Citation: | Wang TR,Qiu YX. Application and prospects of landscape genomics in conservation biology[J]. Plant Science Journal,2023,41(6):741−750. DOI: 10.11913/PSJ.2095-0837.23166 |
Biodiversity serves as the foundation of human survival and development yet faces significant threats from rapid global climate fluctuations. Conservation biology seeks to address this global biodiversity crisis by developing more effective conservation strategies. By analyzing the relationship between genotypes and environmental factors, landscape genomics can reveal the adaptive genetic variations and evolutionary responses of species to climate change, leading to the rapid development of conservation biology. In this review, we discuss the major methodologies used to analyze the distribution patterns of adaptive genetic variation in species. We also summarize recent findings in landscape genomics as applied to the conservation of plants and animals. Finally, we address current challenges and suggest future research directions in the use of landscape genomics for conservation biology, offering targeted recommendations.
[1] |
Maclaurin J, Sterelny K. What is Biodiversity?[M]. Chicago: The University of Chicago Press, 2008: 1-9.
|
[2] |
Jenkins M. Prospects for biodiversity[J]. Science,2003,302 (5648):1175−1177. doi: 10.1126/science.1088666
|
[3] |
Watson R, Baste I, Larigauderie A, Leadley P, Pascual U, et al. Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental science-policy platform on biodiversity and ecosystem services[J]. IPBES Secretariat: Bonn, Germany, 2019: 22-47.
|
[4] |
Ceballos G,Ehrlich PR,Raven PH. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction[J]. Proc Natl Acad Sci USA,2020,117 (24):13596−13602. doi: 10.1073/pnas.1922686117
|
[5] |
Pimm SL,Russell GJ,Gittleman JL,Brooks TM. The future of biodiversity[J]. Science,1995,269 (5222):347−350. doi: 10.1126/science.269.5222.347
|
[6] |
Ellegren H,Galtier N. Determinants of genetic diversity[J]. Nat Rev Genet,2016,17 (7):422−433. doi: 10.1038/nrg.2016.58
|
[7] |
Hughes AR,Inouye BD,Johnson MTJ,Underwood N,Vellend M. Ecological consequences of genetic diversity[J]. Ecol Lett,2008,11 (6):609−623. doi: 10.1111/j.1461-0248.2008.01179.x
|
[8] |
Soulé ME. What is conservation biology? A new synthetic discipline addresses the dynamics and problems of perturbed species,communities,and ecosystems[J]. BioScience,1985,35 (11):727−734. doi: 10.2307/1310054
|
[9] |
蒋志刚, 马克平, 韩兴国. 保护生物学[M]. 杭州: 浙江科学技术出版社, 1997: 3-11.
|
[10] |
马克平. 保护生物学、保护生态学与生物多样性科学[J]. 生物多样性,2016,24(2):125−126. doi: 10.17520/biods.2016058
Ma KP. Conservation biology,conservation ecology and biodiversity science[J]. Biodiversity Science,2016,24 (2):125−126. doi: 10.17520/biods.2016058
|
[11] |
Frankham R. Genetics and conservation biology[J]. C R Biol, 2003, 326 (S1): 22-29.
|
[12] |
Van Dyke F. Conservation Biology: Foundations, Concepts, Applications[M]. 2nd ed. New York: Springer, 2008: 83-119.
|
[13] |
Caughley G. Directions in conservation biology[J]. J Anim Ecol,1994,63 (2):215−244. doi: 10.2307/5542
|
[14] |
Wan QH,Wu H,Fujihara T,Fang SG. Which genetic marker for which conservation genetics issue?[J]. Electrophoresis,2004,25 (14):2165−2176. doi: 10.1002/elps.200305922
|
[15] |
Kinnison MT,Hendry AP,Stockwell CA. Contemporary evolution meets conservation biology Ⅱ: impediments to integration and application[J]. Ecol Res,2007,22 (6):947−954. doi: 10.1007/s11284-007-0416-6
|
[16] |
Pertoldi C,Bijlsma R,Loeschcke V. Conservation genetics in a globally changing environment:present problems,paradoxes and future challenges[J]. Biodivers Conserv,2007,16 (14):4147−4163. doi: 10.1007/s10531-007-9212-4
|
[17] |
Segelbacher G,Cushman SA,Epperson BK,Fortin MJ,Francois O,et al. Applications of landscape genetics in conservation biology:concepts and challenges[J]. Conserv Genet,2010,11 (2):375−385. doi: 10.1007/s10592-009-0044-5
|
[18] |
Hu TS,Chitnis N,Monos D,Dinh A. Next-generation sequencing technologies:an overview[J]. Hum Immunol,2021,82 (11):801−811. doi: 10.1016/j.humimm.2021.02.012
|
[19] |
Fitzpatrick MC,Keller SR. Ecological genomics meets community-level modelling of biodiversity:mapping the genomic landscape of current and future environmental adaptation[J]. Ecol Lett,2015,18 (1):1−16. doi: 10.1111/ele.12376
|
[20] |
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[J]. Tree Genet Genomes,2013,9 (4):901−911. doi: 10.1007/s11295-013-0596-x
|
[21] |
王天瑞,冯力,杜芳. 生态适应研究新方法:从种群遗传学到景观基因组学[J]. 中国科学:生命科学,2021,51(2):167−178. doi: 10.1360/SSV-2020-0265
Wang TR,Feng L,Du F. New approaches for ecological adaptation study:from population genetics to landscape genomics[J]. Sci Sin Vitae,2021,51 (2):167−178. doi: 10.1360/SSV-2020-0265
|
[22] |
Feng L,Du FK. Landscape genomics in tree conservation under a changing environment[J]. Front Plant Sci,2022,13:822217. doi: 10.3389/fpls.2022.822217
|
[23] |
Holderegger R,Kamm U,Gugerli F. Adaptive vs. neutral genetic diversity:implications for landscape genetics[J]. Landscape Ecol,2006,21 (6):797−807. doi: 10.1007/s10980-005-5245-9
|
[24] |
Sork VL. Genomic studies of local adaptation in natural plant populations[J]. J Hered,2018,109 (1):3−15.
|
[25] |
Allendorf FW,Hohenlohe PA,Luikart G. Genomics and the future of conservation genetics[J]. Nat Rev Genet,2010,11 (10):697−709. doi: 10.1038/nrg2844
|
[26] |
Shafer ABA,Wolf JBW,Alves PC,Bergström L,Bruford MW,et al. Genomics and the challenging translation into conservation practice[J]. Trends Ecol Evol,2015,30 (2):78−87. doi: 10.1016/j.tree.2014.11.009
|
[27] |
De Greef E,Einfeldt AL,Miller PJO,Ferguson SH,Garroway CJ,et al. Genomics reveal population structure,evolutionary history,and signatures of selection in the northern bottlenose whale,Hyperoodon ampullatus[J]. Mol Ecol,2022,31 (19):4919−4931. doi: 10.1111/mec.16643
|
[28] |
Kearns AM,Campana MG,Slikas B,Berry L,Saitoh T,et al. Conservation genomics and systematics of a near-extinct island radiation[J]. Mol Ecol,2022,31 (7):1995−2012. doi: 10.1111/mec.16382
|
[29] |
Yang L,Wei FW,Zhan XJ,Fan HZ,Zhao PP,et al. Evolutionary conservation genomics reveals recent speciation and local adaptation in threatened takins[J]. Mol Biol Evol,2022,39 (6):msac111. doi: 10.1093/molbev/msac111
|
[30] |
Sang YP,Long ZQ,Dan XM,Feng JJ,Shi TT,et al. Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia[J]. Nat Commun,2022,13 (1):6541. doi: 10.1038/s41467-022-34206-8
|
[31] |
Excoffier L,Hofer T,Foll M. Detecting loci under selection in a hierarchically structured population[J]. Heredity,2009,103 (4):285−298. doi: 10.1038/hdy.2009.74
|
[32] |
Foll M,Gaggiotti O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers:a Bayesian perspective[J]. Genetics,2008,180 (2):977−993. doi: 10.1534/genetics.108.092221
|
[33] |
Frichot E,Schoville SD,Bouchard G,François O. Testing for associations between loci and environmental gradients using latent factor mixed models[J]. Mol Biol Evol,2013,30 (7):1687−1699. doi: 10.1093/molbev/mst063
|
[34] |
Joost S,Bonin A,Bruford MW,Després L,Conord C,et al. A spatial analysis method (SAM) to detect candidate loci for selection:towards a landscape genomics approach to adaptation[J]. Mol Ecol,2007,16 (18):3955−3969. doi: 10.1111/j.1365-294X.2007.03442.x
|
[35] |
Hohenlohe PA,Bassham S,Etter PD,Stiffler N,Johnson EA,Cresko WA. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags[J]. PLoS Genet,2010,6 (2):e1000862. doi: 10.1371/journal.pgen.1000862
|
[36] |
Whitlock MC,Lotterhos KE. Reliable detection of loci responsible for local adaptation:inference of a null model through trimming the distribution of FST[J]. Am Nat,2015,186 (S1):S24−S36. doi: 10.1086/682949
|
[37] |
Luu K,Bazin E,Blum MGB. Pcadapt:an R package to perform genome scans for selection based on principal component analysis[J]. Mol Ecol Resour,2017,17 (1):67−77. doi: 10.1111/1755-0998.12592
|
[38] |
Privé F,Luu K,Vilhjálmsson BJ,Blum MGB. Performing highly efficient genome scans for local adaptation with R package pcadapt version 4[J]. Mol Biol Evol,2020,37 (7):2153−2154. doi: 10.1093/molbev/msaa053
|
[39] |
Beaumont MA,Nichols RA. Evaluating loci for use in the genetic analysis of population structure[J]. Proc Roy Soc B:Biol Sci,1996,263 (1377):1619−1626. doi: 10.1098/rspb.1996.0237
|
[40] |
Bonhomme M,Chevalet C,Servin B,Boitard S,Abdallah J,et al. Detecting selection in population trees:the Lewontin and Krakauer test extended[J]. Genetics,2010,186 (1):241−262. doi: 10.1534/genetics.110.117275
|
[41] |
Coop G,Witonsky D,Di Rienzo A,Pritchard JK. Using environmental correlations to identify loci underlying local adaptation[J]. Genetics,2010,185 (4):1411−1423. doi: 10.1534/genetics.110.114819
|
[42] |
De Jong MJ,Lovatt F,Hoelzel AR. Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events[J]. Mol Ecol,2021,30 (7):1642−1658. doi: 10.1111/mec.15837
|
[43] |
Eveno E,Collada C,Guevara MA,Léger V,Soto A,et al. Contrasting patterns of selection at Pinus pinaster Ait. drought stress candidate genes as revealed by genetic differentiation analyses[J]. Mol Biol Evol,2008,25 (2):417−437. doi: 10.1093/molbev/msm272
|
[44] |
R Core Team. R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria[EB/OL]. 2016. http: //www.R-project.org/.
|
[45] |
Naimi B,Hamm NAS,Groen TA,Skidmore AK,Toxopeus AG. Where is positional uncertainty a problem for species distribution modelling?[J]. Ecography,2014,37 (2):191−203. doi: 10.1111/j.1600-0587.2013.00205.x
|
[46] |
Günther T,Coop G. Robust identification of local adaptation from allele frequencies[J]. Genetics,2013,195 (1):205−220. doi: 10.1534/genetics.113.152462
|
[47] |
Caye K,Jumentier B,Lepeule J,François O. LFMM 2:fast and accurate inference of gene-environment associations in genome-wide studies[J]. Mol Biol Evol,2019,36 (4):852−860. doi: 10.1093/molbev/msz008
|
[48] |
Gautier M. Genome-wide scan for adaptive divergence and association with population-specific covariates[J]. Genetics,2015,201 (4):1555−1579. doi: 10.1534/genetics.115.181453
|
[49] |
Legendre P, Legendre L. Numerical Ecology[M]. 3rd ed. Amsterdam: Elsevier, 2012: 641-667.
|
[50] |
De Villemereuil P,Gaggiotti OE. A new FST-based method to uncover local adaptation using environmental variables[J]. Methods Ecol Evol,2015,6 (11):1248−1258. doi: 10.1111/2041-210X.12418
|
[51] |
Wright S. Isolation by distance[J]. Genetics,1943,28 (2):114−138. doi: 10.1093/genetics/28.2.114
|
[52] |
Diniz-Filho JAF,Soares TN,Lima JS,Dobrovolski R,Landeiro VL,et al. Mantel test in population genetics[J]. Genet Mol Biol,2013,36 (4):475−485. doi: 10.1590/S1415-47572013000400002
|
[53] |
Van den Wollenberg AL. Redundancy analysis an alternative for canonical correlation analysis[J]. Psychometrika,1977,42 (2):207−219. doi: 10.1007/BF02294050
|
[54] |
Goudet J. HIERFSTAT,a package for R to compute and test hierarchical F-statistics[J]. Mol Ecol Notes,2005,5 (1):184−186. doi: 10.1111/j.1471-8286.2004.00828.x
|
[55] |
Hijmans RJ. Introduction to the "geosphere" package[EB/OL]. R Package Version 1.5.18. (2022-11-15). http: //CRAN.R-project.org/package=geosphere.
|
[56] |
Goslee SC,Urban DL. The ecodist package for dissimilarity-based analysis of ecological data[J]. J Stat Softw,2007,22 (7):1−19.
|
[57] |
Guillot G,Rousset F. Dismantling the Mantel tests[J]. Methods Ecol Evol,2013,4 (4):336−344. doi: 10.1111/2041-210x.12018
|
[58] |
Capblancq T,Luu K,Blum MGB,Bazin E. Evaluation of redundancy analysis to identify signatures of local adaptation[J]. Mol Ecol Resour,2018,18 (6):1223−1233. doi: 10.1111/1755-0998.12906
|
[59] |
Oksanen J. Vegan: community ecology package[EB/OL]. R Package Version 2.6.4. (2022-10-11). http: //CRAN.R-project.org/package=vegan.
|
[60] |
Borcard D, Gillet F, Legendre P. Numerical Ecology with R[M]. New York: Springer, 2011: 175-178.
|
[61] |
Hecht BC,Matala AP,Hess JE,Narum SR. Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range[J]. Mol Ecol,2015,24 (22):5573−5595. doi: 10.1111/mec.13409
|
[62] |
De Mazancourt C,Johnson E,Barraclough TG. Biodiversity inhibits species' evolutionary responses to changing environments[J]. Ecol Lett,2008,11 (4):380−388. doi: 10.1111/j.1461-0248.2008.01152.x
|
[63] |
Keller SR,Levsen N,Olson MS,Tiffin P. Local adaptation in the flowering-time gene network of balsam poplar,Populus balsamifera L.[J]. Mol Biol Evol,2012,29 (10):3143−3152. doi: 10.1093/molbev/mss121
|
[64] |
Ellis N,Smith SJ,Pitcher CR. Gradient forests:calculating importance gradients on physical predictors[J]. Ecology,2012,93 (1):156−168. doi: 10.1890/11-0252.1
|
[65] |
Ferrier S,Manion G,Elith J,Richardson K. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment[J]. Divers Distrib,2007,13 (3):252−264. doi: 10.1111/j.1472-4642.2007.00341.x
|
[66] |
Gougherty AV,Keller SR,Fitzpatrick MC. Maladaptation,migration and extirpation fuel climate change risk in a forest tree species[J]. Nat Climate Change,2021,11 (2):166−171. doi: 10.1038/s41558-020-00968-6
|
[67] |
Manion G, Lisk M, Ferrier S, Nieto-Lugilde D, Fitzpatrick MC. GDM: functions for generalized dissimilarity modeling[EB/OL]. R Package Version 1.5.0. (2022-12-01). https: //CRAN.R-project.org/package=gdm
|
[68] |
Capblancq T,Fitzpatrick MC,Bay RA,Exposito-Alonso M,Keller SR. Genomic prediction of (mal) adaptation across current and future climatic landscapes[J]. Annu Rev Ecol Evol Syst,2020,51:245−269. doi: 10.1146/annurev-ecolsys-020720-042553
|
[69] |
Rellstab C,Zoller S,Walthert L,Lesur I,Pluess AR,et al. Signatures of local adaptation in candidate genes of oaks (Quercus spp. ) with respect to present and future climatic conditions[J]. Mol Ecol,2016,25 (23):5907−5924. doi: 10.1111/mec.13889
|
[70] |
Pina-Martins F,Baptista J,Pappas Jr G,Paulo OS. New insights into adaptation and population structure of cork oak using genotyping by sequencing[J]. Global Change Biol,2019,25 (1):337−350. doi: 10.1111/gcb.14497
|
[71] |
Neale DB,Kremer A. Forest tree genomics:growing resources and applications[J]. Nat Rev Genet,2011,12 (2):111−122. doi: 10.1038/nrg2931
|
[72] |
Eckert CG,Samis KE,Lougheed SC. Genetic variation across species' geographical ranges:the central–marginal hypothesis and beyond[J]. Mol Ecol,2008,17 (5):1170−1188. doi: 10.1111/j.1365-294X.2007.03659.x
|
[73] |
Yuan S,Shi Y,Zhou BF,Liang YY,Chen XY,et al. Genomic vulnerability to climate change in Quercus acutissima,a dominant tree species in East Asian deciduous forests[J]. Mol Ecol,2023,32 (7):1639−1655. doi: 10.1111/mec.16843
|
[74] |
Du FK,Wang TR,Wang YY,Ueno S,de Lafontaine G. Contrasted patterns of local adaptation to climate change across the range of an evergreen oak,Quercus aquifolioides[J]. Evol Appl,2020,13 (9):2377−2391. doi: 10.1111/eva.13030
|
[75] |
Cao YN,Zhu SS,Chen J,Comes HP,Wang IJ,et al. Genomic insights into historical population dynamics,local adaptation,and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae)[J]. Evol Appl,2020,13 (8):2038−2055. doi: 10.1111/eva.12960
|
[76] |
Wang YH,Zhang L,Zhou YC,Ma WX,Li MY,et al. Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China[J]. Front Plant Sci,2023,14:1150704.
|
[77] |
Van Daele F,Honnay O,de Kort H. Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb[J]. Evol Appl,2022,15 (11):1859−1874. doi: 10.1111/eva.13485
|
[78] |
Faske TM,Agneray AC,Jahner JP,Sheta LM,Leger EA,Parchman TL. Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush,a foundational Great Basin shrub[J]. Evol Appl,2021,14 (12):2881−2900. doi: 10.1111/eva.13323
|
[79] |
Maier PA,Vandergast AG,Bohonak AJ. Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)[J]. Evol Appl,2023,16 (1):74−97. doi: 10.1111/eva.13511
|
[80] |
Bay RA,Harrigan RJ,Underwood VL,Gibbs HL,Smith TB,Ruegg K. Genomic signals of selection predict climate-driven population declines in a migratory bird[J]. Science,2018,359 (6371):83−86. doi: 10.1126/science.aan4380
|
[81] |
Jaffé R,Veiga JC,Pope NS,Lanes ÉCM,Carvalho CS,et al. Landscape genomics to the rescue of a tropical bee threatened by habitat loss and climate change[J]. Evol Appl,2019,12 (6):1164−1177. doi: 10.1111/eva.12794
|
[82] |
Dawson TP,Jackson ST,House JI,Prentice IC,Mace GM. Beyond predictions:biodiversity conservation in a changing climate[J]. Science,2011,332 (6025):53−58. doi: 10.1126/science.1200303
|
[83] |
Hylander K,Greiser C,Christiansen DM,Koelemeijer IA. Climate adaptation of biodiversity conservation in managed forest landscapes[J]. Conserv Biol,2022,36 (3):e13847.
|
[84] |
Pacifici M,Foden WB,Visconti P,Watson JEM,Butchart SHM,et al. Assessing species vulnerability to climate change[J]. Nat Climate Change,2015,5 (3):215−224. doi: 10.1038/nclimate2448
|
[85] |
Li Y,Zhang XX,Mao RL,Yang J,Miao CY,et al. Ten years of landscape genomics:challenges and opportunities[J]. Front Plant Sci,2017,8:2136. doi: 10.3389/fpls.2017.02136
|
[86] |
Di Pierro EA,Mosca E,Rocchini D,Binelli G,Neale DB,La Porta N. Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps[J]. Tree Genet Genomes,2016,12 (2):16. doi: 10.1007/s11295-016-0972-4
|
[87] |
Hand BK,Lowe WH,Kovach RP,Muhlfeld CC,Luikart G. Landscape community genomics:understanding eco-evolutionary processes in complex environments[J]. Trends Ecol Evol,2015,30 (3):161−168. doi: 10.1016/j.tree.2015.01.005
|
[88] |
Avise JC. Phylogeography: the History and Formation of Species[M]. Cambridge: Harvard University Press, 2000: 1-10.
|
[89] |
Qiu YX,Fu CX,Comes HP. Plant molecular phylogeography in China and adjacent regions:tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora[J]. Mol Phylogenet Evol,2011,59 (1):225−244. doi: 10.1016/j.ympev.2011.01.012
|
[90] |
邱英雄,鹿启祥,张永华,曹亚男. 东亚第三纪孑遗植物的亲缘地理学:现状与趋势[J]. 生物多样性,2017,25(2):136−146.
Qiu YX,Lu QX,Zhang YH,Cao YN. Phylogeography of East Asia's Tertiary relict plants:current progress and future prospects[J]. Biodiversity Science,2017,25 (2):136−146.
|
[91] |
Arnold B,Corbett-Detig RB,Hartl D,Bomblies K. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling[J]. Mol Ecol,2013,22 (11):3179−3190. doi: 10.1111/mec.12276
|
[92] |
Ceballos G,Ehrlich PR,Barnosky AD,García A,Pringle RM,Palmer TM. Accelerated modern human–induced species losses:Entering the sixth mass extinction[J]. Sci Adv,2015,1 (5):e1400253. doi: 10.1126/sciadv.1400253
|
1. |
周静静,苗灵凤,李大东,田梦洁,杨帆. 旱-盐复合胁迫对降香黄檀幼苗生长和生理生化特性的影响. 热带亚热带植物学报. 2025(02): 197-206 .
![]() |