Evidence for range stasis during the latter Pleistocene for the Atlantic Coastal Plain endemic genus, Pyxidanthera Michaux

Molecular Ecology

Volumn 19, Issue 19, 2010, Pages 4302-4314

  Wall, Wade A ^a   Douglas, Norman A ^a   Xiang, Qiu Yun ^a   Hoffmann, William A ^a   Wentworth, Thomas R ^a   Hohmann, Matthew G ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b U S ARMY ENGINEER RESEARCH AND DEVELOPMENT CENTER   (United States)

Author keywords

amplified fragment length polymorphism; cpDNA; Diapensiaceae; phylogeography; Pleistocene; refugium

Indexed keywords

CHLOROPLAST DNA;

ALLELE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANGIOSPERM; ARTICLE; CPDNA; DIAPENSIACEAE; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; HISTOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION GENETICS; REFUGIUM;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; CPDNA; DIAPENSIACEAE; PHYLOGEOGRAPHY; PLEISTOCENE; REFUGIUM;

ALLELES; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANGIOSPERMS; DNA, CHLOROPLAST; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA;

ANIMALIA; DIAPENSIACEAE; PYXIDANTHERA; PYXIDANTHERA BARBULATA; PYXIDANTHERA BREVIFOLIA;

EID: 77957226352     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04793.x     Document Type: Article

References (90)

1. Ahles HE (1964) New combinations for some vascular plants of southeastern United States. Journal of the Elisha Mitchell Scientific Society, 80, 172 173.
2. Bahlo M, Griffiths RC (2000) Inference from gene trees in a subdivided population. Theoretical Population Biology, 57, 79 95. (Pubitemid 30221281)
3. Bloom AL (1983) Sea level and coastal changes. Late-Quaternary Environments of the United States, 2, 42 51.
4. Bonin A, Bellemain E, Bronken Eidsen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261 3273. (Pubitemid 39415663)
5. Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737 3758. (Pubitemid 47397323)
6. Broyles SB (1998) Postglacial migration and the loss of allozyme variation in northern populations of Asclepias exaltata (Asclepiadaceae). American Journal of Botany, 85, 1091 1097.
7. Buchanan M, Finnegan JT (2008) Natural Heritage Program List of Rare Plant Species of North Carolina, North Carolina Natural Heritage Program
8. Burnham KP, Anderson DR (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer
9. Carstens BC, Stoute HN, Reid NM (2009) An information-theoretical approach to phylogeography. Molecular Ecology, 18, 4270 4282.
10. Church SA, Kraus JM, Mitchell JC, Church DR, Taylor DR (2003) Evidence for multiple Pleistocene refugia in the postglacial expansion of the eastern tiger salamander, Ambystoma tigrinum tigrinum. Evolution, 57, 372 383.
11. Coart E, Lamote V, De Loose M, Van Bockstaele E, Lootens P, Roldán-Ruiz I (2002) AFLP markers demonstrate local genetic differentiation between two indigenous oak species [Quercus robur L. and Quercus petraea (Matt.) Liebl.] in Flemish populations. Theoretical and Applied Genetics, 105, 431 439. (Pubitemid 36072796)
12. Comes HP, Kadereit JW (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science, 3, 432 438.
13. Comps B, Gomory D, Letouzey J, Thiébaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics, 157, 389 397. (Pubitemid 32066324)
14. Cunningham CW, Collins TM (1994) Developing model systems for molecular biogeography: vicariance and interchange in marine invertebrates. In : Molecular Ecology and Evolution: Approaches and Applications (eds B Schierwater, B Streit, P Wagner, R DeSalle). pp. 405 433, Birkhauser Verlag
15. Delcourt PA, Delcourt HR (1981) Vegetation maps for eastern North America: 40,000 yr BP to the present. In : Geobotany II (ed RC Romans). pp. 123 165, Plenum
16. 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.
17. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical bulletin, 19, 11 15.
18. Ehlers J, Gibbard PL (Eds 2004) Quaternary Glaciations : Extent and Chronology. Elsevier
19. Ehrich D (2006) AFLPdat: a collection of R functions for convenient handling of AFLP data. Molecular Ecology Notes, 6, 603 604. (Pubitemid 44252552)
20. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611 2620. (Pubitemid 40886055)
21. Evans MEK, Dolan RW, Menges ES, Gordan DR (2000) Genetic diversity and reproductive biology in Warea carteri (Brassicaceae), a narrowly endemic Florida scrub annual. American Journal of Botany, 87, 372 381.
22. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47 50.
23. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574 578. (Pubitemid 47035522)
24. Fenneman NM (1938) Physiography of Eastern United States. McGraw-Hill
25. Flora of North America Editorial Committee (1993) Flora of North America North of Mexico. Oxford University Press
26. French HM, Demitroff M, Forman SL (2003) Evidence for late-pleistocene permafrost in the New Jersey Pine Barrens (Latitude 39 degrees N), Eastern USA. Permafrost and Periglacial Processes, 14, 259 274. (Pubitemid 37196240)
27. French HM, Demitroff M, Forman SL, Newell WL (2007) A chronology of Late-Pleistocene permafrost events in southern New Jersey, eastern USA. Permafrost and Periglacial Processes, 18, 49 59. (Pubitemid 46403748)
28. Frost C (2006) History and future of the longleaf pine ecosystem. In : The Longleaf Pine Ecosystem: Ecology, Silvacul-ture, and Restoration (eds S Jose, EJ Jokela, DL Miller). pp. 9 42, Springer Science
29. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
30. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics, 133, 693 709.
31. Godt MJW, Hamrick JL (1995) Low levels of allozyme differentiation between Pyxidanthera (pyxie-moss) taxa (Diapensiaceae). Plant Systematics and Evolution, 195, 159 168.
32. Gonzales E, Hamrick JL, Chang S (2008) Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum. Journal of Biogeography, 35, 844 852. (Pubitemid 351551989)
33. Hafner MS, Nadler SA (1990) Cospeciation in host-parasite assemblages: comparative analysis of rates of evolution and timing of cospeciation events. Systematic Biology, 39, 192 204.
34. Herrera CM, Bazaga P (2008) Population-genomic approach reveals adaptive floral divergence in discrete populations of a hawk moth-pollinated violet. Molecular Ecology, 17, 5378 5390.
35. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913. (Pubitemid 30435039)
36. Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, 104, 2785 2790. (Pubitemid 46327957)
37. Hobbs III. CH (2004) Geological history of Chesapeake Bay, USA. Quaternary Science Reviews, 23, 641 661.
38. Holland BR, Clarke AC, Meudt HM (2008) Optimizing automated AFLP scoring parameters to improve phylog-enetic resolution. Systematic Biology, 57, 347 366.
39. Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898 1914.
40. Ikeda H, Senni K, Fujii N, Setoguchi H (2008) Survival and genetic divergence of an arctic-alpine plant, Diapensia lapponica subsp obovata (Fr. Schm.) Hulten (Diapensiaceae), in the high mountains of central Japan during climatic oscillations. Plant Systematics and Evolution, 272, 197 210.
41. Jacobson GL, Webb III. T, Grimm EC (1987) Patterns and rates of vegetation change during the deglaciation of eastern North America. In : North America and Adjacent Oceans during the Last Deglaciation. The Geology of North America (eds WF Ruddiman, HE Wright Jr.). pp. 277 288, Geological Society of America
42. Kimura M (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61, 893 903.
43. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451 1452.
44. Magni CR, Ducousso A, Caron H, Petit RJ, Kremer A (2005) Chloroplast DNA variation of Quercus rubra L in North America and comparison with other Fagaceae. North America and comparison with other Fagaceae. Molecular ecology, 14, 513 524.
45. Maliouchenko O, Palme AE, Buonamici A, Vendramin GG, Lascoux M (2007) Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens. Journal of Biogeography, 34, 1601 1610. (Pubitemid 47300680)
46. McKinnon GE, Vaillancourt RE, Steane DA, Potts BM (2008) An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae). American Journal of Botany, 95, 368 380.
47. McLachlan JS, Clark JS, Manos PS (2005) Molecular indicators of tree migration capacity under rapid climate change. Ecology, 86, 2088 2098.
48. Meudt HM, Bayly MJ (2008) Phylogeographic patterns in the Australasian genus Chionohebe (Veronica s.l., Plantaginaceae) based on AFLP and chloroplast DNA sequences. Molecular Phylogenetics and Evolution, 47, 319 338.
49. Morris AB, Ickert-Bond SM, Brunson DB, Soltis DE, Soltis PS (2008) Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae). Molecular Ecology, 17, 3889 3900.
50. Mylecraine KA, Kuser JE, Smouse PE, Zimmermann GL (2004) Geographic allozyme variation in Atlantic white-cedar, Chamaecyparis thyoides (Cupressaceae). Canadian Journal of Forest Research, 34, 2443 2454.
51. Nei M (1972) Genetic distance between populations. American Naturalist, 106, 283 292.
52. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press
53. Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885 896. (Pubitemid 32552323)
54. Oksanen J, Kindt R, Legendre P et al. (2009) vegan: Community Ecology Package.
55. Oliveira LO, Huck RB, Gitzendanner MA, Judd WS, Soltis DE, Soltis PS (2007) Molecular phylogeny, biogeography, and systematics of Dicerandra (Lamiaceae), a genus endemic to the southeastern United States. American Journal of Botany, 94, 1017 1027.
56. Overpeck JT, Webb RS, Webb III. T (1992) Mapping eastern North American vegetation change of the past 18 ka: No-analogs and the future. Geology, 20, 1071.
57. Palme AE, Semerikov V, Lascoux M (2003) Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L. Heredity, 91, 465 474. (Pubitemid 37399256)
58. Paradis E (2009) pegas: Population and Evolutionary Genetics Analysis System. R package version 0.3.
59. Paun O, Schönswetter P, Winkler M, Intrabiodiv C, Tribsch A (2008) Historical divergence vs. contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians. Molecular Ecology, 17, 4263 4275.
60. Perez-Collazos E, Sanchez-Gomez P, Jimenez JF, Catalan P (2009) The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis. Molecular Ecology, 18, 848 861.
61. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237 1245. (Pubitemid 26378263)
62. Price EW, Carbone I (2005) SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics, 21, 402 404. (Pubitemid 40246616)
63. Primack RB, Wyatt R (1975) Variation and taxonomy of Pyxidanthera (Diapensiaceae). Brittonia, 27, 115 118.
64. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959. (Pubitemid 30397141)
65. R Development Core Team (2009) R: a Language and environment for statistical computing. R Foundation for Statistical Computing
66. Rahmstorf S (2002) Ocean circulation and climate during the past 120,000 years. Nature, 419, 207 214. (Pubitemid 35033480)
67. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092 2100. (Pubitemid 35440445)
68. Reynolds JD (1966) Morphological Studies in Diapensiaceae. The Embryology of Pyxidanthera Mich, PhD thesis, University of South Carolina.
69. Roberts DW (2010) labdsv: Ordination and Multivariate Analysis for Ecology. R package version 1.4-1.
70. Ronblom K, Anderberg AA (2002) Phylogeny of Diapensiaceae based on molecular data and morphology. Systematic Botany, 27, 383 395. (Pubitemid 34617044)
71. Schafale MP, Weakley AS (1990) Classification of the Natural Communities of North Carolina: Third Approximation. North Carolina Natural Heritage Program
72. Schönswetter P, Tribsch A (2005) Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon, 54, 725 732. (Pubitemid 41494607)
73. 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. (Pubitemid 40113117)
74. Shaw J, Lickey EB, Schill EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany, 94, 275 288. (Pubitemid 46955026)
75. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS (2006) Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15, 4261 4293. (Pubitemid 44749551)
76. Sorrie BA, Weakley AS (2001) Coastal plain vascular plant endemics: phytogeographic patterns. Castanea, 66, 50 82.
77. Sorrie BA, Gray JB, Crutchfield PJ (2006) The vascular flora of the longleaf pine ecosystem of Fort Bragg and Weymouth Woods, North Carolina. Castanea, 71, 129 161.
78. Sorrie BA, Weakley AS, Neesom GL (2009) Pyxidanthera. In : Flora of North America North of Mexico Volume 3 (eds Flora of North America Editorial Committee). pp. 336 337, Oxford University Press
79. Stewart JR, Lister AM (2001) Crypitc refugia and the origins of the modern biota. Trends in Ecology and Evolution, 16, 608 613.
80. Takhtajan A (1986) Floristic Regions of the World. University of California Press
81. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596 1599. (Pubitemid 47236692)
82. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619 633.
83. Trybush S, Hanley S, Cho K et al. (2006) Getting the most out of fluorescent amplified fragment length polymorphism. Canadian Journal of Botany, 84, 1347 1354. (Pubitemid 44945386)
84. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139 151. (Pubitemid 34108478)
85. Ward LW (1992) Tertiary molluscan assemblages from the Salisbury embayment of Virginia. Virginia Journal of Science, 43, 85 100.
86. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256.
87. Weakley AS (2008) Flora of the Carolinas, Virginia, Georgia, northern Florida, and surrounding areas (Working Draft of 7 April 2008).
88. Wells BW (1929) A new pixie from North Carolina. Journal of the Elisha Mitchell Scientific Society, 44, 238 239.
89. Wells BW, Shunk IV (1931) The vegetation and habitat factors of the coarser sands of the North Carolina coastal plain: an ecological study. Ecological Monographs, 1, 465 520.
90. Zhang YY, Zhang DY, Barrett SCH (2010) Genetic uniformity characterizes the invasive spread of water hyacinth (Eichhornia crassipes), a clonal aquatic plant. Molecular Ecology, 19, 1774 1786.