Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Molecular Ecology

Volumn 21, Issue 5, 2012, Pages 1255-1270

  Escobar García, Pedro ^a   Winkler, Manuela ^a   Flatscher, Ruth ^a   Sonnleitner, Michaela ^a   Krejčíková, Jana ^b,c   Suda, Jan ^b,c   Hülber, Karl ^a,d   Schneeweiss, Gerald M ^a   Schönswetter, Peter ^e  

^a UNIVERSITY OF VIENNA   (Austria)

^b INSTITUTE OF BOTANY   (Czech Republic)

^c CHARLES UNIVERSITY   (Czech Republic)

^d Vienna Institute for Nature Conservation and Analyses   (Austria)

^e UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

AFLPs; Alps; geographic diffusion models; phylogeography; plastid sequences; Pleistocene refugia; range dynamics; Senecio carniolicus

Indexed keywords

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARCTIC; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; EUROPE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; ICE COVER; PHYLOGEOGRAPHY; SENECIO;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ARCTIC REGIONS; BAYES THEOREM; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; EUROPE; GENETIC VARIATION; GEOGRAPHY; HAPLOTYPES; ICE COVER; PHYLOGEOGRAPHY; SENECIO; SEQUENCE ANALYSIS, DNA;

ASTERACEAE; SENECIO; SENECIO CARNIOLICUS;

EID: 84857637857     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05456.x     Document Type: Article

References (94)

1. Álvarez N, Thiel-Egenter C, Tribsch A, et al. (2009) History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants. Ecology Letters, 12, 632-640.
2. Bettin O, Cornejo C, Edwards PJ, Holderegger R, (2007) Phylogeography of the high alpine plant Senecio halleri (Asteraceae) in the European Alps: in situ glacial survival with postglacial stepwise dispersal into peripheral areas. Molecular Ecology, 16, 2517-2524. (Pubitemid 46897134)
3. Blöch C, Weiss-Schneeweiss H, Schneeweiss GM, et al. (2009) Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae). Molecular Phylogenetics and Evolution, 53, 220-233.
4. 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. (Pubitemid 39415663)
5. Borsch T, Quandt D, (2009) Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Systematics and Evolution, 282, 169-199.
6. Burnier J, Buerki S, Arrigo N, Küpfer P, Álvarez N, (2009) Genetic structure and evolution of Alpine polyploid complexes: Ranunculus kuepferi (Ranunculaceae) as a case study. Molecular Ecology, 18, 3730-3744.
7. Carstens BC, Richards CL, (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439-1454. (Pubitemid 46848830)
8. 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. (Pubitemid 39568278)
9. Chenevard P, (1906) Notes floristiques alpines. Bulletin de l'Herbier Boissier 2me série, 6, 365-370.
10. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
11. Corriveau J, Coleman A, (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany, 75, 1443-1458.
12. Currat M, Ruedi M, Petit RJ, Excoffier L, (2008) The hidden side of invasions: massive introgression by local genes. Evolution, 62, 1908-1920. (Pubitemid 352033252)
13. Després L, Gielly L, Redoutet B, Taberlet P, (2003) Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. Molecular Phylogenetics and Evolution, 27, 185-196. (Pubitemid 36521964)
14. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
15. Drummond A, Rambaut A, Shapiro B, Pybus O, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192. (Pubitemid 40577756)
16. Dyer RJ, Nason JD, (2004) Population graphs: the graph theoretic shape of genetic structure. Molecular Ecology, 13, 1713-1727. (Pubitemid 38847581)
17. Ehrich D, (2006) AFLPdat: a collection of R functions for convenient handling of AFLP data. Molecular Ecology Notes, 6, 603-604. (Pubitemid 44252552)
18. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.11: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
19. 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)
20. Felsenstein J, (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics, 5, 164-166.
21. Flatscher R, (2010) Morphological Differentiation of the Sympatric Di-, Tetra- and Hexaploid Cytotypes of Senecio carniolicus s.l. (syn. Jacobaea carniolica, Asteraceae). Diploma Thesis, University of Vienna, Vienna.
22. Gabrielsen TM, Bachmann K, Jakobsen KS, Brochmann C, (1997) Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia. Molecular Ecology, 6, 831-842. (Pubitemid 27378138)
23. Garrick R, Nason J, Meadows C, Dyer R, (2009) Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Molecular Ecology, 18, 1916-1931.
24. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
25. Hargreaves S, Maxted N, Hirano R, et al. (2010) Islands as refugia of Trifolium repens genetic diversity. Conservation Genetics, 11, 1317-1326.
26. Hess HE, Landolt E, Hirzel R, (1980) Flora der Schweiz und angrenzender Gebiete III. Birkhäuser, Basel.
27. Hewitt GM, (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87-112. (Pubitemid 29485515)
28. Hewitt G, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913. (Pubitemid 30435039)
29. Hewitt GM, (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society London B, 359, 183-195. (Pubitemid 38231471)
30. Holderegger R, Thiel-Egenter C, Parisod C, (2011) Marie Brockmann-Jerosch and her influence on Alpine phylogeography. Alpine Botany, 121, 5-10.
31. Hülber K, Sonnleitner M, Flatscher R, et al. (2009) Ecological segregation drives fine-scale cytotype distribution of Senecio carniolicus in the Eastern Alps. Preslia, 81, 309-319.
32. Ingvarsson PK, Ribstein S, Taylor DR, (2003) Molecular evolution of insertions and deletion in the chloroplast genome of Silene. Molecular Biology and Evolution, 20, 1737-1740. (Pubitemid 37420926)
33. Jakobsson M, Rosenberg NA, (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801-1806. (Pubitemid 47250313)
34. Knowles LL, (2009) Statistical phylogeography. Annual Review of Ecology, Evolution, and Systematics, 40, 593-612.
35. Knowles LL, Maddison WP, (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635. (Pubitemid 35436682)
36. Lemey P, Rambaut A, Drummond AJ, Suchard MA, (2009) Bayesian phylogeography finds its roots. PLoS Computational Biology, 5, e1000520.
37. Lemey P, Rambaut A, Welch JJ, Suchard MA, (2010) Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27, 1877-1885.
38. Lemmon AR, Lemmon EM, (2008) A likelihood framework for estimating phylogeographic history on a continuous landscape. Systematic Biology, 57, 544-561.
39. Lohse K, Nicholls JA, Stone GN, (2011) Inferring the colonization of a mountain range-refugia vs. nunatak survival in high alpine ground beetles. Molecular Ecology, 20, 394-408.
40. Maechler M, Rousseeuw P, Struyf A, Hubert M, (2005) Cluster analysis basics and extensions.
41. 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. (Pubitemid 351439329)
42. Merxmüller H, (1952) Untersuchungen zur Sippengliederung und Arealbildung in den Alpen. I. Jahrbuch des Vereins zum Schutze der Alpenpflanzen und -tiere, 17, 96-133.
43. Merxmüller H, (1953) Untersuchungen zur Sippengliederung und Arealbildung in den Alpen. II. Jahrbuch des Vereins zum Schutze der Alpenpflanzen und -tiere, 18, 138-158.
44. Merxmüller H, (1954) Untersuchungen zur Sippengliederung und Arealbildung in den Alpen. III. Jahrbuch des Vereins zum Schutze der Alpenpflanzen und -tiere, 19, 97-139.
45. Nei M, (1972) Genetic distance between populations. American Naturalist, 106, 283-292.
46. Nieto Feliner G, Rossellõ JA, (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution, 44, 911-919. (Pubitemid 47048931)
47. Nordborg M, Hu TT, Ishino Y, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology, 3, e196.
48. Parisod C, Besnard G, (2007) Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae). Molecular Ecology, 16, 2755-2767. (Pubitemid 47012146)
49. Paun O, Schönswetter P, Winkler M, Intrabiodiv Consortium, 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.
50. Pawłowski B, (1970) Remarques sur l'endémisme dans la flore des Alpes et des Carpates. Vegetatio, 21, 181-243.
51. Pelser P, Gravendeel B, van der Meijden R, (2003) Phylogeny reconstruction in the gap between too little and too much divergence: the closest relatives of Senecio jacobaea (Asteraceae) according to DNA sequences and AFLPs. Molecular Phylogenetics and Evolution, 29, 613-628. (Pubitemid 37491901)
52. Pelser PB, van den Hof K, Gravendeel B, van der Meijden R, (2004) The systematic value of morphological characters in Senecio sect. Jacobaea (Asteraceae) as compared to DNA sequences. Systematic Botany, 29, 790-805. (Pubitemid 39175561)
53. Pelser PB, Veldkamp JF, van der Meijden R, (2006) New combinations in Jacobaea Mill. (Asteraceae-Senecioneae). Compositae Newsletter, 44, 1-11.
54. Petit RJ, Duminil J, Fineschi S, et al. (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology, 14, 689-701. (Pubitemid 40346461)
55. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256. (Pubitemid 351882013)
56. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959. (Pubitemid 30397141)
57. Provan J, Bennett KD, (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology and Evolution, 23, 564-571.
58. Rebernig CA, Schneeweiss GM, Bardy KE, et al. (2010a) Multiple Pleistocene refugia and Holocene range expansion of an abundant southwestern American desert plant species (Melampodium leucanthum, Asteraceae). Molecular Ecology, 19, 3421-3443.
59. Rebernig CA, Weiss-Schneeweiss H, Schneeweiss GM, et al. (2010b) Quaternary range dynamics and polyploid evolution in an arid brushland plant species (Melampodium cinereum, Asteraceae). Molecular Phylogenetics and Evolution, 54, 594-606.
60. Reisigl H, Pitschmann H, (1958) Obere Grenzen von Flora und Vegetation in der Nivalstufe der zentralen Ötztaler Alpen (Tirol). Plant Ecology, 8, 93-129.
61. Rohlf FJ, (1997) NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.2. Applied Biostatistics, New York.
62. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. (Pubitemid 37038874)
63. Schneeweiss GM, Schönswetter P, (2010) The wide but disjunct range of the European mountain plant Androsace lactea L. (Primulaceae) reflects Late Pleistocene range fragmentation and post-glacial distributional stasis. Journal of Biogeography, 37, 2016-2025.
64. Schneeweiss GM, Schönswetter P, (2011) A re-appraisal of nunatak survival in arctic-alpine phylogeography. Molecular Ecology, 20, 190-192.
65. Schönswetter P, Tribsch A, (2005) Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon, 54, 725-732. (Pubitemid 41494607)
66. Schönswetter P, Tribsch A, Barfuss M, Niklfeld H, (2002) Several Pleistocene refugia detected in the high alpine plant Phyteuma globulariifolium Sternb. & Hoppe (Campanulaceae) in the European Alps. Molecular Ecology, 11, 2637-2647. (Pubitemid 35436683)
67. Schönswetter P, Tribsch A, Schneeweiss GM, Niklfeld H, (2003) Disjunctions in relict alpine plants: phylogeography of Androsace brevis and A. wulfeniana (Primulaceae). Botanical Journal of the Linnean Society, 141, 437-446. (Pubitemid 36463425)
68. Schönswetter P, Tribsch A, Stehlik I, Niklfeld H, (2004) Glacial history of high alpine Ranunculus glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context. Biological Journal of the Linnean Society, 81, 183-195. (Pubitemid 38231151)
69. Schönswetter P, Stehlik I, Holderegger R, Tribsch A, (2005) Molecular evidence for glacial refugia of mountain plants in the European Alps. Molecular Ecology, 14, 3547-3555.
70. Schönswetter P, Lachmayer M, Lettner C, et al. (2007) Sympatric diploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps are separated along an altitudinal gradient. Journal of Plant Research, 120, 721-725. (Pubitemid 350172329)
71. Schönswetter P, Solstad H, Escobar García P, Elven R, (2009) A combined molecular and morphological approach to the taxonomically intricate European mountain plant Papaver alpinum s.l. (Papaveraceae). Taxa or informal phylogeographical groups? Taxon, 17, 1326-1343.
72. 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)
73. Shaw J, Lickey EB, Schilling 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)
74. Smith CI, Pellmyr O, Althoff DM, et al. (2008) Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification. Proceedings of the Royal Society B: Biological Sciences, 275, 249-258. (Pubitemid 350295704)
75. Sonnleitner M, Flatscher R, Escobar García P, et al. (2010) Distribution and habitat segregation on different spatial scales among diploid, tetraploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps. Annals of Botany, 106, 967-978.
76. Spellman GM, Klicka J, (2006) Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea). Proceedings of the Royal Society B: Biological Sciences, 273, 3057-3063. (Pubitemid 46622446)
77. Stehlik I, (2000) Nunataks and peripheral refugia for alpine plants during Quaternary glaciation in the middle part of the Alps. Botanica Helvetica, 110, 25-30. (Pubitemid 30448412)
78. Stehlik I, Schneller JJ, Bachmann K, (2001) Resistance or emigration: response of the high-alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps. Molecular Ecology, 10, 357-370. (Pubitemid 32232343)
79. Stehlik I, Blattner F, Holderegger R, Bachmann K, (2002) Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages. Molecular Ecology, 11, 2027-2036.
80. Stewart JR, Lister AM, Barnes I, Dalén L, (2010) Refugia revisited: individualistic responses of species in space and time. Proceedings of the Royal Society B: Biological Sciences, 277, 661-671.
81. Suda J, Weiss-Schneeweiss H, Tribsch A, et al. (2007) Complex distribution patterns of di-, tetra-, and hexaploid cytotypes in the European high mountain plant Senecio carniolicus (Asteraceae). American Journal of Botany, 94, 1391-1401. (Pubitemid 47282128)
82. Svenning JC, Normand S, Skov F, (2008) Postglacial dispersal limitation of widespread forest plant species in nemoral Europe. Ecography, 31, 316-326. (Pubitemid 351799692)
83. Swofford DL, (2003) PAUP*: Phylogenetic Analysis Using Parsimony, Version 4.0 b10. Sinauer, Sunderland, Massachusetts.
84. Taberlet P, (1998) Biodiversity at the intraspecific level: the comparative phylogeographic approach. Journal of Biotechnology, 64, 91-100. (Pubitemid 29027787)
85. Tackenberg O, Stöcklin J, (2008) Wind dispersal of alpine plant species: a comparison with lowland species. Journal of Vegetation Science, 19, 109-118. (Pubitemid 351448467)
86. Tajima F, (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460. (Pubitemid 14247444)
87. Thiel-Egenter C, Holderegger R, Brodbeck S, Gugerli F, (2009) Concordant genetic breaks, identified by combining clustering and tessellation methods, in two co-distributed alpine plant species. Molecular Ecology, 18, 4495-4507.
88. Tribsch A, Schönswetter P, Stuessy TF, (2002) Saponaria pumila (Caryophyllaceae) and the ice age in the European Alps. American Journal of Botany, 89, 2024-2033. (Pubitemid 36080474)
89. Vachon N, Freeland JR, (2011) Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences. Molecular Ecology Resources, 11, 279-285.
90. Victoriano PF, Ortiz JC, Benavides E, Adams BJ, Sites Jr JW, (2008) Comparative phylogeography of codistributed species of Chilean Liolaemus (Squamata: Tropiduridae) from the central-southern Andean range. Molecular Ecology, 17, 2397-2416. (Pubitemid 351623773)
91. Vos P, Hogers R, Bleeker M, et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.
92. Westergaard KB, Alsos IG, Popp M, et al. (2011) Glacial survival may matter after all: nunatak signatures in the rare European populations of two west-arctic species. Molecular Ecology, 20, 376-393.
93. Yamane K, Yasui Y, Ohnishi O, (2003) Intraspecific cpDNA variations of diploid and tetraploid perennial buckwheat, Fagopyrum cymosum (Polygonaceae). American Journal of Botany, 90, 339-346. (Pubitemid 38170887)
94. Zhou R, Shi S, Wu CI, (2005) Molecular criteria for determining new hybrid species-an application to the Sonneratia hybrids. Molecular Phylogenetics and Evolution, 35, 595-601. (Pubitemid 40607952)