1932

Abstract

At the heart of the analyses of landscape genetics are isolation models seeking to explain either interindividual or interpopulation connectivity. These models use spatial, ecological, and topographic predictor variables measured between sites in an attempt to explain observed genetic variation. During the past decade, these models have adopted an increasingly sophisticated set of techniques to quantify intervening physical and ecological spaces, although they are restrained by rather mundane approaches to characterizing the genetic components of connectivity. Population Graphs are one approach to improving the quantification of genetic covariance used in models of landscape genetics. I explain the construction of the Population Graph framework, explain its strengths and weaknesses, and provide examples of how it has been used during the past decade within the contexts of landscape and population genetics.

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2015-12-04
2024-12-05
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Literature Cited

  1. Albert EM, Fortuna MA, Godoy JA, Bascompte J. 2013. Assessing the robustness of networks of spatial genetic variation. Ecol. Lett. 16:86–93 [Google Scholar]
  2. Baker SA, Dyer RJ. 2011. Invasion genetics of Microstegium vimineum (Poaceae) within the James River Basin of Virginia, USA. Conserv. Genet. 12:793–803 [Google Scholar]
  3. Cushman SA, McKelvey KS, Hayden J, Schwartz MK. 2006. Gene flow in complex landscapes: testing multiple models with causal modeling. Am. Nat. 168:2553–64 [Google Scholar]
  4. Dell'Acqua M, Zuccolo A, Tuna M, Gianfranceschi L, ME. 2014. Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach. BMC Genom. 15:801 [Google Scholar]
  5. DiLeo MF, Siu JC, Rhodes MK, López-Villalobos A, Redwine A. et al. 2014. The gravity of pollination: integrating at-site features into spatial analyses of contemporary pollen movement. Mol. Ecol. 23:3345–61 [Google Scholar]
  6. Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol. Ecol. 11:2571–81 [Google Scholar]
  7. Dyer RJ. 2007. The evolution of genetic topologies. Theor. Popul. Biol. 71:71–78 [Google Scholar]
  8. Dyer RJ. 2015. Is there such a thing as landscape genetics?. Mol. Ecol. 24:3518–28 [Google Scholar]
  9. Dyer RJ, Chan DM, Gardiakos VA, Meadows CA. 2012. Pollination networks: quantifying pollen pool covariance networks and the influence of intervening landscape on genetic connectivity in the North American understory tree, Cornus florida L. Landsc. Ecol. 27:239–51 [Google Scholar]
  10. Dyer RJ, Nason JD. 2004. Population Graphs: the graph theoretic shape of genetic structure. Mol. Ecol. 13:1713–28 [Google Scholar]
  11. Dyer RJ, Nason JD, Garrick RC. 2010. Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Mol. Ecol. 19:3746–59 [Google Scholar]
  12. Dyer RJ, Westfall RD, Sork VL, Smouse PE. 2004. Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure. Heredity 92:204–11 [Google Scholar]
  13. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–20 [Google Scholar]
  14. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–91 [Google Scholar]
  15. Falconer DR. 1981. Introduction to Quantitative Genetics. London: Longman, 2nd ed.. [Google Scholar]
  16. Falk DA, Holsinger K. 1991. Genetics and Conservation of Rare Plants New York: Oxford Univ. Press [Google Scholar]
  17. Fitzpatrick JM, Carlon DB, Lippe C, Robertson DR. 2011. The West Pacific diversity hotspot as a sink for new species? Population genetic insights from the Indo-Pacific parrotfish Scarus rubroviolaceus. Mol. Ecol. 20:219–34 [Google Scholar]
  18. Foley CJ, Holland JD. 2010. Do flying beetles perceive human-dominated landscapes as complex mosaics or binary patterns?. Landsc. Online 16:1–18 [Google Scholar]
  19. Fortuna MA, Albaladejo RG, Fernández L, Aparicio A, Bascompte J. 2009. Networks of spatial genetic variation across species. PNAS 106:19044–49 [Google Scholar]
  20. Fraser DJ, Lippé C, Bernatchez L. 2004. Consequences of unequal population size, asymmetric gene flow, and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Mol. Ecol. 13:67–80 [Google Scholar]
  21. Garrick RC, Nason JD, Fernández-Manjarrés JF, Dyer RJ. 2013. Ecological co-associations influence species' response to past climatic change: an example from a Sonoran Desert bark beetle. Mol. Ecol. 22:3345–61 [Google Scholar]
  22. Garrick RC, Nason JD, Meadows CA, Dyer RJ. 2009. Not just vicariance: Phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Mol. Ecol. 18:1916–31 [Google Scholar]
  23. Giordano AR, Ridenhour BJ, Storfer A. 2007. The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym). Mol. Ecol. 16:1625–37 [Google Scholar]
  24. Gomulkiewicz R, Thompson JN, Holt RD, Nuismer SL, Hochberg ME. 2000. Hot spots, cold spots, and the geographic mosaic theory of coevolution. Am. Nat. 156:156–74 [Google Scholar]
  25. Greve C, Gimnich F, Hutterer R, Misof B, Haase M. 2012. Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826). PLOS ONE 7:e34339 [Google Scholar]
  26. Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59:1633–38 [Google Scholar]
  27. Herrera-Arroyo ML, Sork VL, González-Rodríguez, Rocha-Ramírez V, Vega E, Oyama K. 2013. Seed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape. Am. J. Bot. 100:1663–71 [Google Scholar]
  28. Jost L. 2008. GST and its relatives do not measure differentiation. Mol. Ecol. 17:4015–26 [Google Scholar]
  29. Kimura M, Weiss WH. 1964. The stepping stone model of genetic structure and the decrease of genetic correlation with distance. Genetics 49:561–76 [Google Scholar]
  30. Klütsch CFC, Dyer RJ, Misof B. 2011. Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera). Conserv. Genet. 13:21–37 [Google Scholar]
  31. Koen EL, Bowman J, Garroway CJ, Wilson PJ. 2013. The sensitivity of genetic connectivity measures to unsampled and under-sampled sites. PLOS ONE 8:e56204 [Google Scholar]
  32. Krafsur ES, Cummings MA, Endsley MA, Marquez JG, Nason JD. 2005. Geographic differentiation in the house fly estimated by microsatellite and mitochondrial variation. J. Hered. 96:502–12 [Google Scholar]
  33. Kutnjak DD, Kuttner M, Niketic, Dullinger S, Schøonswetter, Frajman B. 2014. Escaping to the summits: phylogeography and predicting range dynamics of Cerastium dinaricum, an endangered high mountain plant endemic to the western Balkan Peninsula. Mol. Phylogenetics Evol. 78:365–74 [Google Scholar]
  34. Landguth EL, Cushman SA, Schwartz MK, McKelvey KS, Murphy M, Luikart G. 2010. Quantifying the lag time to detect barriers in landscape genetics. Mol. Ecol. 19:4179–91 [Google Scholar]
  35. Landguth EL, Fedy BC, Oyler-McCance SJ, Gearey AL, Emel SL. et al. 2012. Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern. Mol. Ecol. Resour. 12:276–84 [Google Scholar]
  36. Li J, Coates BS, Kim KS, Bourguet D, Ponsard S. et al. 2014. The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize. J. Hered. 105:642–55 [Google Scholar]
  37. Li MH, Tapio I, Vilkki J, Ivanova Z, Kiselyova T. et al. 2007. The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation. Mol. Ecol. 16:3839–53 [Google Scholar]
  38. Malécot G. 1948. Les mathématiques de l'hérédité Paris: Masson [Google Scholar]
  39. Manel S, Schwartz MK, Luikart G, Taberlet P. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 18:189–97 [Google Scholar]
  40. McRae BH. 2006. Isolation by resistance. Evolution 60:1551–61 [Google Scholar]
  41. McRae BH, Dickson BG, Keitt TH, Shah VB. 2008. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89:2712–24 [Google Scholar]
  42. Milligan BG, Leebens-Mac J, Strand AE. 1994. Conservation genetics: beyond the maintenance of marker diversity. Mol. Ecol. 3:423–35 [Google Scholar]
  43. Murphy MA, Evans JS, Storfer A. 2010. Quantifying Bufo boreas connectivity in Yellowstone National Park with landscape genetics. Ecology 91:1129–37 [Google Scholar]
  44. Nei M. 1973. Analysis of gene diversity in subdivided populations. PNAS 70:3321–23 [Google Scholar]
  45. Neigel JE. 1997. A comparison of alternative strategies for estimating gene flow from genetic markers. Ann. Rev. Ecol. Syst. 28:105–28 [Google Scholar]
  46. Nosil P, Egan SP, Funk DJ. 2008. Heterogeneous genomic differentiation between walking-stick ecotypes: “isolation by adaptation” and multiple roles for divergent selection. Evolution 62:316–36 [Google Scholar]
  47. Noutsos C, Borevitz JO, Hodges SA. 2014. Gene flow between nascent species: genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens. Mol. Ecol. 23:5589–98 [Google Scholar]
  48. Pagán I, Holguín Á. 2013. Reconstructing the timing and dispersion routes of HIV-1 subtype B epidemics in the Caribbean and Central America. PLOS ONE 8:e69218 [Google Scholar]
  49. Papa R, Gepts P. 2003. Asymmetry of gene flow and differential geographic structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor. Appl. Genet. 106:239–50 [Google Scholar]
  50. Paz-Vinas I, Quéméré E, Chikhi L, Loot S, Blanchet S. 2013. The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data. Mol. Ecol. 22:3279–91 [Google Scholar]
  51. Pinto N, Keitt TH. 2009. Beyond the least-cost path: evaluating corridor redundancy using a graph-theoretic approach. Land. Ecol. 24:253–66 [Google Scholar]
  52. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–59 [Google Scholar]
  53. Pritchard JK, Wen X, Falush D. 2007. Documentation for structure software: Version 2.2 Tech. Doc., Univ. Chicago [Google Scholar]
  54. Quintela M, Johansson MP, Kristjánsson, Barreiro R, Laurila A. 2014. AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod. PLOS ONE 9:e101821 [Google Scholar]
  55. Schwartz MK, McKelvey KS. 2009. Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv. Gen. 10:441–52 [Google Scholar]
  56. Schwartz MK, Mills LS, McKelvey K, Ruggiero LS, Allendorf FW. 2002. DNA reveals high dispersal synchronizing the population dynamics of Canada lynx. Nature 415:520–22 [Google Scholar]
  57. Slatkin M. 1993. Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264–79 [Google Scholar]
  58. Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–62 [Google Scholar]
  59. Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape. I. Male gamete heterogeneity among females. Evolution 55:260–71 [Google Scholar]
  60. Smouse PE, Wood JW. 1987. The genetic demography of the Gainj of Papua New Guinea: functional models of migration and their genetic implications. Mammalian Dispersal Patterns: The Effects of Social Structure on Population Genetics DB Chepko-Sade, ZT Halpin Chicago: Chicago Univ. Press [Google Scholar]
  61. Wang IJ, Glor RE, Losos JB. 2013. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol. Lett. 16:175–82 [Google Scholar]
  62. Wasserman S, Faust K. 2005. Social Network Analysis: Methods and Applications Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  63. Wegier A, Piñeyro-Nelson A, Alarcón J, Gálvez-Mariscal A, Álvarez-Buylla ER, Pinero D. 2011. Recent long-distance transgene flow into wild populations conforms to historical patterns of gene flow in cotton (Gossypium hirsutum) at its centre of origin. Mol. Ecol. 20:4182–94 [Google Scholar]
  64. Widmer I, Del Grande F, Excoffier L, Holderegger R, Keller C. et al. 2012. European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiont. Mol. Ecol. 21:5827–44 [Google Scholar]
  65. Whitlock M. 2011. GST and D do not replace FST. Mol. Ecol. 20:1083–91 [Google Scholar]
  66. Wright S. 1931. Evolution in Mendelian populations. Genetics 16:97–159 [Google Scholar]
  67. Wright S. 1943. Isolation by distance. Genetics 28:114–38 [Google Scholar]
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