. Elsevier, Amsterdam.
63. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
64. Rambaut A (1996) se-al: Sequence alignment editor. Available from http://tree.bio.ed.ac.uk/software/seal/.
65. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223 225.
66. Riddle BR (1996) The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology and Evolution, 11, 207 211.
67. Roalson EH, Columbus JT, Friar EA (2001) Phylogenetic relationships in Cariceae (Cyperaceae) based on ITS (nrDNA) and trnT-L-F (cpDNA) region sequences: assessment of subgeneric and sectional relationships in Carex with emphasis on section Acrocystis. Systematic Botany, 26, 318 341.
68. Schönswetter P, Popp M, Brochmann C (2006) Central Asian origin of and strong genetic differentiation among populations of the rare and disjunct Carex atrofusca (Cyperaceae) in the Alps. Journal of Biogeography, 33, 948 956.
69. Shaw J, Lickey EB, Beck JT et al. (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany, 92, 142 166.
70. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15, 4261 4293.
71. Standley LA (1985) Paradioecy and gender ratios in Carex macrocephala Cyperaceae. American Midland Naturalist, 113, 283 286.
72. Steele CA, Storfer A (2006) Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Molecular Ecology, 15, 2477 2487.
73. Stenström A, Jonsson BO, Jónsdóttir IS, Fagerström T, Augner M (2001) Genetic variation and clonal diversity in four clonal sedges (Carex) along the Arctic coast of Eurasia. Molecular Ecology, 10, 497 513.
74. Twichell DC, Cross VA (2002) Holocene evolution of the southern Washington and northern Oregon shelf and coast: Geologic discussion and GIS data release. USGS Open-File Report 01-076. Available from http://pubs.usgs.gov/of/ of01-076/index.htm.
75. Tyler T (2002) Geographical distribution of allozyme variation in relation to post-glacial history in Carex digitata, a widespread European woodland sedge. Journal of Biogeography, 29, 919 930.
76. Weckworth BV, Talbot S, Sage GK, Person DK, Cook JA (2005) A signal for independent coastal and continental histories among North American wolves. Molecular Ecology, 14, 917 931.
77. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
78. Widmer A, Lexer C (2001) Glacial refugia: sanctuaries for allelic richness, but not for gene diversity. Trends in Ecology and Evolution, 16, 267 268.
79. Williams T, Kelley C (2004) gnuplot 4.2.2. Available from http://www.gnuplot.info/.
80. Willyard A, Syring J, Gernandt DS, Liston A, Cronn R (2007) Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution, 24, 90 101.
81. Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA, 84, 9054 9058.
82. Wright S (1951) The genetical structure of populations. Annals of Eugenics, 15, 323 354.