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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations

  • Niko Balkenhol
  • Rachael Y. Dudaniec
  • Konstantin V. Krutovsky
  • Jeremy S. Johnson
  • David M. Cairns
  • Gernot Segelbacher
  • Kimberly A. Selkoe
  • Sophie von der Heyden
  • Ian J. Wang
  • Oliver Selmoni
  • Stéphane Joost
Chapter
Part of the Population Genomics book series

Abstract

Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.

Keywords

Adaptive landscape genetics Environmental association analysis (EAA) Functional connectivity Genome-wide association studies (GWAS) Genotype-environment association (GEA) Landscape resistance Local adaptation Outlier loci Seascape genomics 

References

  1. Abrahms B, Sawyer SC, Jordan NR, McNutt JW, Wilson AM, Brashares JS. Does wildlife resource selection accurately inform corridor conservation? J Appl Ecol. 2017;54(2):412–22.  https://doi.org/10.1111/1365-2664.12714.CrossRefGoogle Scholar
  2. Adriaensen F, Chardon JP, De Blust G, Swinnen E, Villalba S, Gulinck H, Matthysen E. The application of ‘least-cost’ modelling as a functional landscape model. Landsc Urban Plan. 2003;64(4):233–47.CrossRefGoogle Scholar
  3. Afán I, Chiaradia A, Forero MG, Dann P, Ramírez F. A novel spatio-temporal scale based on ocean currents unravels environmental drivers of reproductive timing in a marine predator. Proc R Soc B. 2015;282(1810):20150721.PubMedPubMedCentralCrossRefGoogle Scholar
  4. Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S. Adaptation, migration or extirpation: climate change outcomes for tree populations. Evol Appl. 2008;1:95–111.PubMedPubMedCentralCrossRefGoogle Scholar
  5. Alamouti SM, Haridas S, Feau N, Robertson G, Bohlmann J, Breuil C. Comparative genomics of the pine pathogens and beetle symbionts in the genus Grosmannia. Mol Biol Evol. 2014;31(6):1454–74.  https://doi.org/10.1093/molbev/msu102.CrossRefGoogle Scholar
  6. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.PubMedPubMedCentralCrossRefGoogle Scholar
  7. Allen CD, Macalady AK, Chenchouni H, Bachelet D, McDowell N, Vennetier M, Kitzberger T, Rigling A, Breshears DD, Hogg EH, Gonzalez P, Fensham R, Zhang Z, Castro J, Demidova N, Lim J-H, Allard G, Running SW, Semerci A, Cobb N. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For Ecol Manage. 2010;259:660–84.CrossRefGoogle Scholar
  8. Ally D, Ritland K. A case study: looking at the effects of fragmentation on genetic structure in different life history stages of old-growth Mountain Hemlock (Tsuga mertensiana). J Hered. 2007;98:73–8.PubMedCrossRefGoogle Scholar
  9. Ally D, El-Kassaby Y, Ritland K. Genetic diversity, differentiation and mating system in Mountain Hemlock (Tsuga mertensiana) across British Columbia. For Genet. 2000;7:97–108.Google Scholar
  10. Anderson K, Gaston KJ. Lightweight unmanned aerial vehicles will revolutionize spatial ecology. Front Ecol Environ. 2013;11:138–146.CrossRefGoogle Scholar
  11. Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81–92.PubMedPubMedCentralCrossRefGoogle Scholar
  12. Anselin L. Local Indicators of Spatial Association-LISA. Geogr Anal. 1995;27:93–115.CrossRefGoogle Scholar
  13. Ashley MV, Abraham ST, Backs JR, Koenig WD. Landscape genetics and population structure in Valley Oak (Quercus lobata Nee). Am J Bot. 2015;102:2124–31.PubMedCrossRefGoogle Scholar
  14. Balkenhol N, Fortin M-J. Basics of study design: sampling landscape heterogeneity and genetic variation for landscape genetic studies. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 58–75.Google Scholar
  15. Balkenhol N, Waits LP, Dezzani RJ. Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography. 2009;32:818–30.CrossRefGoogle Scholar
  16. Balkenhol N, Holbrook J, Zager P, Rachael J, Onorate D, DeSimone R, White C, Waits LP. A multi-method approach for analyzing hierarchical genetic structures: a case study with cougars (Puma concolor). Ecography. 2014;37:552–63.CrossRefGoogle Scholar
  17. Balkenhol N, Cushman S, Storfer A, Waits LP. Introduction to landscape genetics: defining, learning and applying an interdisciplinary field. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016a. p. 1–17.Google Scholar
  18. Balkenhol N, Cushman S, Storfer A, Waits LP. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016b.Google Scholar
  19. Balkenhol N, Cushman S, Storfer A, Waits LP. Current status, future opportunities and remaining challenges in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016c. p. 247–55.Google Scholar
  20. Barbujani G, Sokal RR. Zones of sharp genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci U S A. 1990;87:1816–9.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  21. Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of microevolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol. 2015;24:1696–712.PubMedCrossRefGoogle Scholar
  22. Bashalkhanov S, Eckert AJ, Rajora OP. Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae). Mol Ecol. 2013;22:5877–89.PubMedCrossRefGoogle Scholar
  23. Belanger CL, Jablonski D, Roy K, Berke SK, Krug AZ, Valentine JW. Global environmental predictors of benthic marine biogeographic structure. Proc Natl Acad Sci U S A. 2012;109:14046–51.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  24. Benestan L, Quinn BK, Maaroufi H, Laporte M, Clark FK, Greenwood SJ, Rochette R, Bernatchez L. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Mol Ecol. 2016;25:5073–92.PubMedCrossRefGoogle Scholar
  25. Benomar L, Lamhamedi MS, Rainville A, Beaulieu J, Bousquet J, Margolis HA. Genetic adaptation vs. ecophysiological plasticity of photosynthetic-related traits in young Picea glauca trees along a regional climatic gradient. Front Plant Sci. 2016;7:48.PubMedPubMedCentralCrossRefGoogle Scholar
  26. Benz RA, Boyce MS, Thurfjell H, Paton DG, Musiani M, Dormann CF, Ciuti S. Dispersal ecology informs design of large-scale wildlife corridors. PLoS One. 2016;11:e0162989.  https://doi.org/10.1371/journal.pone.0162989.PubMedPubMedCentralCrossRefGoogle Scholar
  27. Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, Andre C. Adaptation to low salinity promotes genomic divergence in Atlantic cod (Gadus morhua L.). Genome Biol Evol. 2015;7:1644–63.PubMedPubMedCentralCrossRefGoogle Scholar
  28. Biek R, Real LA. The landscape genetics of infectious disease emergence and spread. Mol Ecol. 2010;19:3515–31.PubMedPubMedCentralCrossRefGoogle Scholar
  29. Blair C, Weigel DE, Balazik M, Keeley ATH, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N. A simulation-based evaluation of methods for inferring linear barriers to gene flow. Mol Ecol Resour. 2012;12:822–33.PubMedCrossRefGoogle Scholar
  30. Bolnick DI, Otto SP. The magnitude of local adaptation under genotype-dependent dispersal. Ecol Evol. 2013;3:4722–35.PubMedPubMedCentralCrossRefGoogle Scholar
  31. Bolnick DI, Snowberg LK, Patenia C, et al. Phenotype-dependent native habitat preference facilitates divergence between parapatric lake and stream stickleback. Evolution. 2009;63:2004–16.PubMedCrossRefGoogle Scholar
  32. Borevitz JO, Chory J. Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol. 2004;7:132–6.PubMedCrossRefGoogle Scholar
  33. Bowen BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, et al. Comparative phylogeography of the ocean planet. Proc Natl Acad Sci U S A. 2016;113:7962–9.PubMedPubMedCentralCrossRefGoogle Scholar
  34. Bradburd GS, Ralph PL, Coop GM. Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution. 2013;67:3258–73.PubMedCrossRefGoogle Scholar
  35. Bradbury D, Smithson A, Krauss SL. Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations. Mol Ecol. 2013a;22:5112–29.PubMedCrossRefGoogle Scholar
  36. Bradbury IR, Hubert S, Higgins B, Bowman S, Borza T, Paterson IG, et al. Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evol Appl. 2013b;6:450–61.PubMedPubMedCentralCrossRefGoogle Scholar
  37. Bragg JG, Supple RL, Andrew RL, Borevitz JO. Genomic variation across landscapes: insights and applications. New Phytol. 2015;207:953–67.PubMedCrossRefGoogle Scholar
  38. Buckley J, Butlin RK, Bridle JR. Evidence for evolutionary change associated with the recent range expansion of the British butterfly, Aricia agestis, in response to climate change. Mol Ecol. 2012;21:267–80.PubMedCrossRefGoogle Scholar
  39. Caldwell IR, Gergel SE. Thresholds in seascape connectivity: influence of mobility, habitat distribution, and current strength on fish movement. Landsc Ecol. 2013;28:1937–48.CrossRefGoogle Scholar
  40. Calic I, Bussotti F, Martinez-Garcia PJ, Neale DB. Recent landscape genomics studies in forest trees-what can we believe? Tree Genet Genomes. 2016;12:3.CrossRefGoogle Scholar
  41. Carl G, Kühn I. Analyzing spatial autocorrelation in species distributions using Gaussian and logit models. Ecol Model. 2007;207:159–70.CrossRefGoogle Scholar
  42. Ceron-Souza I, Bermingham E, McMillan WO, Jones FA. Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama. BMC Evol Biol. 2012;12:205.PubMedPubMedCentralCrossRefGoogle Scholar
  43. Chavez-Pesqueira M, Suarez-Montes P, Castillo G, Nunez-Farfan J. Habitat fragmentation threatens wild populations of Carica papaya (Caricaceae) in a lowland rainforest. Am J Bot. 2014;101:1092–101.PubMedCrossRefGoogle Scholar
  44. Chhatre VE. Population structure, association mapping of economic traits and landscape genomics of east Texas loblolly pine (Pinus taeda L.). PhD thesis, Texas A&M University; 2013. 157 pp.Google Scholar
  45. Chhatre VE, Rajora OP. Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, eastern white pine (Pinus strobus) from northern Ontario. PLoS One. 2014;9(5):e97291.  https://doi.org/10.1371/journal.pone.0097291.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  46. Chhatre VE, Byram TD, Neale DB, Wegrzyn JL, Krutovsky KV. Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations. Tree Genet Genomes. 2013;9:1161–78.  https://doi.org/10.1007/s11295-013-0624-x.CrossRefGoogle Scholar
  47. Conover DO, Clarke LM, Munch SB, Wagner GN. Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation. J Fish Biol. 2006;69:21–47.CrossRefGoogle Scholar
  48. Coop G, Witonsky D, Di Rienzo A, Pritchard JK. Using environmental correlations to identify loci underlying local adaptation. Genetics. 2010;185:1411–23.PubMedPubMedCentralCrossRefGoogle Scholar
  49. Costanza R, D'Arge R, De Groot R, Farber S, Grasso M, Hannon B, et al. The value of the world’s ecosystem services and natural capital. Nature. 1997;387:253–60.ADSCrossRefGoogle Scholar
  50. Cox K, Broeck AV, Van Calster H, Mergeay J. Temperature-related natural selection in a wind-pollinated tree across regional and continental scales. Mol Ecol. 2011;20:2724–38.PubMedCrossRefGoogle Scholar
  51. Craft KJ, Ashley MV. Landscape genetic structure of bur oak (Quercus macrocarpa) savannas in Illinois. For Ecol Manage. 2007;239:13–20.CrossRefGoogle Scholar
  52. Crida A, Manel S. WOMBSOFT: a R package that implements the wombling method to identify genetic boundary. Mol Ecol Notes. 2007;7:588–91.CrossRefGoogle Scholar
  53. Cuervo-Alarcon LC. Genetic analysis of European beech populations across precipitation gradients: understanding the adaptive potential to climate change. PhD thesis, Georg-August University of Göttingen, Göttingen; 2017. 153 pp.Google Scholar
  54. Cushman SA, Lewis JS. Movement behavior explains genetic differentiation in American black bears. Landsc Ecol. 2010;25:1613–25.CrossRefGoogle Scholar
  55. Cushman SA, McKelvey KS, Hayden J, Schwartz MK. Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am Nat. 2006;168:486–99.PubMedCrossRefGoogle Scholar
  56. Cushman SA, Max T, Meneses N, Evans LM, Ferrier S, Honchak B, et al. Landscape genetic connectivity in a riparian foundation tree is jointly driven by climatic gradients and river networks. Ecol Appl. 2014;24:1000–14.PubMedCrossRefGoogle Scholar
  57. Dale VH, Joyce LA, McNulty S, Neilson RP, Ayres MP, Flannigan MD, et al. Climate change and forest disturbances. Bioscience. 2001;51:723–34.CrossRefGoogle Scholar
  58. Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One. 2015;10:e0116528.PubMedPubMedCentralCrossRefGoogle Scholar
  59. Davis JM, Stamps JA. The effect of natal experience on habitat preferences. Trends Ecol Evol. 2004;19:411–6.PubMedCrossRefGoogle Scholar
  60. De Kort H, Vandepitte K, Bruun HH, Closset-Kopp D, Honnay O, Mergeay J. Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa. Mol Ecol. 2014;23:4709–21.PubMedCrossRefGoogle Scholar
  61. De Mita S, Thuillet AC, Ahmadi N, Manel S, Ronfort J, Vigouroux Y. Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations. Mol Ecol. 2013;22:1383–99.PubMedCrossRefGoogle Scholar
  62. de Villemereuil P, Gaggiotti OE. A new FST-based method to uncover local adaptation using environmental variables. Methods Ecol Evol. 2015;6:1248–58.CrossRefGoogle Scholar
  63. DeLong JP, Forbe VE, Galic N, Gibert JP, Laport RG, Phillips JS, Vavra JM. How fast is fast? Eco-evolutionary dynamics and rates of change in populations and phenotypes. Ecol Evol. 2016;6:573–81.PubMedPubMedCentralCrossRefGoogle Scholar
  64. DiLeo MF, Wagner HH. A landscape ecologist’s agenda for landscape genetics. Curr Landsc Ecol Rep. 2016;1:115–26.CrossRefGoogle Scholar
  65. Diniz-Filho JAF, Nabout JC, Bini LM, Soares TN, de Campos Telles MP, de Marco P Jr, Collevatti RG. Niche modelling and landscape genetics of Caryocar brasiliense (“Pequi” tree: Caryocaraceae) in Brazilian Cerrado: an integrative approach for evaluating central-peripheral population patterns. Tree Genet Genomes. 2009;5:617–27.CrossRefGoogle Scholar
  66. Ducatez S, Crossland M, Shine R. Differences in developmental strategies between long-settled and invasion-front populations of the cane toad in Australia. J Evol Biol. 2016;29:335–43.PubMedCrossRefGoogle Scholar
  67. Dudaniec RY, Tesson SVM. Applying landscape genetics to the microbial world. Mol Ecol. 2016;25:3266–75.  https://doi.org/10.1111/mec.13691.PubMedCrossRefGoogle Scholar
  68. Dudaniec RY, Rhodes JR, Worthington-Wilmer J, Lyons M, Lee K, McAlpine CA, Carrick FN. Using multi-level models to identify drivers of landscape genetic structure among management areas. Mol Ecol. 2013;22:3752–65.PubMedCrossRefGoogle Scholar
  69. Dudaniec RY, Worthington-Wilmer J, Hanson J, Warren M, Bell S, Rhodes JR. Dealing with uncertainty in landscape genetic resistance models: a case of three co-occurring marsupials. Mol Ecol. 2016;25:470–86.  https://doi.org/10.1111/mec.13482.PubMedCrossRefGoogle Scholar
  70. Duforet-Frebourg N, Blum MGB. Nonstationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging. Evolution. 2014;68:1110–23.PubMedPubMedCentralCrossRefGoogle Scholar
  71. Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MGB. Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Mol Biol Evol. 2016;33:1082.  https://doi.org/10.1093/molbev/msv334.PubMedCrossRefGoogle Scholar
  72. Dyer RJ. Is there such a thing as landscape genetics? Mol Ecol. 2015a;24:3518–28.PubMedCrossRefGoogle Scholar
  73. Dyer RJ. Population graphs and landscape genetics. Annu Rev Ecol Evol Syst. 2015b;46:327–42.CrossRefGoogle Scholar
  74. Dyer RJ. Landscapes and plant populations genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 183–98.Google Scholar
  75. Dyer RJ, Nason JD. Population graphs: the graph theoretic shape of genetic structure. Mol Ecol. 2004;13:1713–27.PubMedCrossRefGoogle Scholar
  76. Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, et al. Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics. 2009;182:1289–302.PubMedPubMedCentralCrossRefGoogle Scholar
  77. Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB. Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol Ecol. 2010a;19:3789–805.PubMedCrossRefGoogle Scholar
  78. Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics. 2010b;185:969–82.PubMedPubMedCentralCrossRefGoogle Scholar
  79. Eckert AJ, Maloney PE, Vogler DR, Jensen CE, Mix AD, Neale DB. Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae). Tree Genet Genomes. 2015;11:1–17.CrossRefGoogle Scholar
  80. Edelaar P, Bolnick DI. Non-random gene flow: an underappreciated force in evolution and ecology. Trends Ecol Evol. 2012;27:659–65.PubMedCrossRefGoogle Scholar
  81. Edelaar P, Siepielski AM, Clobert J. Matching habitat choice causes directed gene flow: a neglected dimension in evolution and ecology. Evolution. 2008;62:2462–72.PubMedCrossRefGoogle Scholar
  82. Edelhoff H, Signer J, Balkenhol N. Path segmentation for beginners: an overview of current methods for detecting changes in animal movement patterns. Mov Ecol. 2016;4:21.PubMedPubMedCentralCrossRefGoogle Scholar
  83. Ehrenreich IM, Purugganan MD. The molecular genetic basis of plant adaptation. Am J Bot. 2006;93:953–62.PubMedCrossRefGoogle Scholar
  84. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  85. Engler J, Rödder D, Filz K, Habel J, Balkenhol N. Comparative landscape genetics in three closely related sympatric Hesperid butterflies with diverging ecological traits. PLoS One. 2014;9(9):e106526.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  86. Fageria MS, Rajora OP. Effects of harvesting of increasing intensities on genetic diversity and population structure of white spruce. Evol Appl. 2013;6:778–94.CrossRefGoogle Scholar
  87. Feder JL, Forbes AA. Habitat avoidance and speciation for phytophagous insect specialists. Funct Ecol. 2007;21:585–97.CrossRefGoogle Scholar
  88. Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, et al. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Mol Ecol. 2013;22:5594–607.PubMedPubMedCentralCrossRefGoogle Scholar
  89. Fitzpatrick MC, Keller SR. Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecol Lett. 2015;18:1–16.PubMedCrossRefGoogle Scholar
  90. Flaxman SM, Feder JL, Nosil P. Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow. Evolution. 2013;67:2577–91.PubMedCrossRefGoogle Scholar
  91. Foll M, Gaggiotti OA. Genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics. 2008;180:977.PubMedPubMedCentralCrossRefGoogle Scholar
  92. Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol Ecol. 2016;25:104–20.PubMedCrossRefGoogle Scholar
  93. Forester BR, Lasky JR, Wagner HH, Urban DL. Using genotype-environment associations to identify multilocus local adaptation. bioRxiv. 2017; 129460.  https://doi.org/10.1101/129460.
  94. Fotheringham AS, Brunsdon C, Charlton M. Geographically weighted regression: the analysis of spatially varying relationships. West Sussex: Wiley; 2002.zbMATHGoogle Scholar
  95. Fountain T, Nieminen M, Sirén J, et al. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly. Proc Natl Acad Sci U S A. 2016;113:2678–83.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  96. François O, Waits LP. Clustering and assignment methods in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 247–55.Google Scholar
  97. Freedman AH, Thomassen HA, Buermann W, Smith TB. Genomic signals of diversification along ecological gradients in a tropical lizard. Mol Ecol. 2010;19:3773–88.PubMedCrossRefGoogle Scholar
  98. Frichot E, Schoville SD, Bouchard G, Francois O. Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol. 2013;30:1687–99.PubMedPubMedCentralCrossRefGoogle Scholar
  99. Frichot E, Schoville SD, de Villemereuil P, Gaggiotti OE, François O. Detecting adaptive evolution based on association with ecological gradients: orientation matters! Heredity. 2015;115:22–8.PubMedPubMedCentralCrossRefGoogle Scholar
  100. Fronhofer EA, Altermatt F. Eco-evolutionary feedbacks during experimental range expansions. Nat Commun. 2015;6:6844.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  101. Funk WC, Lovich RE, Hohenlohe PA, Hofman CA, Morrison SA, Sillett TS, Ghalambor CK, Maldonado JE, Rick TC, Day MD, Polato NR, Fitzpatrick SW, Coonan TJ, Crooks KR, Dillon A, Garcelon DK, King JL, Boser CL, Gould N, Andelt WF. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol. 2016;25:2176–94.PubMedPubMedCentralCrossRefGoogle Scholar
  102. Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl. 2015;8:769–86.PubMedPubMedCentralCrossRefGoogle Scholar
  103. Gaines MS, Diffendorfer JE, Tamarin RH, Whittam TS. The effects of habitat fragmentation on the genetic structure of small mammal population. J Hered. 1997;88:294–304.PubMedCrossRefGoogle Scholar
  104. Gaither MR, Bowen BW, Rocha LA, Briggs JC. Fishes that rule the world: circumtropical distributions revisited. Fish Fish. 2016;17:664–79.CrossRefGoogle Scholar
  105. Gaston KJ. Geographic range limits: achieving synthesis. Proc R Soc Lond B Bio Sci. 2009;276:1395–406.CrossRefGoogle Scholar
  106. Gauffre B, Estoup A, Bretangnolle V, Cosson JF. Spatial genetic structure of a small rodent in a heterogeneous landscape. Mol Ecol. 2008;17:4619–29.PubMedCrossRefGoogle Scholar
  107. Gautier M. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics. 2015;201:1555–79.PubMedPubMedCentralCrossRefGoogle Scholar
  108. González-Martínez SC, Krutovsky KV, Neale DB. Forest-tree population genomics and adaptive evolution. New Phytol. 2006;170:227–38.PubMedCrossRefGoogle Scholar
  109. Gralka M, Stiewe F, Farrell F, Möbius W, Waclaw B, Hallatschek O. Allele surfing promotes microbial adaptation from standing variation. Ecol Lett. 2016;19:889–98.PubMedPubMedCentralCrossRefGoogle Scholar
  110. Guillot G, Rousset F. Dismantling the Mantel tests. Methods Ecol Evol. 2013;4:336–44.CrossRefGoogle Scholar
  111. Guillot G, Vitalis R, le Rouzic A, Gautier M. Detecting correlation between allele frequencies and environmental variables as a signature of selection. A fast computational approach for genome-wide studies. Spat Stat. 2014;8:145–55.MathSciNetCrossRefGoogle Scholar
  112. Günther T, Coop G. Robust identification of local adaptation from allele frequencies. Genetics. 2013;195:205–20.PubMedPubMedCentralCrossRefGoogle Scholar
  113. Guo B, DeFaveri J, Sotelo G, Nair A, Merilä J. Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol. 2015;13:19.PubMedPubMedCentralCrossRefGoogle Scholar
  114. Haddad NM, Brudvig LA, Clobert J, Davies KF, Gonzalez A, Holt RD, et al. Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci Adv. 2015;1:e1500052.ADSPubMedPubMedCentralCrossRefGoogle Scholar
  115. Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperona G, Toomajian C, et al. Adaptation to climate across the Arabidopsis thaliana genome. Science. 2011;334(6052):83–6.ADSPubMedCrossRefGoogle Scholar
  116. Hand BK, Lowe WH, Kovach RP, Muhlfeld CC, Luikart G. Landscape community genomics: understanding eco-evolutionary processes in complex environments. Trends Ecol Evol. 2015;30:161–8.PubMedCrossRefGoogle Scholar
  117. Hauser L, Carvalho GR. Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish. 2008;9:333–62.CrossRefGoogle Scholar
  118. Hedrick PW, Ginevan ME, Ewing EP. Genetic polymorphism in heterogeneous environments. Annu Rev Ecol Syst. 1976;7:1–32.CrossRefGoogle Scholar
  119. Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. Biol Bull. 2014;227:117–32.PubMedCrossRefGoogle Scholar
  120. Henriques R, von der Heyden S, Lipinski MR, du Toit N, Kainge P, Bloomer P, Matthee CA. Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes. Mol Ecol. 2016;25:5843–61.PubMedCrossRefGoogle Scholar
  121. Hitchings SP, Beebee, Trevor JCT. Genetic substructuring as a result of barriers to gene flow in urban Rana temporaria (common frog) populations: implications for biodiversity conservation. Heredity. 1997;79:117–27.PubMedCrossRefGoogle Scholar
  122. Hoban S, Bertorelle G, Gaggiotti OE. Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet. 2012;13:110–22.PubMedGoogle Scholar
  123. Hoban SM, Hauffe H, Pérez-Espona S, Arntzen J, Bertorelle G, Bryja J, et al. Bringing genetic diversity to the forefront of conservation policy and management. Conserv Genet Resour. 2013;5:593–8.CrossRefGoogle Scholar
  124. Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions. Am Nat. 2016;188(4):379–97.PubMedPubMedCentralCrossRefGoogle Scholar
  125. Hoekstra HE, Hirschmann RJ, Bundey RJ, Insel P, Crossland JP. A single amino acid mutation contributes to adaptive color pattern in beach mice. Science. 2006;313:101–4.ADSPubMedCrossRefGoogle Scholar
  126. Hoffmann A, Griffin P, Dillon S, Catullo R, Rane R, Byrne M, Jordan R, Oakeshott J, Weeks A, Joseph L, Lockhart P, Borevitz J, Sgrò C. A framework for incorporating evolutionary genomics into biodiversity conservation and management. Clim Change Resp. 2015;2:1.  https://doi.org/10.1186/s40665-014-0009-x.CrossRefGoogle Scholar
  127. Holderegger R, Wagner HH. Landscape genetics. BioScience. 2008;58:199–207.CrossRefGoogle Scholar
  128. Holderegger R, Kamm U, Gugerli F. Adaptive vs. neutral genetic diversity: implications for landscape genetics. Landsc Ecol. 2006;21:797–807.CrossRefGoogle Scholar
  129. Holderegger R, Herrmann D, Poncet B, Gugerli F, Thuiller W, Taberlet P, Gielly L, Rioux D, Brodbeck S, Aubert S, Manel S. Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol Divers. 2008;1:273–83.CrossRefGoogle Scholar
  130. Holderegger R, Buehler D, Gugerli F, Manel S. Landscape genetics of plants. Trends Plant Sci. 2010;15:675–83.PubMedCrossRefGoogle Scholar
  131. Holliday JA, Suren H, Aitken SN. Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proc R Soc Lond B Biol Sci. 2012;279:1675–83.CrossRefGoogle Scholar
  132. Hu L-J, Uchiyama K, Shen H-L, Ide Y. Multiple-scaled spatial genetic structures of Fraxinus mandshurica over a riparian-mountain landscape in Northeast China. Conserv Genet. 2010;11:77–87.CrossRefGoogle Scholar
  133. Jaquiery J, Broquet T, Hirzel AH, Yearsley J, Perrin N. Inferring landscape effects on dispersal from genetic distances: how far can we go? Mol Ecol. 2011;20:692–705.PubMedCrossRefGoogle Scholar
  134. Johnson JS, Gaddis KD, Cairns DM, Lafon CW, Krutovsky KV. Plant responses to global change: next generation biogeography. Phys Geogr. 2016;37:93–119.  https://doi.org/10.1080/02723646.2016.1162597.CrossRefGoogle Scholar
  135. Johnson JS, Gaddis KD, Cairns DM, Konganti K, Krutovsky KV. Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change. Am J Bot. 2017a;104(3):439–50.  https://doi.org/10.3732/ajb.1600262.PubMedCrossRefGoogle Scholar
  136. Johnson JS, Gaddis KD, Cairns DM, Krutovsky KV. Seed dispersal at alpine treeline: an assessment of seed movement within the alpine treeline ecotone. Ecosphere. 2017b;8(1):e01649.  https://doi.org/10.1002/ecs2.1649.CrossRefGoogle Scholar
  137. Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E. The genomic basis of adaptive evolution in three-spine sticklebacks. Nature. 2012;484:55–61.PubMedPubMedCentralCrossRefGoogle Scholar
  138. Jones MR, Forester BR, Teufel AI, Adams RV, Anstett DN, Goodrich BA, Landguth EL, Joost S, Manel S. Integrating spatially explicit approaches to detect adaptive loci in a landscape genomics context. Evolution. 2013;67:3455–68.PubMedCrossRefGoogle Scholar
  139. Joost S, Bonin A, Bruford MW, Després L, Conord C, Erhardt G, et al. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol. 2007;16:3955–69.PubMedCrossRefGoogle Scholar
  140. Joost S, Vuilleumier S, Denson JD, Schoville S, Leempoel K, Stucki S, et al. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Mol Ecol. 2013;22:3659–65.PubMedCrossRefGoogle Scholar
  141. Kamm U, Rotach P, Gugerli F, Siroky M, Edwards P, Holderegger R. Frequent long-distance gene flow in a rare temperate forest tree (Sorbus domestica) at the landscape scale. Heredity. 2009;103:476–82.PubMedCrossRefGoogle Scholar
  142. Kamm U, Gugerli F, Rotach P, Edwards P, Holderegger R. Open areas in a landscape enhance pollen-mediated gene flow of a tree species: evidence from northern Switzerland. Landsc Ecol. 2010;25:903–11.CrossRefGoogle Scholar
  143. Kawecki TJ, Ebert D. Conceptual issues in local adaptation. Ecol Lett. 2004;7:1225–41.CrossRefGoogle Scholar
  144. Keller SR, Levsen N, Olson MS, Tiffin P. Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L. Mol Biol Evol. 2012;29:3143–52.PubMedCrossRefGoogle Scholar
  145. Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet. 2016;17:523–34.PubMedCrossRefGoogle Scholar
  146. Kelly E, Phillips BL. Targeted gene flow for conservation. Conserv Biol. 2016;30:259–67.PubMedCrossRefGoogle Scholar
  147. Keyghobadi N. The genetic implications of habitat fragmentation for animals. Can J Zool. 2007;85:1049–64.CrossRefGoogle Scholar
  148. Kidd MK, Ritchie MG. Phylogeographic information systems: putting the geography into phylogeography. J Biogeogr. 2006;33:1851–65.CrossRefGoogle Scholar
  149. Kirkpatrick M, Barton NH. Evolution of a species’ range. Am Nat. 1997;150:1–23.PubMedCrossRefGoogle Scholar
  150. Klopfstein S, Currat M, Excoffier L. The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol. 2006;23:482–90.PubMedCrossRefGoogle Scholar
  151. Kremer A, Ronce O, Robledo-Arnuncio JJ, Guillaume F, Bohrer G, Nathan R, Bridle JR, Gomulkiewicz R, Klein EK, Ritland K, Kuparinen A, Gerber S, Schueler S. Long-distance gene flow and adaptation of forest trees to rapid climate change. Ecol Lett. 2012;15:378–92.PubMedPubMedCentralCrossRefGoogle Scholar
  152. Krutovsky KV, Burczyk J, Chybicki I, Finkeldey R, Pyhäjärvi T, Robledo-Arnuncio JJ. Gene flow, spatial structure, local adaptation and assisted migration in trees. In: Schnell RJ, Priyadarshan PM, editors. Genomics of tree crops. New York: Springer; 2012. p. 71–116.  https://doi.org/10.1007/978-1-4614-0920-5_4.CrossRefGoogle Scholar
  153. Kubisch A, Holt RD, Poethke H-J, Fronhofer EA. Where am I and why? Synthesizing range biology and the eco-evolutionary dynamics of dispersal. Oikos. 2014;123:5–22.CrossRefGoogle Scholar
  154. Lancaster LT. Widespread range expansions shape latitudinal variation in insect thermal limits. Nat Clim Chang. 2016;6:618.  https://doi.org/10.1038/nclimate2945.ADSCrossRefGoogle Scholar
  155. Landguth EL, Fedy B, Garey A, Mumma M, Emel S, Oyler-McCance S, et al. Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern. Mol Ecol Resour. 2012;12:276–84.CrossRefGoogle Scholar
  156. Landguth E, Cushman S, Balkenhol N. Simulation modeling in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 101–13.Google Scholar
  157. Landguth EL, Bearlin A, Day CC, Dunham J. CDMetaPOP: an individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics. Methods Ecol Evol. 2017;8:4–11.CrossRefGoogle Scholar
  158. Lee C-R, Mitchell-Olds T. Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol Ecol. 2011;20:4631–42.PubMedPubMedCentralCrossRefGoogle Scholar
  159. Legendre P, Fortin MJ. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol Ecol Resour. 2010;10:831–44.PubMedCrossRefGoogle Scholar
  160. Legendre P, Legendre LP. Numerical ecology. London: Elsevier; 2012.zbMATHGoogle Scholar
  161. Legendre P, Borcard D, Roberts DW. Variation partitioning involving orthogonal spatial eigenfunction submodels. Ecology. 2012;93:1234–40.PubMedCrossRefGoogle Scholar
  162. Legendre P, Fortin MJ, Borcard D. Should the Mantel test be used in spatial analysis? Methods Ecol Evol. 2015;6:1239–47.CrossRefGoogle Scholar
  163. Legrand D, Cote J, Fronhofer EA, Holt RD, Ronce O, Schtickzelle N, Travis JMJ, Clobert J. Eco-evolutionary dynamics in fragmented landscapes. Ecography. 2016.  https://doi.org/10.1111/ecog.0253.
  164. Lenormand T. Gene flow and the limits to natural selection. Trends Ecol Evol. 2002;17:183–9.CrossRefGoogle Scholar
  165. Lepais O, Bacles CF. Two are better than one: combining landscape genomics and common gardens for detecting local adaptation in forest trees. Mol Ecol. 2014;23:4671–3.PubMedCrossRefGoogle Scholar
  166. Lhuillier E, Butaud J-F, Bouvet J-M. Extensive clonality and strong differentiation in the insular pacific tree Santalum insulare: implications for its conservation. Ann Bot. 2006;98:1061–72.PubMedPubMedCentralCrossRefGoogle Scholar
  167. Loiselle BA, Sork VL, Nason J, Graham C. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot. 1995;82:1420–5.CrossRefGoogle Scholar
  168. Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour. 2017;17:142–52.PubMedCrossRefGoogle Scholar
  169. Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics. 2016;17:730.  https://doi.org/10.1186/s12864-016-3081-8.PubMedPubMedCentralCrossRefGoogle Scholar
  170. Lu M, Krutovsky KV, Nelson CD, West JB, Reilly NA, Loopstra CA. Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms. Tree Genet Genomes. 2017;13:57.  https://doi.org/10.1007/s11295-017-1140-1.CrossRefGoogle Scholar
  171. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet. 2003;4:981–94.PubMedCrossRefGoogle Scholar
  172. Manel S, Holderegger R. Ten years of landscape genetics. Trends Ecol Evol. 2013;28:614–21.PubMedCrossRefGoogle Scholar
  173. Manel S, Schwartz MK, Luikart G, Taberlet P. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol. 2003;18:189–97.CrossRefGoogle Scholar
  174. Manel S, Gugerli F, Thuiller W, Alvarez N, Legendre P, Holderegger R, et al. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol. 2010;19:3760–72.PubMedCrossRefGoogle Scholar
  175. Manel S, et al. Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation. Mol Ecol. 2012;21:3729–38.PubMedPubMedCentralCrossRefGoogle Scholar
  176. Manicacci D, Olivieri I, Perrot V, Atlan A, Gouyon PH, Prosperi JM, Couvet D. Landscape ecology: population genetics at the metapopulation level. Landsc Ecol. 1992;6:147–59.CrossRefGoogle Scholar
  177. Marko PB, Hart MW. The complex analytical landscape of gene flow inference. Trends Ecol Evol. 2011;26:448–56.PubMedCrossRefGoogle Scholar
  178. Martin MA, Mattioni C, Molina JR, Alvarez JB, Cherubini M, Herrera MA, Villani F, Martin LM. Landscape genetic structure of chestnut (Castanea sativa Mill.) in Spain. Tree Genet Genomes. 2012;8:127–36.CrossRefGoogle Scholar
  179. Mateo-Sanchéz M, Balkenhol N, Cushman S, Pérez T, Domínguez P, Saura S. A comparative framework to infer landscape effects on population genetic structure: are habitat suitability models effective in explaining gene flow? Landsc Ecol. 2015;8:1405–20.CrossRefGoogle Scholar
  180. Mayr E, O’Hara RJ. The biogeographic evidence supporting the Pleistocene forest refuge hypothesis. Evolution. 1986;40:55–67.PubMedCrossRefGoogle Scholar
  181. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hitschhorn JN. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356–69.PubMedCrossRefGoogle Scholar
  182. McKown AD, Guy RD, Klapste J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. New Phytol. 2014;201:1263–76.PubMedCrossRefGoogle Scholar
  183. McRae BH. Isolation by resistance. Evolution. 2006;60:1551–61.PubMedCrossRefGoogle Scholar
  184. McRae BH, Dickson BG, Keitt TH, Shah VB. Using circuit theory to model connectivity in ecology and conservation. Ecology. 2008;10:2712–24.CrossRefGoogle Scholar
  185. Merilä J, Hendry AP. Climate change, adaptation, and phenotypic plasticity: the problem and the evidence. Evol Appl. 2014;7:1–14.PubMedPubMedCentralCrossRefGoogle Scholar
  186. Merriam G, Kozakiewicz M, Tsuchiya E, Hawley K. Barriers as boundaries for metapopulations and demes of Peromyscus leucopus in farm landscapes. Landsc Ecol. 1989;2:227–35.CrossRefGoogle Scholar
  187. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 2007;17:240–8.PubMedPubMedCentralCrossRefGoogle Scholar
  188. Monmonier M. Maximum–difference barriers: an alternative numerical regionalization method. Geogr Anal. 1973;3:245–61.Google Scholar
  189. Montgelard C, Zenboudji S, Ferchaud A, Arnal V, van Vuuren BJ. Landscape genetics in mammals. Mammalia. 2014;78:139–57.CrossRefGoogle Scholar
  190. Moran PAP. Notes on continuous stochastic phenomena. Biometrika. 1950;37:17–23.zbMATHMathSciNetPubMedCrossRefGoogle Scholar
  191. Morgan SG. Behaviorally mediated larval transport in upwelling systems. Adv Oceanogr. 2014;2014:364214.CrossRefGoogle Scholar
  192. Moritz C, Patton JL, Schneider CJ, Smith TB. Diversification of rainforest faunas: an integrated molecular approach. Annu Rev Ecol Syst. 2000;31:533–63.CrossRefGoogle Scholar
  193. Morris GP, et al. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci. 2013;110:453–8.ADSPubMedCrossRefGoogle Scholar
  194. Mosca E, Eckert AJ, Di Pierro EA, Rocchini D, La Porta N, Belletti P, Neale DB. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Mol Ecol. 2012;21:5530–45.PubMedCrossRefGoogle Scholar
  195. Mosca E, González-Martínez SC, Neale DB. Environmental versus geographical determinants of genetic structure in two subalpine conifers. New Phytol. 2014;201:180–92.PubMedCrossRefGoogle Scholar
  196. Mosca E, Gugerli F, Eckert AJ, Neale DB. Signatures of natural selection on Pinus cembra and P. mugo along elevational gradients in the Alps. Tree Genet Genomes. 2016;12:9.  https://doi.org/10.1007/s11295-015-0964-9.CrossRefGoogle Scholar
  197. Murphy M, Dyer R, Cushman SA. Graph theory and network models in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 165–80.Google Scholar
  198. Namroud M-C, Beaulieu J, Juge N, Laroche J, Bousquet J. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol. 2008;17:3599–613.PubMedPubMedCentralCrossRefGoogle Scholar
  199. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol. 2013;22:2841–7.PubMedPubMedCentralCrossRefGoogle Scholar
  200. Neale DB, Kremer A. Forest tree genomics: growing resources and applications. Nat Rev Genet. 2011;12:111–22.PubMedCrossRefGoogle Scholar
  201. Nielsen EE, Hemmer-Hansen JA, Larsen PF, Bekkevold D. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol. 2009;18:3128–50.PubMedCrossRefGoogle Scholar
  202. Nosil P. Reproductive isolation caused by visual predation on migrants between divergent environments. Proc R Soc Lond B. 2004;271:1521–8.CrossRefGoogle Scholar
  203. Nosil P, Vines TH, Funk DJ. Reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution. 2005;59:705–19.PubMedGoogle Scholar
  204. Nosil P, Egan SP, Funk DJ. Heterogeneous genomic differentiation between walking-stick ecotypes: “isolation by adaptation” and multiple roles for divergent selection. Evolution. 2008;62:316–36.PubMedCrossRefGoogle Scholar
  205. Nosil P, Funk DJ, Ortiz-Barrientos D. Divergent selection and heterogeneous genomic divergence. Mol Ecol. 2009;18:375–402.PubMedCrossRefGoogle Scholar
  206. O’Connell LM, Mosseler A, Rajora OP. Impacts of forest fragmentation on the matting system and genetic diversity of white spruce (Picea glauca) at the landscape level. Heredity. 2006;97:418–26.PubMedCrossRefGoogle Scholar
  207. O’Connell LM, Mosseler A, Rajora OP. Extensive long-distance pollen dispersal in a fragmented landscape maintains genetic diversity in white spruce. J Hered. 2007;98:640–5.PubMedCrossRefGoogle Scholar
  208. Orsini L, Vanoverbeke J, Swillen I, Mergeay J, Meester L. Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol Ecol. 2013;22:5983–99.PubMedCrossRefGoogle Scholar
  209. Pamilo P. Genetic variation in heterogeneous environments. Ann Zool Fenn. 1988;25:99–106.Google Scholar
  210. Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol. 2012;21:2991–3005.PubMedCrossRefGoogle Scholar
  211. Paris CB, Cherubin LM, Cowen RK. Surfing, spinning, or diving from reef to reef: effects on population connectivity. Mar Ecol Prog Ser. 2007;347:285–300.ADSCrossRefGoogle Scholar
  212. Parisod C, Holderegger R. Adaptive landscape genetics: pitfalls and benefits. Mol Ecol. 2012;21:3644–6.PubMedCrossRefGoogle Scholar
  213. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2:e190.PubMedPubMedCentralCrossRefGoogle Scholar
  214. Paul J, Song YS. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics. 2012;28:2008–15.PubMedPubMedCentralCrossRefGoogle Scholar
  215. Pel MA, Foster SJ, Rietman H, van Arkel G, Jones JD, Van Eck HJ, et al. Mapping and cloning of late blight resistance genes from Solanum venturii using an interspecific candidate gene approach. Mol Plant-Microbe Interact. 2009;22:601–15.PubMedCrossRefGoogle Scholar
  216. Pelletier F, Garant D, Hendry AP. Eco-evolutionary dynamics. Philos Trans R Soc B Biol Sci. 2009;364:1483–9.CrossRefGoogle Scholar
  217. Pettorelli N, Vik JO, Mysterud A, Gaillard J-M, Tucker CJ, Stenseth NC. Using the satellite-derived NDVI to assess ecological responses to environmental change. Trends Ecol Evol. 2005;20:503–10.PubMedCrossRefGoogle Scholar
  218. Pflieger S, Lefebvre V, Causse M. The candidate gene approach in plant genetics: a review. Mol Breed. 2001;7:275–91.CrossRefGoogle Scholar
  219. Pflüger F, Balkenhol N. A plea for simultaneously considering matrix quality and local environmental conditions when analyzing landscape impacts on effective dispersal. Mol Ecol. 2014;23:2146–56.PubMedCrossRefGoogle Scholar
  220. Poelchau MF, Hamrick JL. Differential effects of landscape-level environmental features on genetic structure in three codistributed tree species in Central America. Mol Ecol. 2012;21(20):4970–82.PubMedCrossRefGoogle Scholar
  221. Porth I, Klápště J, McKown AD, La Manita J, Guy RD, Ingvrasson PK, et al. Evolutionary quantitative genomics of Populus trichocarpa. PLoS One. 2015;10:e0142864.PubMedPubMedCentralCrossRefGoogle Scholar
  222. Primack RB. Essentials of conservation biology. 6th ed. Sunderland: Sinaur Associates; 2014.Google Scholar
  223. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.PubMedPubMedCentralGoogle Scholar
  224. Prunier J, Laroche J, Beaulieu J, Bousquet J. Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce. Mol Ecol. 2011;20:1702–16.PubMedCrossRefGoogle Scholar
  225. Prunier JG, Kaufmann B, Fenet S, Picard D, Pompanon F, Joly P, Lena JP. Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme. Mol Ecol. 2013;22:5516–30.PubMedCrossRefGoogle Scholar
  226. Rajora OP, Eckert AJ, Zinck JWR. Single-locus versus multilocus patterns of local adaptation to climate in eastern white pine (Pinus strobus, Pinaceae). PLoS One. 2016;11(7):e0158691.PubMedPubMedCentralCrossRefGoogle Scholar
  227. Rasic G, Filipovic I, Weeks AR, Hoffmann AA. Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti. BMC Genomics. 2014;15:275.PubMedPubMedCentralCrossRefGoogle Scholar
  228. Ratnam W, Rajora OP, Finkeldey R, Aravanopoulos F, Bouvet J-M, Vallancourt RE, Kanashiro M. Genetic effects of forest management practices: global synthesis and perspectives. For Ecol Manage. 2014;333:52–65.CrossRefGoogle Scholar
  229. Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R. A practical guide to environmental association analysis in landscape genomics. Mol Ecol. 2015;24:4348–70.PubMedCrossRefGoogle Scholar
  230. Richardson JL, Urban MC, Bolnick DI, Skelly DK. Microgeographic adaptation and the spatial scale of evolution. Trends Ecol Evol. 2014;29:165–76.PubMedCrossRefGoogle Scholar
  231. Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml E. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool. 2016;62:581–601.  https://doi.org/10.1093/cz/zow067.CrossRefGoogle Scholar
  232. Roberts DR, Hamann A. Glacial refugia and modern genetic diversity of 22 western North American tree species. Proc R Soc B. 2015;282(1804):20142903.PubMedPubMedCentralCrossRefGoogle Scholar
  233. Roffler GH, Amish SJ, Smith S, Cosart T, Kardos M, Schwartz MK, Luikart G. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate. Mol Ecol Resour. 2016a;16:1147–64.PubMedCrossRefGoogle Scholar
  234. Roffler GH, Schwartz MK, Pilgrim MK, Talbot SL, Sage GK, Adams LG, Luikart G. Identification of landscape features influencing gene flow: how useful are habitat selection models? Evol Appl. 2016b;9:805–17.PubMedPubMedCentralCrossRefGoogle Scholar
  235. Roschanski AM, Csillery K, Liepelt S, Oddou-Muratorio S, Ziegenhagen B, Huard F, Ulrich KK, Postolache D, Vendramin GG, Fady B. Evidence of divergent selection at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps. Mol Ecol. 2016;25:776–94.Google Scholar
  236. Rosenblum EB, Harmon LJ. “Same same but different”: replicated ecological speciation at white sands. Evolution. 2011;65:946–60.PubMedCrossRefGoogle Scholar
  237. Safran RJ, Scordato ESC, Symes LB, Rodríguez RL, Mendelson TC. Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda. Trends Ecol Evol. 2013;28:643–50.PubMedCrossRefGoogle Scholar
  238. Savolainen O, Pyhäjärvi T, Knürr T. Gene flow and local adaptation in trees. Annu Rev Ecol Evol Syst. 2007;38:595–619.CrossRefGoogle Scholar
  239. Schoville SD, Bonin A, François O, Lobreaux S, MeloDelima C, Manel S. Adaptive genetic variation on the landscape: methods and cases. Annu Rev Ecol Evol Syst. 2012;43:23–43.CrossRefGoogle Scholar
  240. Schumaker NH. HexSim Version 2.5.7. Corvallis: U.S. Environmental Protection Agency, Environmental Research Laboratory; 2013. http://hexsim.net Google Scholar
  241. Schupp EW, Fuentes M. Spatial patterns of seed dispersal and the unification of plant population ecology. Ecoscience. 1995;2:267–75.CrossRefGoogle Scholar
  242. Schwabl P, Llewellyn MS, Landguth EL, Andersson B, Kitron U, Costales JA, et al. Prediction and prevention of parasitic diseases using a landscape genomics framework. Trends Parasitol. 2017;33(4):264–75.PubMedCrossRefGoogle Scholar
  243. Schwartz MK, Luikart G, McKelvey KS, Cushman SA. Landscape genomics: a brief perspective. In: Cushman SA, Huettmann F, editors. Spatial complexity, informatics, and wildlife conservation. Tokyo: Springer; 2009. p. 165–74.Google Scholar
  244. Selkoe KA, Toonen RJ. Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal. Mar Ecol Prog Ser. 2011;436:291–305.ADSCrossRefGoogle Scholar
  245. Selkoe KA, D’Aloia CC, Crandall ED, Iacchei M, Liggins L, Puritz JB, von der Heyden S, Toonen RJ. A decade of seascape genetics: contributions to basic and applied marine connectivity. Mar Ecol Prog Ser. 2016a;554:1–19.ADSCrossRefGoogle Scholar
  246. Selkoe KA, Scribner KT, Galindo HM. Waterscape genetics – applications of landscape genetics to rivers, lakes, and seas. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016b. p. 220–46.Google Scholar
  247. Servedio MR. The evolution of premating isolation: local adaptation and natural and sexual selection against hybrids. Evolution. 2004;58:913–24.PubMedCrossRefGoogle Scholar
  248. Sexton JP, Hangartner SB, Hoffmann AA. Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution. 2014;68:1–15.PubMedCrossRefGoogle Scholar
  249. Shafer ABA, Wolf JBW, Alves PC, Bergström L, Bruford M, Brännström I, et al. Genomics and the challenging translation into conservation practice. Trends Ecol Evol. 2015;30:78–87.PubMedCrossRefGoogle Scholar
  250. Smith TB, Wayne RK, Girman DJ, Bruford MW. A role for ecotones in generating rainforest biodiversity. Science. 1997;276:1855–7.CrossRefGoogle Scholar
  251. Smouse PE, Sork VL. Measuring pollen flow in forest trees: an exposition of alternative approaches. For Ecol Manage. 2004;197:21–38.CrossRefGoogle Scholar
  252. Sodeland M, Jorde PE, Lien S, Jentoft S, Berg PR, Grove H, et al. ‘Islands of divergence’ in the Atlantic cod represent polymorphic chromosomal rearrangements. Genome Biol Evol. 2016;8:1012–22.  https://doi.org/10.1093/gbe/evw057.PubMedPubMedCentralCrossRefGoogle Scholar
  253. Sork V, Smouse P. Genetic analysis of landscape connectivity in tree populations. Landsc Ecol. 2006;21:821–36.CrossRefGoogle Scholar
  254. Sork VL, Nason J, Campbell DR, Fernandez JF. Landscape approaches to historical and contemporary gene flow in plants. Trends Ecol Evol. 1999;14:219–24.PubMedCrossRefGoogle Scholar
  255. Sork VL, Davis FW, Westfall R, Flint A, Ikegami M, Wang H, Grivet D. Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change. Mol Ecol. 2010;19:3806–23.PubMedCrossRefGoogle Scholar
  256. Sork VL, Aitken SN, Dyer RJ, Eckert AJ, Legendre P, Neale DB. Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genet Genomes. 2013;9:901–11.CrossRefGoogle Scholar
  257. Sork VL, Squire K, Gugger PF, Steele SE, Levy ED, Eckert AJ. Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata. Am J Bot. 2016;103:33–46.PubMedCrossRefGoogle Scholar
  258. Spear SF, Balkenhol N, McRae B, Scribner K, Fortin M-J. Modeling resistance surfaces for landscape genetics: considerations for parameterization and analysis. Mol Ecol. 2010;19:3576–91.PubMedCrossRefGoogle Scholar
  259. Spear SF, Cushman SA, McRae BM. Resistance surface modeling in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 129–48.Google Scholar
  260. Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity. 2008;100:158–70.PubMedCrossRefGoogle Scholar
  261. Storfer A, Murphy MA, Evans JS, Goldberg CS, Robinson S, Spear SF, et al. Putting the ‘landscape’ in landscape genetics. Heredity. 2007;98:128–42.PubMedCrossRefGoogle Scholar
  262. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP. Landscape genetics: where are we now? Mol Ecol. 2010;19:3496–514.PubMedCrossRefGoogle Scholar
  263. Storfer A, Antolin MF, Manel S, et al. Genomic approaches in landscape genetics. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 249–164.Google Scholar
  264. Stucki S, Orozco-terWengel P, Bruford MW, Colli L, Masembe C, Negrini R, Taberlet P, Joost S, The NEXTGEN Consortium. High performance computation of landscape genomic models including local indicators of spatial association. Mol Ecol Resour. 2016; arXiv:1405.7658. https://arxiv.org/abs/1405.7658
  265. Suren H, Hodgins KA, Yeaman S, Nurkowski KA, Smets P, Rieseberg LH, Aitken SN, Holliday JA. Exome capture from the spruce and pine giga-genomes. Mol Ecol Resour. 2016;16:1136–46.PubMedCrossRefGoogle Scholar
  266. Swaegers J, Mergeay J, Van Geystelen A, Therry L, Larmuseau MHD, Stoks R. Neutral and adaptive genomic signatures of rapid poleward range expansion. Mol Ecol. 2015;24:6163–76. https://doi.org/10.1111/mec.13462.
  267. Taylor HR, Soanes K. Breaking out of the echo chamber: missed opportunities for genetics at conservation conferences. Biodivers Conserv. 2016;25:1987–93.CrossRefGoogle Scholar
  268. Taylor P, Fahrig L, With K. Landscape connectivity: a return to basics. In: Crooks KR, Sanjayan M, editors. Connectivity conservation. Cambridge: Cambridge University Press; 2006. p. 29–43.CrossRefGoogle Scholar
  269. Travis JMJ, Munkemuller T, Burton OJ, et al. Deleterious mutations can surf to high densities on the wave front of an expanding population. Mol Biol Evol. 2007;24:2334–43.PubMedCrossRefGoogle Scholar
  270. Truong C, Palmé AE, Felber F. Recent invasion of the mountain birch Betula pubescens ssp. tortuosa above the treeline due to climate change: genetic and ecological study in northern Sweden. J Evol Biol. 2007;20:369–80.PubMedCrossRefGoogle Scholar
  271. Tsuda Y, Sawada H, Ohsawa T, Nakao K, Nishikawa H, Ide Y. Landscape genetic structure of Betula maximowicziana in the Chichibu mountain range, central Japan. Tree Genet Genomes. 2010;6:377–87.CrossRefGoogle Scholar
  272. Turner TL, Hahn MW. Genomic islands of speciation or genomic islands and speciation? Mol Ecol. 2010;19:848–50.PubMedCrossRefGoogle Scholar
  273. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet. 2010;42:260–3.PubMedCrossRefGoogle Scholar
  274. van Strien MJ, Keller D, Holderegger R. A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Mol Ecol. 2012;21:4010–23.CrossRefGoogle Scholar
  275. Vangestel C, Vazquez-Lobo A, Martinez-Garcia PJ, Calic I, Wegrzyn JL, Neale DB. Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.). Tree Genet Genomes. 2016;12:51.CrossRefGoogle Scholar
  276. Via S. The ecological genetics of speciation. Am Nat. 2002;159(S3):S1–7.PubMedCrossRefGoogle Scholar
  277. von der Heyden S, Lipinski MR, Matthee CA. Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus. Mol Phylogenet Evol. 2007;42:517–27.PubMedCrossRefGoogle Scholar
  278. von der Heyden S, Beger M, Toonen RJ, van Herwerden L, Juinio-Meñez MA, Ravago-Gotanco R, Fauvelot C, Bernardi G. The application of genetics to marine management and conservation: examples from the Indo-Pacific. Bull Mar Sci. 2014;90:123–58.CrossRefGoogle Scholar
  279. Wagner H, Fortin M-J. A conceptual framework for the spatial analysis of landscape genetic data. Conserv Genet. 2013;14:253–61.CrossRefGoogle Scholar
  280. Wagner HH, Fortin MJ. Basics of spatial data analysis: linking landscape and genetic data for landscape genetic studies. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 77–98.Google Scholar
  281. Waits LP, Storfer A. Basics of population genetics: quantifying neutral and adaptive genetic variation for landscape genetic studies. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 35–57.Google Scholar
  282. Waits LP, Cushman SA, Spear SF. Applications of landscape genetics to connectivity research in terrestrial animals. In: Balkenhol N, Cushman S, Storfer A, Waits L, editors. Landscape genetics: concepts, methods, applications. West Sussex: Wiley; 2016. p. 199–219.Google Scholar
  283. Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol. 2014;23:5649–62.PubMedCrossRefGoogle Scholar
  284. Wang Y-H, Yang KC, Bridgman CL, Lin LK. Habitat suitability modelling to correlate gene flow with landscape connectivity. Landsc Ecol. 2008;23:989–1000.Google Scholar
  285. Wang R, Compton SG, Chen X-Y. Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree. Mol Ecol. 2011;20:4421–32.PubMedCrossRefGoogle Scholar
  286. Wang R, Compton SG, Shi Y-S, Chen X-Y. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed. Ecol Evol. 2012;2:2250–61.PubMedPubMedCentralCrossRefGoogle Scholar
  287. Wang IJ, Glor RE, Losos JB. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol Lett. 2013;16:175–82.PubMedCrossRefGoogle Scholar
  288. Wang Z-F, Lian J-Y, Ye W-H, Cao H-L, Zhang Q-M, Wang Z-M. Pollen and seed flow under different predominant winds in wind-pollinated and wind-dispersed species Engelhardia roxburghiana. Tree Genet Genomes. 2016;12:19.CrossRefGoogle Scholar
  289. Wee AKS, Takayama K, Asakawa T, Thompson B, Onrizal, Sungkaew S, Tung NX, Nazre M, Soe KK, Tan HTW, Watano Y, Baba S, Kajita T, Webb EL. Oceanic currents, not land masses, maintain the genetic structure of the mangrove Rhizophora mucronata Lam. (Rhizophoraceae) in Southeast Asia. J Biogeogr. 2014;41:954–64.CrossRefGoogle Scholar
  290. Wenzel MA, Piertney SB. Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species. J Evol Biol. 2015;28:807–25.PubMedCrossRefGoogle Scholar
  291. White C, Selkoe KA, Watson J, Siegel DA, Zacherl DC, Toonen RJ. Ocean currents help explain population genetic structure. Proc R Soc B. 2010;277:1685–94.PubMedPubMedCentralCrossRefGoogle Scholar
  292. White TA, Perkins SE, Heckel G, Searle JB. Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Mol Ecol. 2013;22:2971–85.PubMedCrossRefGoogle Scholar
  293. Whitham TG, Bailey JK, Schweitzer JA, Shuster SM, Bangert RK, LeRoy VJ, et al. A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet. 2006;7:510–23.PubMedCrossRefGoogle Scholar
  294. Whitlock MC, Lotterhos KE. Reliable detection of loci responsible for local adaptation: inference of a neutral model through trimming the distribution of FST. Am Nat. 2015;186(S1):S24–36.PubMedCrossRefGoogle Scholar
  295. Womble W. Differential systematics. Science. 1951;28:315–22.ADSCrossRefGoogle Scholar
  296. Wright S. Isolation by distance. Genetics. 1943;28:114–38.PubMedPubMedCentralGoogle Scholar
  297. Zeller KA, McGarigal K, Whiteley AR. Estimating landscape resistance to movement: a review. Landsc Ecol. 2012;27:777–97.CrossRefGoogle Scholar
  298. Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL. Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow. Ecol Evol. 2016;6:4115–28.PubMedPubMedCentralCrossRefGoogle Scholar
  299. Zhou Y, Zhang L, Liu J, Wu G, Savolainen O. Climatic adaptation and ecological divergence between two closely related pine species in Southeast China. Mol Ecol. 2014;23:3504–22.PubMedCrossRefGoogle Scholar
  300. Zinck JWR, Rajora OP. Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes. BMC Evol Biol. 2016;16:56.  https://doi.org/10.1186/s12862-016-0624-1.PubMedPubMedCentralCrossRefGoogle Scholar
  301. Ziólkowska E, Ostapowicz K, Radeloff VC, et al. Assessing differences in connectivity based on habitat versus movement models for brown bears in the Carpathians. Landsc Ecol. 2016;31:1863.  https://doi.org/10.1007/s10980-016-0368-8.CrossRefGoogle Scholar
  302. Zulliger D, Schnyder E, Gugerli F. Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species. Mol Ecol. 2013;23:1626–39.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Niko Balkenhol
    • 1
  • Rachael Y. Dudaniec
    • 2
  • Konstantin V. Krutovsky
    • 3
    • 4
    • 5
    • 6
  • Jeremy S. Johnson
    • 7
    • 8
    • 9
  • David M. Cairns
    • 7
  • Gernot Segelbacher
    • 10
  • Kimberly A. Selkoe
    • 11
  • Sophie von der Heyden
    • 12
  • Ian J. Wang
    • 13
  • Oliver Selmoni
    • 14
  • Stéphane Joost
    • 14
  1. 1.Wildlife SciencesUniversity of GoettingenGöttingenGermany
  2. 2.Department of Biological SciencesMacquarie UniversitySydneyAustralia
  3. 3.Department of Forest Genetics and Forest Tree BreedingUniversity of GoettingenGöttingenGermany
  4. 4.Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationUSA
  5. 5.N. I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
  6. 6.Genome Research and Education CenterSiberian Federal UniversityKrasnoyarskRussia
  7. 7.Department of GeographyTexas A&M UniversityCollege StationUSA
  8. 8.School of ForestryNorthern Arizona UniversityAZUSA
  9. 9.Dorena Genetic Resource CenterORUSA
  10. 10.Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
  11. 11.Bren School of Environmental Science & Management, National Center for Ecological Analysis and Synthesis, University of California Santa BarbaraSanta BarbaraUSA
  12. 12.Evolutionary Genomics Group, Department of Botany and ZoologyUniversity of StellenboschStellenboschSouth Africa
  13. 13.Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyUSA
  14. 14.Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland

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