Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Molecular Ecology

Volumn 21, Issue 13, 2012, Pages 3210-3223

  Ortego, Joaquín ^a,b,c   Riordan, Erin C ^a   Gugger, Paul F ^a   Sork, Victoria L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INSTITUTO DE INVESTIGACIÓN EN RECURSOS CINEGÉTICOS IREC CSIC UCLM JCCM   (Spain)

^c MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

Author keywords

causal modelling; ecological niche modelling; genetic diversity; genetic structure; landscape genetics; species distribution models

Indexed keywords

MICROSATELLITE DNA; PLANT DNA;

ARTICLE; BIOLOGICAL MODEL; CELL NUCLEUS; CLIMATE; DNA SEQUENCE; ECOSYSTEM; GENE FLOW; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; OAK; POPULATION GENETICS; UNITED STATES;

CALIFORNIA; CELL NUCLEUS; CLIMATE; DNA, PLANT; ECOSYSTEM; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; MICROSATELLITE REPEATS; MODELS, GENETIC; QUERCUS; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

QUERCUS ENGELMANNII;

EID: 84862759230     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05591.x     Document Type: Article

References (116)

1. Aitken SN, Yeaman S, Holliday JA, Wang TL, Curtis-McLane S, (2008) Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications, 1, 95-111.
2. Alleaume-Benharira M, Pen IR, Ronce O, (2006) Geographical patterns of adaptation within a species' range: interactions between drift and gene flow. Journal of Evolutionary Biology, 19, 203-215.
3. Anderson CD, Epperson BK, Fortin MJ, et al. (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology, 19, 3565-3575.
4. Avise JC, (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
5. Beier P, Majka DR, Spencer WD, (2008) Forks in the road: choices in procedures for designing wildland linkages. Conservation Biology, 22, 836-851.
6. Bonnet E, Van de Peer Y, (2002) ZT: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 10, 1-12.
7. Borash DJ, Gibbs AG, Joshi A, Mueller LD, (1998) A genetic polymorphism maintained by natural selection in a temporally varying environment. American Naturalist, 151, 148-156.
8. Bull RAS, Cushman SA, Mace R, et al. (2011) Why replication is important in landscape genetics: American black bear in the Rocky Mountains. Molecular Ecology, 20, 1092-1107.
9. Burczyk JL, Prat D, (1997) Male reproductive success in Pseudotsuga menziesii (Mirb.) France: the effects of spatial structure and flowering characteristics. Heredity, 79, 638-647.
10. 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.
11. 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.
12. Collins WD, Bitz CM, Blackmon ML, et al. (2006) The community climate system model version 3 (CCSM3). Journal of Climate, 19, 2122-2143.
13. Coulon A, Fitzpatrick JW, Bowman R, Lovette IJ, (2010) Effects of habitat fragmentation on effective dispersal of Florida scrub-jays. Conservation Biology, 24, 1080-1088.
14. Cushman SA, Landguth EL, (2010) Spurious correlations and inference in landscape genetics. Molecular Ecology, 19, 3592-3602.
15. Cushman SA, McKelvey KS, Hayden J, Schwartz MK, (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. American Naturalist, 168, 486-499.
16. Davis EB, Koo MS, Conroy C, Patton JL, Moritz C, (2008) The California Hotspots Project: identifying regions of rapid diversification of mammals. Molecular Ecology, 17, 120-138.
17. Dow BD, Ashley MV, Howe HF, (1995) Characterization of highly variable (Ga/Ct)(N) microsatellites in the bur oak, Quercus macrocarpa. Theoretical and Applied Genetics, 91, 137-141.
18. Dyer RJ, Nason JD, Garrick RC, (2010) Landscape modeling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology, 19, 3746-3759.
19. Eckert AJ, van Heerwaarden J, Wegrzyn JL, et al. (2010) Patterns of population structure and environmental associations to aridity across the range of Loblolly pine (Pinus taeda L., Pinaceae). Genetics, 185, 969-982.
20. Elith J, Graham CH, Anderson RP, et al. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography, 29, 129-151.
21. Endler JA, (1986) Natural Selection in the Wild. Princeton University Press, Princeton, New Jersey.
22. Ersts PJ, 2011 [Internet] Geographic Distance Matrix Generator (version 1.2.3). American Museum of Natural History, Center forBiodiversity and Conservation. Downloaded on 18 March 2011.
23. 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.
24. 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.
25. 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.
26. Fielding AH, Bell JF, (1997) A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation, 24, 38-49.
27. eFloras. (2011) Flora of North America. Missouri Botanical Garden, St. Louis, Missouri, USA, and Harvard University Herbaria, Cambridge, Massachusetts, USA.
28. Frankham R, (1996) Relationship of genetic variation to population size in wildlife. Conservation Biology, 10, 1500-1508.
29. Frankham R, (2005) Genetics and extinction. Biological Conservation, 126, 131-140.
30. Freedman AH, Thomassen HA, Buermann W, Smith TB, (2010) Genomic signals of diversification along ecological gradients in a tropical lizard. Molecular Ecology, 19, 3773-3788.
31. Freeland JR, Biss P, Conrad KF, Silvertown J, (2010) Selection pressures have caused genome-wide population differentiation of Anthoxanthum odoratum despite the potential for high gene flow. Journal of Evolutionary Biology, 23, 776-782.
32. Funk WC, Cannatella DC, Ryan MJ, (2009) Genetic divergence is more tightly related to call variation than landscape features in the Amazonian frogs Physalaemus petersi and P. freibergi. Journal of Evolutionary Biology, 22, 1839-1853.
33. Garant D, Kruuk LEB, Wilkin TA, McCleery RH, Sheldon BC, (2005) Evolution driven by differential dispersal within a wild bird population. Nature, 433, 60-65.
34. García-Ramos G, Kirkpatrick M, (1997) Genetic models of adaptation and gene flow in peripheral populations. Evolution, 51, 21-28.
35. Goudet J, (1995) Fstat (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
36. Goudet J, (2001) Fstat, a Program to Estimate and Test Gene Diversities and Fixation Indices (Version 2.9.3). Institut d'Ecologie, Universite' de Lausanne, Dorigny, Switzerland.
37. Grivet D, Smouse PE, Sork VL, (2005) A novel approach to an old problem: tracking dispersed seeds. Molecular Ecology, 14, 3585-3595.
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. Grivet D, Robledo-Arnuncio JJ, Smouse PE, Sork VL, (2009) Relative contribution of contemporary pollen and seed dispersal to the effective parental size of seedling population of California valley oak (Quercus lobata Née). Molecular Ecology, 18, 3967-3979.
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, 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.
42. Guo SW, Thompson EA, (1992) A Monte-Carlo method for combined segregation and linkage analysis. American Journal of Human Genetics, 51, 1111-1126.
43. Hampe A, Petit RJ, (2005) Conserving biodiversity under climate change: the rear edge matters. Ecology Letters, 8, 461-467.
44. Hedrick PW, (2001) Conservation genetics: where are we now? Trends in Ecology & Evolution, 16, 629-636.
45. Hendry AP, Day T, (2005) Population structure attributable to reproductive time: isolation by time and adaptation by time. Molecular Ecology, 14, 901-916.
46. Hewitt G, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
47. 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.
48. Hirao AS, Kudo G, (2008) The effect of segregation of flowering time on fine-scale spatial genetic structure in an alpine-snowbed herb Primula cuneifolia. Heredity, 100, 424-430.
49. Holderegger R, Wagner HH, (2008) Landscape genetics. BioScience, 58, 199-207.
50. Holzhauer SIJ, Wolff K, Wolters V, (2009) Changes in land use and habitat availability affect the population genetic structure of Metrioptera roeselii (Orthoptera: Tettigoniidae). Journal of Insect Conservation, 13, 543-552.
51. Hubisz MJ, Falush D, Stephens M, Pritchard JK, (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322-1332.
52. 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.
53. Isagi Y, Suhandono S, (1997) PCR primers amplifying microsatellite loci of Quercus myrsinifolia Blume and their conservation between oak species. Molecular Ecology, 6, 897-899.
54. IUCN. (2010) IUCN Red List of Threatened Species. Version 2010.4. Downloaded on 17 April 2011.
55. Jenkins DG, Carey M, Czerniewska J, et al. (2010) A meta-analysis of isolation by distance: relic or reference standard for landscape genetics? Ecography, 33, 315-320.
56. Kalinowski ST, (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes, 5, 187-189.
57. Kampfer S, Lexer C, Glossl J, Steinkellner H, (1998) Characterization of (GA)(n) microsatellite loci from Quercus robur. Hereditas, 129, 183-186.
58. Kiehl JT, Gent PR, (2004) The community climate system model, version 2. Journal of Climate, 17, 3666-3682.
59. 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.
60. Lammi A, Siikamaki P, Mustajarvi K, (1999) Genetic diversity, population size, and fitness in central and peripheral populations of a rare plant Lychnis viscaria. Conservation Biology, 13, 1069-1078.
61. Legendre P, (1993) Spatial autocorrelation-trouble or new paradigm. Ecology, 74, 1659-1673.
62. Legendre P, Troussellier M, (1988) Aquatic heterotrophic bacteria-modelling in the presence of spatial auto-correlation. Limnology and Oceanography, 33, 1055-1067.
63. Leppig G, White JW, (2006) Conservation of peripheral plant populations in California. Madroño, 53, 264-274.
64. Lynch M, Ritland K, (1999) Estimation of pairwise relatedness with molecular markers. Genetics, 152, 1753-1766.
65. Manel S, Schwartz MK, Luikart G, Taberlet P, (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189-197.
66. Manel S, Poncet BN, Legendre P, Gugerli F, Holderegger R, (2010) Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Molecular Ecology, 19, 3824-3835.
67. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
68. Nei M, Chakravarti A, (1977) Drift variances of Fst and Gst statistics obtained from a finite number of isolated populations. Theoretical Population Biology, 11, 307-325.
69. Ortego J, Bonal R, (2010) Natural hybridisation between kermes (Quercus coccifera L.) and holm oaks (Q. ilex L.) revealed by microsatellite markers. Plant Biology, 12, 234-238.
70. Ortego J, Bonal R, Muñoz A, (2010a) Genetic consequences of habitat fragmentation in long-lived tree species: the case of the Mediterranean holm oak (Quercus ilex, L.). Journal of Heredity, 101, 717-726.
71. Ortego J, Aguirre MP, Cordero PJ, (2010b) Population genetics of Mioscirtus wagneri, a grasshopper showing a highly fragmented distribution. Molecular Ecology, 19, 472-483.
72. Ortego J, Yannic G, Shafer ABA, et al. (2011) Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Molecular Ecology, 20, 1601-1611.
73. Otto-Bliesner BL, Marsha SJ, Overpeck JT, et al. (2006) Simulating arctic climate warmth and icefield retreat in the last interglaciation. Science, 311, 1751-1753.
74. Pastorini J, Thalmann U, Martin RD, (2003) A molecular approach to comparative phylogeography of extant Malagasy lemurs. Proceedings of the National Academy of Sciences of the United States of America, 100, 5879-5884.
75. Pearse IS, Hipp AL, (2009) Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks. Proceedings of the National Academy of Sciences of the United States of America, 106, 18097-18102.
76. 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.
77. Pérez-Espona S, Pérez-Barbería FJ, McLeod JE, et al. (2008) Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus). Molecular Ecology, 17, 981-996.
78. Pérez-Tris J, Carbonell R, Telleria JL, (2000) Abundance distribution, morphological variation and juvenile condition of robins, Erithacus rubecula (L.), in their Mediterranean range boundary. Journal of Biogeography, 27, 879-888.
79. Petit RJ, Aguinagalde I, de Beaulieu JL, et al. (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563-1565.
80. Phillips SJ, Dudik M, (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175.
81. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
82. Pluess AR, Sork VL, Dolan B, et al. (2009) Short distance pollen movement in a wind-pollinated tree, Quercus lobata (Fagaceae). Forest Ecology and Management, 258, 735-744.
83. Postma E, Van Noordwijk AJ, (2005) Gene flow maintains a large genetic difference in clutch size at a small spatial scale. Nature, 433, 65-68.
84. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
85. Pyron RA, Burbrink FT, (2009) Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula. Molecular Ecology, 18, 3443-3457.
86. Ramírez-Valiente JA, Lorenzo Z, Soto A, et al. (2009) Elucidating the role of genetic drift and natural selection in cork oak differentiation regarding drought tolerance. Molecular Ecology, 18, 3803-3815.
87. Ramírez-Valiente JA, Lorenzo Z, Soto A, et al. (2010) Natural selection on cork oak: allele frequency reveals divergent selection in cork oak populations along a temperature cline. Evolutionary Ecology, 24, 1031-1044.
88. Raven PH, Axelrod DI, (1978) Origin and relationships of the California flora. University of California Publications in Botany, 72, 1-134.
89. Rice WR, (1989) Analyzing tables of statistical tests. Evolution, 43, 223-225.
90. Richards-Zawacki CL, (2009) Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius. Diversity and Distributions, 15, 796-806.
91. Roberts FM, (1995) The Oaks of the Southern California Floristic Province. F. M. Roberts Publications, Encinitas, California.
92. Rodríguez-Robles JA, Jezkova T, Leal M, (2010) Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican 'Lagartijo Jardinero de la Montana'. Molecular Ecology, 19, 1860-1876.
93. Sacks BN, Brown SK, Ernest HB, (2004) Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history. Molecular Ecology, 13, 1265-1275.
94. Schneider CJ, Cunningham M, Moritz C, (1998) Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Molecular Ecology, 7, 487-498.
95. Schuster WS, Alles DL, Mitton JB, (1989) Gene flow in limber pine-evidence from pollination phenology and genetic differentiation along an elevational transect. American Journal of Botany, 76, 1395-1403.
96. Scott TA, (1991) The distribution of Engelmann oak (Quercus engelmannii) in California. In: Proceedings of the Symposium on Oak Woodlands and Hardwood Rangeland Management (ed., Standiford RB,), pp. 351-359. US Deptartment of Agriculture, Forest Service Pacific Southwest Forest & Range Experimental Station, Berkeley.
97. Shafer ABA, Côté SD, Coltman DW, (2011) Hot spots of genetic diversity descended from multiple Pleistocene refugia in an Alpine ungulate. Evolution, 65, 125-138.
98. Slatkin M, (1993) Isolation by distance in equilibrium and nonequilibrium populations. Evolution, 47, 264-279.
99. Smith TB, Wayne RK, Girman DJ, Bruford MW, (1997) A role for ecotones in generating rainforest biodiversity. Science, 276, 1855-1857.
100. Sork VL, Waits L, (2010) Contributions of landscape genetics-approaches, insights, and future potential. Molecular Ecology, 19, 3489-3495.
101. Sork VL, Davis FW, Smouse PE, et al. (2002) Pollen movement in declining populations of California Valley oak, Quercus lobata: where have all the fathers gone? Molecular Ecology, 11, 1657-1668.
102. Sork VL, Davis FW, Grivet D, (2009) Incorporating genetic information into conservation planning for California valley oak. Gen. Tech. Rep. PSW-GTR-217 497-509.
103. Sork VL, Davis FW, Westfall R, et al. (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change. Molecular Ecology, 19, 3806-3823.
104. Spielman D, Brook BW, Frankham R, (2004) Most species are not driven to extinction before genetic factors impact them. Proceedings of the National Academy of Sciences of the United States of America, 101, 15261-15264.
105. Steinkellner H, Fluch S, Turetschek E, et al. (1997) Identification and characterization of (GA/CT)(n)-microsatellite loci from Quercus petraea. Plant Molecular Biology, 33, 1093-1096.
106. Storfer A, Murphy MA, Evans JS, et al. (2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128-142.
107. Swenson NG, Howard DJ, (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist, 166, 581-591.
108. Thomassen HA, Cheviron ZA, Freedman AH, Harrigan RJ, Wayne RK, Smith TB, (2010) Spatial modeling and landscape-level approaches for visualizing intra-specific variation. Molecular Ecology, 19, 3532-3548.
109. Vähä JP, Primmer CR, (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Molecular Ecology, 15, 63-72.
110. Walker D, Avise JC, (1998) Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States. Annual Review of Ecology and Systematics, 29, 23-58.
111. 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.
112. Wang IJ, Johnson JR, Johnson BB, Shaffer HB, (2011) Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense. Conservation Genetics, 12, 911-920.
113. Waples RS, (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity, 89, 438-450.
114. Willi Y, Van Buskirk J, Hoffmann AA, (2006) Limits to the adaptive potential of small populations. Annual Review of Ecology Evolution and Systematics, 37, 433-458.
115. Winkler KA, Pamminger-Lahnsteiner B, Wanzenbock J, Weiss S, (2011) Hybridization and restricted gene flow between native and introduced stocks of Alpine whitefish (Coregonus sp.) across multiple environments. Molecular Ecology, 20, 456-472.
116. Wright S, (1943) Isolation by distance. Genetics, 28, 114-138.