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Applications of Landscape Genetics to Study the Effect of Varying Landscapes and Environmental Challenges in Plant Populations

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Molecular Approaches in Plant Biology and Environmental Challenges

Part of the book series: Energy, Environment, and Sustainability ((ENENSU))

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Abstract

Evolutionary processes like adaptation, dispersal and genetic drift play an important role in shaping a geographical habitat of the organisms and species. To study these processes in a geographical context is fundamental for the biogeographical studies. Nevertheless, the introduction of new molecular methods allowed a stronger assessment of the associations between the patterns of genetic diversity between populations and the micro-evolutionary processes governing them. Traditionally the use of molecular methods has been applied to study the evolutionary biology, phylogenetics and population structure of the plant species to formulate conservation programs for declining populations and these approaches are collectively referred to as Molecular Ecology. Recently a more robust approach, which has emerged as an altogether separate discipline known as Landscape Genetics has been used for studying the effects of changing environment due to human intervention, habitat fragmentation and effect of varying landscapes. This approach takes help from the disciplines of Molecular Ecology, Population Genetics and Biogeography, aided by the recent advances in simulation and remote sensing technology. Landscape genetics has recently evolved as a discipline, through which, we can incorporate the effect of local habitats and connectivity of the landscapes to analysis of gene flow. It also allows us to have a better understanding of local adaptation processes by helping to develop novel hypothesis on impending selection forces. It plays ever more significant role in species conservation and management studies. Recent advances in molecular tools and statistic has also aided researchers to device more precise strategies for these type of studies. The improvements in sequencing technologies have profoundly enhanced our ability to study genetic variation in wild species, which has opened up new and unparalleled opportunities for genetic analysis in conservation biology. In this chapter we will have an insight on the basic aspects of this discipline, tools and methods used in it and the advent of molecular biology techniques, which serve as the backbone of the research projects in this discipline.

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References

  • Allendorf FW, Luikart G (2009) Conservation and the genetics of populations. Wiley. ISBN 1444309056

    Google Scholar 

  • Arthur G (1935) Tansley the use and abuse of vegetational concepts and terms. Ecology 16:284–307

    Article  Google Scholar 

  • Balkenhol N, Cushman S, Storfer A, Waits L (2015) Landscape genetics: concepts, methods, applications. John Wiley & Sons. ISBN 1118525280

    Google Scholar 

  • Balloux F, Brunner H, Lugon-Moulin N, Hausser J, Goudet J (2000) Microsatellites can be misleading: an empirical and simulation study. Evolution (N. Y) 54:1414–1422

    Google Scholar 

  • Bender DJ, Contreras TA, Fahrig L (1998) Habitat loss and population decline: a meta-analysis of the patch size effect. Ecology 79:517–533

    Article  Google Scholar 

  • Birky CW (1978) Transmission genetics of mitochondria and chloroplasts. Annu Rev Genet 12:471–512

    Article  PubMed  Google Scholar 

  • Blair C, Weigel DE, Balazik M, Keeley ATH, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N (2012) A simulation-based evaluation of methods for inferring linear barriers to gene flow. Mol Ecol Resour 12:822–833

    Article  PubMed  Google Scholar 

  • Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 16:3737–3758

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Franklin JF, Spies TA (1992) Vegetation responses to edge environments in old-growth douglas-fir forests. Ecol Appl 2:387–396

    Article  PubMed  Google Scholar 

  • Chen C, Durand E, Forbes F, François O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7:747–756

    Article  Google Scholar 

  • Coop G, Witonsky D, Di Rienzo A, Pritchard JK (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics 185:1411–1423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Corander J, Marttinen P, Sirén J, Tang J (2008) Enhanced bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinform 9:539

    Article  Google Scholar 

  • Cushman SA, Landguth EL (2012) Multi-taxa population connectivity in the Northern Rocky Mountains. Ecol Modell 231:101–112

    Article  Google Scholar 

  • de Casenave JL, Pelotto J, Protomastro J (1995) Edge-interior differences in vegetation structure and composition in a Chaco semi-arid forest, Argentina. Ecol Manag 72:61–69

    Google Scholar 

  • Dyer R (2014) GSTUDIO: analyses and functions related to the spatial analysis of genetic marker data. R package version 1.3

    Google Scholar 

  • Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB (2010) Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol Ecol 19:3789–3805

    Google Scholar 

  • El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839

    Google Scholar 

  • Fahrig L (2003) Effects of habitat fragmentation on biodiversity. Annu Rev Ecol Evol Syst 34:487–515

    Article  Google Scholar 

  • Flather C, Bevers M (2002) Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement. Am Nat 159:40–56

    Article  PubMed  Google Scholar 

  • Frankham R, Briscoe DA, Ballou JD (2002) Introduction to conservation genetics. Cambridge university press, ISBN 0521639859

    Google Scholar 

  • Gaines M, Diffendorfer J, Tamarin RH (1997) The effects of habitat fragmentation on the genetic structure of small mammal populations. J Hered 88:194–304

    Article  Google Scholar 

  • García-Ramos G, Rodríguez D (2002) Evolutionary speed of species invasions. Evolution (N.Y) 56:661–669

    Google Scholar 

  • Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 10:915–934

    Article  CAS  PubMed  Google Scholar 

  • Gates J, Mosher JA (1981) A functional approach to estimating habitat edge width for birds. Am Midl Nat 189–192

    Google Scholar 

  • Gillham NW (1974) Genetic analysis of the chloroplast and mitochondrial genomes. Annu Rev Genet 8:347–391

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Google Scholar 

  • Guillot G, Mortier F, Estoup A (2005) GENELAND: a computer package for landscape genetics. Mol Ecol Notes 5:712–715

    Article  CAS  Google Scholar 

  • Hanski I (1998) Metapopulation dynamics. Nature 396:41

    Article  CAS  Google Scholar 

  • Hartl DL, Clark AG, Clark AG (1997) Principles of population genetics Sinauer Associates, vol 116. Sunderland, MA

    Google Scholar 

  • Hedrick PW (1995) Gene flow and genetic restoration: the Florida panther as a case study. Conserv Biol 9:996–1007

    Article  PubMed  Google Scholar 

  • Hill MF, Caswell H (1999) Habitat fragmentation and extinction thresholds on fractal landscapes. Ecol Lett 2:121–127

    Article  Google Scholar 

  • Johnson A, Wiens J, Milne B (1992) TO crist animal movements and population dynamics in heterogeneous landscapes. Landsc Ecol 7:63–75

    Article  Google Scholar 

  • Joost S, Bonin A, Bruford MW, Després L, Conord C, Erhardt G, Taberlet P (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol 16:3955–3969

    Article  CAS  PubMed  Google Scholar 

  • Jost L (2008) GST and its relatives do not measure differentiation. Mol Ecol 17:4015–4026

    Article  PubMed  Google Scholar 

  • Kalinowski ST (2004) Counting alleles with rarefaction private alleles and hierarchical sampling designs. Conserv Genet 5:539–543

    Article  CAS  Google Scholar 

  • Kranstauber B, Safi K, Bartumeus F (2014) Bivariate Gaussian bridges: directional factorization of diffusion in Brownian bridge models. Mov Ecol 2:5

    Article  PubMed  PubMed Central  Google Scholar 

  • Latch E, Rhodes OE (2005) The effects of gene flow and population isolation on the genetic structure of reintroduced wild turkey populations: agenetic signatures of source populations. Conserv Genet 6:981–997

    Article  CAS  Google Scholar 

  • Leberg PL (2008) Estimating allelic richness: effects of sample size and bottlenecks. Mol Ecol 11:2445–2449

    Article  Google Scholar 

  • Levin SA (1992) The problem of pattern and scale in ecology: the Robert H. MacArthur Award Lecture Ecology 73:1943–1967

    Google Scholar 

  • Levins R (1969) Some demographic and genetic consequences of environmental heterogeneity for biological control. Am Entomol 15:237–240

    Google Scholar 

  • Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197

    Article  Google Scholar 

  • Manel S, Poncet BN, Legendre P, Gugerli F, Holderegger R (2010a) Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Mol Ecol 19:3824–3835

    Google Scholar 

  • Manel S, Joost S, Epperson BK (2010b) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol 19:3760–3772

    Article  CAS  PubMed  Google Scholar 

  • Mangel M, Clark CW (1996) Towards a unifield foraging theory. Ecology 67:1127–1138

    Article  Google Scholar 

  • Manicacci D, Olivieri I, Perrot V, Atlan A, Gouyon P-H, Prosperi J-M, Couvet D (1992) Landscape ecology: population genetics at the metapopulation level. Landsc Ecol 6:147–159

    Article  Google Scholar 

  • McCoy ED, Mushinsky HR (1999) Habitat fragmentation and the abundances of vertebrates in the Florida scrub. Ecology 80:2526–2538

    Article  Google Scholar 

  • McGarigal K, Cushman SA (2002) Comparative evaluation of experimental approaches to the study of habitat fragmentation effects. Ecol Appl 12:335–345

    Article  Google Scholar 

  • Meirmans PG, Hedrick PW (2011) Assessing population structure: FST and related measures. Mol Ecol Resour 11:5–18

    Article  PubMed  Google Scholar 

  • Merow C, Dahlgren J, Metcalf CJE (2014) Advancing population ecology with integral projection models: a practical guide. Methods Ecol Evol 5:99–110

    Article  Google Scholar 

  • Merriam G, Kozakiewicz M, Tsuchiya E, Hawley K (1989) Barriers as boundaries for metapopulations and demes of Peromyscus leucopus in farm landscapes. Landsc Ecol 2:227–235

    Article  Google Scholar 

  • Monmonier MS (2010) Maximum-difference barriers: an alternative numerical regionalization method. Geogr Anal 5:245–261

    Article  Google Scholar 

  • Morin P, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  • Murphy MA, Evans JS, Cushman SA, Storfer A (2008) Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies. Ecography (Cop.) 31:685–697

    Google Scholar 

  • Naveh Z, Lieberman AS (2013) Landscape ecology: theory and application. Springer Science & Business Media, ISBN 1475723318

    Google Scholar 

  • Neale DB, Marshall KA, Sederoff RR (1989) Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens. In: Don Endl D (ed) Proceedings of the National Academy of Sciences, vol 86, pp 9347–9349

    Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    Google Scholar 

  • Pamilo P (1988) Genetic variation in heterogeneous environments. In: Proceedings of the annales zoologici fennici. JSTOR, pp 99–106

    Google Scholar 

  • Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  • Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Robbins C, Dawson D, Dowell BA (1989) Habitat area requirements of breeding forest birds of the middle Atlantic states. Wildl Monogr 3–34

    Google Scholar 

  • Rousset F (2008) Genepop’007: a complete re‐implementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Google Scholar 

  • Rukke BA (2000) Effects of habitat fragmentation: increased isolation and reduced habitat size reduces the incidence of dead wood fungi beetles in a fragmented forest landscape. Ecography (Cop.) 23:492–502

    Google Scholar 

  • Safner T, Miller M, McRae B, Fortin MJ (2011) Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics. Int J Mol Sci 12:865–889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmiegelow F, Mönkkönen M (2002) Habitat loss and fragmentation in dynamic landscapes: avian perspectives from the boreal forest. Ecol Appl 12:375–389

    Google Scholar 

  • Segelbacher G, Cushman SA, Epperson BK, Fortin MJ, Francois O, Hardy OJ, Holderegger R, Taberlet P, Waits LP, Manel S (2010) Applications of landscape genetics in conservation biology: concepts and challenges. Conserv Genet 11:375–385

    Google Scholar 

  • Shirk AJ, Cushman SA (2011) sGD: software for estimating spatially explicit indices of genetic diversity. Mol Ecol Resour 11:922–934

    Article  CAS  PubMed  Google Scholar 

  • Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    Google Scholar 

  • Stinchcombe J, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity (Edinb) 100:158

    Article  CAS  Google Scholar 

  • Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP (2010) Landscape genetics: where are we now? Mol Ecol 19:3496–3517

    Google Scholar 

  • Tischendorf L, Bender DJ, Fahrig L (2003) Evaluation of patch isolation metrics in mosaic landscapes for specialist versus generalist dispersers. Landsc Ecol 18:41–50

    Google Scholar 

  • Turner MG (2005) Landscape ecology: what is the state of the science? Annu Rev Ecol Evol Syst 36:319–344

    Article  Google Scholar 

  • Vance MD, Fahrig L, Flather CH (2003) Effect of reproductive rate on minimum habitat requirements of forest-breeding birds. Ecology 84:2643–2653

    Article  Google Scholar 

  • Virgós E (2001) Role of isolation and habitat quality in shaping species abundance: a test with badgers (Meles meles L.) in a gradient of forest fragmentation. J Biogeogr 28:381–389

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wales BA (1972) Vegetation analysis of north and south edges in a mature oak-hickory forest. Ecol Monogr 42:451–471

    Article  Google Scholar 

  • Warnes G (2015) With contributions from Gregor Gorjanc; Friedrich Leisch and Michael Man. genetics: Population Genetics. R package version 1.3. 8.1

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F‐statistics for the analysis of population structure. Evolution (N.Y) 38:1358–1370

    Google Scholar 

  • Wiens J, Chr N, Van Horne B, Ims RA (1993) Ecological mechanisms and landscape ecology. Oikos 66:369–380

    Article  Google Scholar 

  • Wilcove DS, McLellan CH, Dobson AP (1986) Habitat fragmentation in the temperate zone. Conserv Biol 6:237–256

    Google Scholar 

  • With K, King AW (1999) Extinction thresholds for species in fractal landscapes. Conserv Biol 13:314–326

    Article  Google Scholar 

  • Womble WH (1951) Differential systematics. Science (80-.) 114:315–322

    Google Scholar 

  • Wright S (1931) Evolution in Mendelian populations. Genetics 16:97

    Google Scholar 

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Correspondence to Kashmir Singh .

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Nag, A., Alok, A., Singh, K. (2019). Applications of Landscape Genetics to Study the Effect of Varying Landscapes and Environmental Challenges in Plant Populations. In: Singh, S., Upadhyay, S., Pandey, A., Kumar, S. (eds) Molecular Approaches in Plant Biology and Environmental Challenges. Energy, Environment, and Sustainability. Springer, Singapore. https://doi.org/10.1007/978-981-15-0690-1_9

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