Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Molecular Ecology

Volumn 22, Issue 13, 2013, Pages 3598-3612

  Gugger, Paul F ^a   Ikegami, Makihiko ^b,c   Sork, Victoria L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LINCOLN UNIVERSITY   (New Zealand)

Author keywords

ecological niche modelling; genetic diversity; phylogeography; Pleistocene; Quercus; redundancy analysis

Indexed keywords

MICROSATELLITE DNA; PLANT DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLIMATE; CLIMATE CHANGE; DNA SEQUENCE; ECOSYSTEM; GENE FLOW; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OAK; PHYLOGEOGRAPHY; POPULATION DYNAMICS; UNITED STATES;

BAYES THEOREM; CALIFORNIA; CLIMATE; CLIMATE CHANGE; DNA, PLANT; ECOSYSTEM; GENE FLOW; GENETIC VARIATION; HAPLOTYPES; MICROSATELLITE REPEATS; MODELS, BIOLOGICAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; POPULATION DYNAMICS; QUERCUS; SEQUENCE ANALYSIS, DNA;

QUERCUS; QUERCUS ALBA; QUERCUS LOBATA;

EID: 84876783965     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12317     Document Type: Article

References (104)

1. Adam DP, Sims JD, Throckmorton CK, (1981) 130,000-yr continuous pollen record from Clear Lake, Lake County, California. Geology, 9, 373-377.
2. Andrew RL, Ostevik KL, Ebert DP, Rieseberg LH, (2012) Adaptation with gene flow across the landscape in a dune sunflower. Molecular Ecology, 21, 2078-2091.
3. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
4. Azaiez A, Bouchard EF, Jean M, Belzile FJ, (2006) Length, orientation, and plant host influence the mutation frequency in microsatellites. Genome, 49, 1366-1373.
5. Baldwin BG, Kalisz S, Armbruster WS, (2011) Phylogenetic perspectives on diversification, biogeography, and floral evolution of Collinsia and Tonella (Plantaginaceae). American Journal of Botany, 98, 731-753.
6. Bandelt HJ, Forster P, Röhl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
7. Barry RG, (1983) Late-Pleistocene climatology. In: Late-Quaternary Environments of the United States: The Late Pleistocene (eds, Wright HE, Porter SC,), pp. 390-407. University of Minnesota Press, Minneapolis, Minnesota.
8. Bartlein PJ, Anderson KH, Anderson PM, et al,. (1998) Paleoclimate simulations for North America over the past 21,000 years: features of the simulated climate and comparisons with paleoenvironmental data. Quaternary Science Reviews, 17, 549-585.
9. Borcard D, Legendre P, Drapeau P, (1992) Partialling out the spatial component of ecological variation. Ecology, 73, 1045-1055.
10. ter Braak CJF, (1986) Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology, 67, 1167-1179.
11. Braconnot P, Otto-Bliesner B, Harrison S, et al,. (2007) Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum-Part 1: experiments and large-scale features. Climate of the Past, 3, 261-277.
12. Bürger R, Lynch M, (1995) Evolution and extinction in a changing environment: a quantitative genetic analysis. Evolution, 49, 151-163.
13. Byrne R, Edlund E, Mensing S, (1991) Holocene changes in the distribution and abundance of oaks in California. USDA Forest Service Pacific Southwest Research Station. General Technical Report, 126, 182-191.
14. Calsbeek R, Thompson JN, Richardson JE, (2003) Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Molecular Ecology, 12, 1021-1029.
15. Carnaval AC, Hickerson MJ, Haddad CFB, Rodrigues MT, Moritz C, (2009) Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science, 323, 785-789.
16. Carstens BC, Richards CL, (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439-1454.
17. Cavender-Bares J, González-Rodríguez A, Pahlich A, Koehler K, Deacon N, (2011) Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone. Journal of Biogeography, 38, 962-981.
18. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
19. Collins WD, Bitz CM, Blackmon ML, et al,. (2006) The community climate system model version 3 (CCSM3). Journal of Climate, 19, 2122-2143.
20. Corander J, Marttinen P, Siren J, Tang J, (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics, 9, 539.
21. Davis MB, (1981) Quaternary history and the stability of forest communities. In: Forest Succession: Concepts and Application (eds, West DC, Shugart HH, Botkin DB,), pp. 132-153. Springer-Verlag, New York, New York.
22. Davis OK, (1999) Pollen analysis of Tulare Lake, California: Great Basin-like vegetation in Central California during the full-glacial and early Holocene. Review of Palaeobotany and Palynology, 107, 249-257.
23. Davis MB, Shaw RG, (2001) Range shifts and adaptive responses to Quaternary climate change. Science, 292, 673-679.
24. Davis FW, Stoms DM, Hollander AD, et al,. (1998) The California Gap Analysis Project-Final Report. University of California, Santa Barbara, California.
25. Davis MB, Shaw RG, Etterson JR, (2005) Evolutionary responses to changing climate. Ecology, 86, 1704-1714.
26. Derory J, Scotti-Saintagne C, Bertocchi E, et al,. (2010) Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks. Heredity, 104, 438-448.
27. Dobrowski SZ, (2011) A climatic basis for microrefugia: the influence of terrain on climate. Global Change Biology, 17, 1022-1035.
28. Earl DA, vonHoldt BM, (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361.
29. Elith J, Graham CH, Anderson RP, et al,. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography, 29, 129-151.
30. Endler JA, (1986) Natural Selection in the Wild. Princeton University Press, Princeton, New Jersey.
31. 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.
32. Excoffier L, Smouse P, Quattro J, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
33. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
34. Franklin J, Wejnert KE, Hathaway SA, Rochester CJ, Fisher RN, (2009) Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California. Diversity and Distributions, 15, 167-177.
35. Geffen ELI, Anderson MJ, Wayne RK, (2004) Climate and habitat barriers to dispersal in the highly mobile grey wolf. Molecular Ecology, 13, 2481-2490.
36. Griffin JR, Critchfield WB, (1972) The Distribution of the Forest Trees in California. Pacific Southwest Forest and Range Experiment Station, U.S. Department of Agriculture Forest Service, Berkeley, California.
37. Grivet D, Deguilloux M-F, Petit RJ, Sork VL, (2006) Contrasting patterns of historical colonization in white oaks (Quercus spp.) in California and Europe. Molecular Ecology, 15, 4085-4093.
38. Grivet D, Sork VL, Westfall RD, Davis FW, (2008) Conserving the evolutionary potential of California valley oak (Quercus lobata Nee): a multivariate genetic approach to conservation planning. Molecular Ecology, 17, 139-156.
39. Gugger PF, Cavender-Bares J, (2013) Molecular and morphological support for a Florida origin of the Cuban oak. Journal of Biogeography, 40, 632-645.
40. Gugger PF, Sugita S, (2010) Glacial populations and postglacial migration of Douglas-fir based on fossil pollen and macrofossil evidence. Quaternary Science Reviews, 29, 2052-2070.
41. Gugger PF, Sugita S, Cavender-Bares J, (2010) Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record. Molecular Ecology, 19, 1877-1897.
42. Gugger PF, González-Rodríguez A, Rodríguez-Correa H, Sugita S, Cavender-Bares J, (2011) Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of 'rear edge' populations. New Phytologist, 189, 1185-1199.
43. Hampe A, Petit RJ, (2005) Conserving biodiversity under climate change: the rear edge matters. Ecology Letters, 8, 461-467.
44. Hasumi H, Emori S, (2004) K-1 coupled GCM (MIROC) Description. Center for Climate System Research, University of Tokyo, Tokyo.
45. Heusser LE, (1995) Pollen stratigraphy and paleoecologic interpretation of the 160-k.y. record from Santa Barbara Basin, Hole 893A. In: Proceedings of the Ocean Drilling Program, Scientific Results (eds, Kennet JP, Baldauf JG, &, Lyle M,), pp. 265-279. Texas A&M University, College Station, Texas.
46. 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.
47. Hewitt G, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
48. Hey J, (2010) Isolation with migration models for more than two populations. Molecular Biology and Evolution, 27, 905-920.
49. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
50. Hudson RR, Kaplan NL, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
51. James PMA, Coltman DW, Murray BW, Hamelin RC, Sperling FAH, (2011) Spatial genetic structure of a symbiotic beetle-fungal system: toward multi-taxa integrated landscape genetics. PLoS ONE, 6, e25359.
52. Jiménez-Valverde A, Lobo JM, (2007) Threshold criteria for conversion of probability of species presence to either-or presence-absence. Acta Oecologica, 31, 361-369.
53. Kalinowski ST, (2005) HP-Rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes, 5, 187-189.
54. Kimura M, (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61, 893-903.
55. Knight TM, Steets JA, Vamosi JC, et al,. (2005) Pollen limitation of plant reproduction: pattern and process. Annual Review of Ecology Evolution and Systematics, 36, 467-497.
56. Knowles LL, Alvarado-Serrano DF, (2010) Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Molecular Ecology, 19, 3727-3745.
57. Kuchta SR, Parks DS, Mueller RL, Wake DB, (2009) Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii. Journal of Biogeography, 36, 982-995.
58. Lapointe F-J, Rissler LJ, (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. The American Naturalist, 166, 290-299.
59. Legendre P, Legendre L, (1998) Numerical Ecology, 2nd English edn. Elsevier, Amsterdam.
60. Li N, Stephens M, (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics, 165, 2213-2233.
61. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
62. Little EL Jr, (1971) Atlas of United States Trees, Volume 1: Conifers and Important Hardwoods. U.S. Department of Agriculture, Washington, District of Columbia.
63. Liu Q, (1997) Variation partitioning by partial redundancy analysis (RDA). Environmetrics, 8, 75-85.
64. Macey JR, Strasburg JL, Brisson JA, Vrendenburg VT, Jennings M, Larson A, (2001) Molecular phylogenetics of western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution, 19, 131-143.
65. 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. Molecular Ecology, 14, 513-524.
66. Marriage TN, Hudman S, Mort ME, Orive ME, Shaw RG, Kelly JK, (2009) Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae). Heredity, 103, 310-317.
67. Martínez-Solano I, Jockusch EL, Wake DB, (2007) Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America. Molecular Ecology, 16, 4335-4355.
68. McLachlan JS, Clark JS, Manos PS, (2005) Molecular indicators of tree migration capacity under rapid climate change. Ecology, 86, 2088-2098.
69. McLaughlin BC, Zavaleta ES, (2012) Predicting species responses to climate change: demography and climate microrefugia in California valley oak (Quercus lobata). Global Change Biology, 18, 2301-2312.
70. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
71. Nosil P, Egan SP, Funk DJ, (2008) Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selection. Evolution, 62, 316-336.
72. Ohta T, Kimura M, (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research, 22, 201-204.
73. Økland RH, (1999) On the variation explained by ordination and constrained ordination axes. Journal of Vegetation Science, 10, 131-136.
74. Oksanen J, Kindt R, Legendre P, et al,. (2009) vegan: Community Ecology Package. Available from http://cran.r-project.org/web/packages/vegan/index.html
75. Ortego J, Riordan EC, Gugger PF, Sork VL, (2012) Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak. Molecular Ecology, 21, 3210-3223.
76. Otto-Bliesner BL, Marshall SJ, Overpeck JT, et al,. (2006) Simulating Arctic climate warmth and icefield retreat in the last interglaciation. Science, 311, 1751-1753.
77. Peabody FE, Savage JM, (1958) Evolution of the coast range corridor in California and its effect on the origin and dispersal of living amphibians and reptiles. In: Zoogeography (ed., Hubbs CL,), pp. 159-186. American Association for the Advancement of Science, Washington, District of Columbia.
78. Peakall R, Smouse PE, (2006) GENALEX 6: genetic analysis in Excel: population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
79. Pease CM, Lande R, Bull JJ, (1989) A model of population growth, dispersal and evolution in a changing environment. Ecology, 70, 1657-1664.
80. Pease KM, Freedman AH, Pollinger JP, et al,. (2009) Landscape genetics of California mule deer (Odocoileus hemionus): the roles of ecological and historical factors in generating differentiation. Molecular Ecology, 18, 1848-1862.
81. Petit RJ, Pineau E, Demesure B, Bacilieri R, Ducousso A, Kremer A, (1997) Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences, 94, 9996-10001.
82. Petit RJ, Brewer S, Bordács S, et al,. (2002a) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Forest Ecology and Management, 156, 49-74.
83. Petit RJ, Csaikl UM, Bordács S, et al,. (2002b) Chloroplast DNA variation in European white oaks: phylogeography and patterns of diversity based on data from over 2600 populations. Forest Ecology and Management, 156, 5-26.
84. Phillips SJ, Dudik M, Schapire RE, (2004) A maximum entropy approach to species distribution modeling. ACM International Proceedings Series, 69, 655.
85. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
86. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
87. Sage R, Koenig W, McLaughlin B, (2011) Fitness consequences of seed size in the valley oak Quercus lobata Née (Fagaceae). Annals of Forest Science, 68, 477-484.
88. Satler JD, Starrett J, Hayashi CY, Hedin M, (2011) Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS ONE, 6, e25355.
89. Smouse PE, Williams RC, (1982) Multivariate analysis of HLA-disease associations. Biometrics, 38, 757-768.
90. Sork VL, Davis FW, Westfall R, et al,. (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Nee) in the face of climate change. Molecular Ecology, 19, 3806-3823.
91. Stebbins RC, (1949) Speciation in salamanders of the plethodontid genus Ensatina. In: University of California Publications in Zoölogy (eds, Daniel JF, Eakin RM, Hall ER, Kirby H, Light SF, Miller AH,), pp. 377-532. University of California, Berkeley, California.
92. Stebbins GL, Major J, (1965) Endemism and speciation in the California flora. Ecological Monographs, 35, 2-35.
93. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
94. Svenning J-C, Normand S, Kageyama M, (2008) Glacial refugia of temperate trees in Europe: insights from species distribution modelling. Journal of Ecology, 96, 1117-1127.
95. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
96. Thornthwaite C, (1953) A charter for climatology. World Meteorological Organization Bulletin, 2, 40-46.
97. Tzedakis PC, Lawson IT, Frogley MR, Hewitt GM, Preece RC, (2002) Buffered tree population changes in a Quaternary refugium: evolutionary implications. Science, 297, 2044-2047.
98. Via S, Bouck AC, Skillman S, (2000) Reproductive isolation between divergent races of pea aphids on two hosts. II. Selection against migrants and hybrids in the parental environments. Evolution, 54, 1626-1637.
99. Waltari E, Hijmans RJ, Peterson AT, Nyári ÁS, Perkins SL, Guralnick RP, (2007) Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE, 2, e563.
100. Wang IJ, Summers K, (2010) Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Molecular Ecology, 19, 447-458.
101. Werth S, Sork VL, (2008) Local genetic structure in a North American epiphytic lichen, Ramalina menziesii (Ramalinaceae). American Journal of Botany, 95, 568-576.
102. Westfall RD, Conkle MT, (1992) Allozyme markers in breeding zone designation. Population Genetics of Forest Trees, 42, 279-309.
103. Whipple AA, Grossinger RM, Davis FW, (2011) Shifting baselines in a California oak savanna: nineteenth Century data to inform restoration scenarios. Restoration Ecology, 19, 88-101.
104. Won YJ, Hey J, (2005) Divergence population genetics of chimpanzees. Molecular Biology and Evolution, 22, 297-307.