电路理论在植物景观遗传学研究中的应用潜力分析
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摘要
景观遗传学的迅速发展为研究异质性系统中的进化生物学问题提供了新颖的理论和方法。本文以电路理论(circuit theory)在植物景观遗传研究中的应用为主题,系统解析理论框架,明确其核心概念和生态学过程间的映射关系,从研究主题、方法和模型验证3方面综述近十年的相关文献,并在此基础上归纳了该理论的优势和局限性。其优势主要为:(1)可对多条潜在传播路径进行通盘考察并予以比较,有助于鉴别影响连接度的关键区域或廊道;(2)对哈迪-温伯格平衡假设和栅格大小不敏感,保证了模型的适应性;(3)模型要求物种对生境无明显经验积累,特别适合分布区形状不规则,以及连续广泛分布的物种,与许多植物的生物学特点相契合。该理论要求物种具有随机漫游和传播各向同性2个前提条件,限制了生物媒介类植物的适用度。在传播过程具有方向偏好的生态系统中,其应用也需慎重考虑。结合未来发展趋势,本文认为电路理论在植物景观遗传学研究中具有很好的潜力,但还需要依据具体的研究问题、物种习性、空间尺度和系统性质来进行科学的应用。
The rapid development of landscape genetics provides innovative concepts and methodologies for evolutionary biology research in heterogeneous systems.This paper focused on the current application of circuit theory in plant landscape genetics.We demonstrated the theoretical framework of the model,explored the ecological meaning of the core concepts,and reviewed the related literature on three aspects:research theme,method and model validation.The advantages and limitations of this theory were summarized.We found the theory to be suitable for research on plant landscape genetics based on:(1) inclusion of multiple pathways enabling comparison and identification of critical habitats and corridors;(2)insensitivity for HW equilibrium and cell size making the model robust;and(3) no priorknowledge for intermediate habitat and broad range(or irregular range shape) prerequisite coinciding with many plant species.The theory has two premises:random walk and isotropic dispersal.Plants dispersing through a biotic agent may be less suitable for the circuit theory.Application in ecosystems with direct dispersal also needs prudence.Considering the prospect of circuit theory in plant landscape genetics,we argue a more rigorous model based on sophisticated consideration for research theme,species behavior,spatial scale,and system character.
The rapid development of landscape genetics provides innovative concepts and methodologies for evolutionary biology research in heterogeneous systems.This paper focused on the current application of circuit theory in plant landscape genetics.We demonstrated the theoretical framework of the model,explored the ecological meaning of the core concepts,and reviewed the related literature on three aspects:research theme,method and model validation.The advantages and limitations of this theory were summarized.We found the theory to be suitable for research on plant landscape genetics based on:(1) inclusion of multiple pathways enabling comparison and identification of critical habitats and corridors;(2)insensitivity for HW equilibrium and cell size making the model robust;and(3) no priorknowledge for intermediate habitat and broad range(or irregular range shape) prerequisite coinciding with many plant species.The theory has two premises:random walk and isotropic dispersal.Plants dispersing through a biotic agent may be less suitable for the circuit theory.Application in ecosystems with direct dispersal also needs prudence.Considering the prospect of circuit theory in plant landscape genetics,we argue a more rigorous model based on sophisticated consideration for research theme,species behavior,spatial scale,and system character.
引文
[1]陈利顶,李秀珍,傅伯杰,肖笃宁,赵文武.中国景观生态学发展历程与未来研究重点[J].生态学报,2014,34(12):3129-3141.Chen LD,Li XZ,Fu BJ,Xiao DN,Zhao WW.Development history and future research priorities of landscape ecology in China[J].Acta Ecologica Sinica,2014,34(12):3129-3141.
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[6]丁兆红,卢君婷,卢剑波.景观破碎化对植物种群的遗传学效应及其研究方法进展[J].杭州师范大学学报:自然科学版,2016,15(5):502-508.Ding ZH,Lu JT,Lu JB.On the genetic effects of landscape fragmentation on plant populations and research methods[J].Journal of Hangzhou Normal University:Natural Science Edition,2016,15(5):502-508.
[7]宋有涛,孙子程,朱京海.植物景观遗传学研究进展[J].生态学报,2017,37(22):7410-7417.Song YT,Sun ZC,Zhu JH.Advances in landscape genetics of plants[J].Acta Ecologica Sinica,2017,37(22):7410-7417.
[8]Adriaensen F,Chardon JP,De Blust G,Swinnen E,Villalba S,et al.The application of‘least-cost'modelling as a functional landscape model[J].Landscape Urban Plan,2003,64(4):2045-2056.
[9]Shirk AJ,Wallin DO,Cushman SA,Rice CG,Warheit KIet al.Inferring landscape effects on gene flow:a new model selection framework[J].Mol Ecol,2010,19(17):3603-3619.
[10]Rayfield B,Fortin MJ,Fall A.The sensitivity of least-cost habitat graphs to relative cost surface values[J].Landscape Ecol,2010,25(4):519-532.
[11]Dickson BG,Albano CM,Gray ME,McClure M,Theobald D,et al.Circuit-theory applications to connectivity science and conservation[J].Conserv Biol,2018,DOI:10.1111/cobi.13230.
[12]McRae BH,Dickson BG,Keitt TH,Viral BS.Using circuit theory to model connectivity in ecology,evolution and conservation[J].Ecology,2008,89(10):2712-2724.
[13]McRae BH,Beier P.Circuit theory predicts gene flow in plant and animal populations[J].Proc Natl Acad Sci USA,2007,104(50):19885-19890.
[14]McRae BH.Isolation by resistance[J].Evolution,2006,60(8):1551-1561.
[15]Urban D,Keitt T.Landscape connectivity:a graph-theoretic perspective[J].Ecology,2001,82(5):1205-1218.
[16]刘佳,尹海伟,孔繁花,李沐寒.基于电路理论的南京城市绿色基础设施格局优化[J].生态学报,2018,38(12):4363-4372.Liu J,Yin HW,Kong FH,Li MH.Structure optimization of circuit theory-based green infrastructure in Nanjing,China[J].Acta Ecologica Sinica,2018,38(12):4363-4372.
[17]宋利利,秦明周.整合电路理论的生态廊道及其重要性识别[J].应用生态学报,2016,27(10):3344-3352.Song LL,Qin MZ.Identification of ecological corridors and its importance by integrating circuit theory[J].Chinese Journal of Applied Ecology,2016,27(10):3344-3352.
[18]Saeki I,Hirao AS,Kenta T,Nagamitsu T,Hiura T.Landscape genetics of a threatened maple,Acer miyabei:implications for restoring riparian forest connectivity[J].Biol Conserv,2018,220:299-307.
[19]Gharehaghaji M,Minor ES,Ashley MV,Abraham ST,Koenig WD.Effects of landscape features on gene flow of valley oaks(Quercus lobata)[J].Plant Ecol,2017,218(4):487-499.
[20]Ortego J,Gugger PF,Sork VL.Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak[J].J Biogeogr,2015,42(2):328-338.
[21]Yu HB,Zhang YL,Liu LS,Qi W,Li SC,et al.Combining the least cost path method with population genetic data and species distribution models to identify landscape connectivity during the late Quaternary in Himalayan hemlock[J].Ecol Evol,2015,5(24):S781-S791.
[22]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[J].Am J Bot,2017,104(3):439-450.
[23]Lee SR,Jo YS,Park CH,Friedman JM,Olson MS.Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States[J].Mol Ecol,2018,27(3):636-646.
[24]Tumas HR,Shamblin BM,Woodrey M,Nibbelink NP,Chandler R,et al.Landscape genetics of the foundational salt marsh plant species black needlerush(Juncus roemerianus Scheele)across the northeastern Gulf of Mexico[J].Landscape Ecol,2018,33(9):1585-1601.
[25]Fant JB,Havens K,Keller JM,Radosavljevic A,Yates ED.The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic,Cirsium pitcheri(Asteraceae)[J].Heredity,2014,112(5):519-523.
[26]李小白,向林,罗洁,胡标林,田胜平,等.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J].中国细胞生物学学报,2013,35(5):720-726.Li XB,Xiang L,Luo J,Hu BL,Tian SP,et al.The strategy of RNA-seq,application and development of molecular marker derived from RNA-seq[J].Chinese Journal of Cell Biology,2013,35(5):720-726.
[27]Helyar SJ,Hemmerhansen J,Bekkevold D,Taylor M,Ogden R,et al.Application of SNPs for population genetics of nonmodel organisms:new opportunities and challenges[J].Mol Ecol Res,2011,11(s1):123-129.
[28]Zeller KA,McGarigal K,Whiteley AR.Estimating landscape resistance to movement:a review[J].Landscape Ecol,2012,27(6):777-797.
[29]Andrew RL,Ostevik KL,Ebert DP,Rieseberg LH.Adaptation with gene flow across the landscape in a dune sunflower[J].Mol Ecol,2012,21(9):2078-2091.
[30]Cruickshank TE,Hahn MW.Reanalysis suggests that genomic islands of speciation are due to reduced diversity,not reduced gene flow[J].Mol Ecol,2014,23(13):3133-3157.
[31]Thiele J,Buchholz S,Schirmel J.Using resistance distance from circuit theory to model dispersal through habitat corridors[J].J Plant Ecol,2018,11(3):385-393.
[32]Grafius DR,Corstanje R,Siriwardena GM,Plummer KE,Harris JA.A bird's eye view:using circuit theory to study urban landscape connectivity for birds[J].Landscape Ecol,2017,32(9):1771-1787.
[33]Simpkins CE,Dennis TE,Etherington TR,Perry GLW.Assessing the performance of common landscape connectivity metrics using a virtual ecologist approach[J].Ecol Model,2018,367:13-23.
[34]Mcclure ML,Hansen AJ,Inman RM.Connecting models to movements:testing connectivity model predictions against empirical migration and dispersal data[J].Landscape Ecol,2016,31(7):1419-1432.
[35]Poor EE,Loucks C,Jakes A,Urban DL.Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations[J].PLo S One,2012,7(11):e49390.
[36]Anderson CD,Epperson BK,Fortin MJ,Holderegger R,James PMA.Considering spatial and temporal scale in landscape-genetic studies of gene flow[J].Mol Ecol,2010,19(17):3565-3575.
[37]Bezanson J,Edelman A,Karpinski S,Shah VB.Julia:Afresh approach to numerical computing[J].Siam Rev,2017,59(1):65-98.
[38]Creech TG,Epps CW,Landguth EL,Wehausen JD,Crowhurst RS,et al.Simulating the spread of selectiondriven genotypes using landscape resistance models for desert bighorn sheep[J].PLo S One,2017,12(5):e176960.
[2]薛亚东,李丽,吴巩胜,周跃.景观遗传学:概念与方法[J].生态学报,2011,31(6):1756-1762.Xue YD,Li L,Wu GS,Zhou Y.Concepts and techniques of landscape genetics[J].Acta Ecologica Sinica,2011,31(6):1756-1762.
[3]Bolliger J,Lander T,Balkenhol N.Landscape genetics since 2003:status,challenges and future directions[J].Landscape Ecol,2014,29(3):361-366.
[4]Schoville SD,Dalongeville A,Viennois G,Gugerli F,Taberlet P,et al.Preserving genetic connectivity in the European Alps protected area network[J].Biol Conserv,2018,218:99-109.
[5]Gagnaire PA,Broquet T,Aurelle D,Viard F,Souissi A,et al.Using neutral,selected,and hitchhiker loci to assess connectivity of marine populations in the genomic era[J].Evol Appl,2015,8(8):769-786.
[6]丁兆红,卢君婷,卢剑波.景观破碎化对植物种群的遗传学效应及其研究方法进展[J].杭州师范大学学报:自然科学版,2016,15(5):502-508.Ding ZH,Lu JT,Lu JB.On the genetic effects of landscape fragmentation on plant populations and research methods[J].Journal of Hangzhou Normal University:Natural Science Edition,2016,15(5):502-508.
[7]宋有涛,孙子程,朱京海.植物景观遗传学研究进展[J].生态学报,2017,37(22):7410-7417.Song YT,Sun ZC,Zhu JH.Advances in landscape genetics of plants[J].Acta Ecologica Sinica,2017,37(22):7410-7417.
[8]Adriaensen F,Chardon JP,De Blust G,Swinnen E,Villalba S,et al.The application of‘least-cost'modelling as a functional landscape model[J].Landscape Urban Plan,2003,64(4):2045-2056.
[9]Shirk AJ,Wallin DO,Cushman SA,Rice CG,Warheit KIet al.Inferring landscape effects on gene flow:a new model selection framework[J].Mol Ecol,2010,19(17):3603-3619.
[10]Rayfield B,Fortin MJ,Fall A.The sensitivity of least-cost habitat graphs to relative cost surface values[J].Landscape Ecol,2010,25(4):519-532.
[11]Dickson BG,Albano CM,Gray ME,McClure M,Theobald D,et al.Circuit-theory applications to connectivity science and conservation[J].Conserv Biol,2018,DOI:10.1111/cobi.13230.
[12]McRae BH,Dickson BG,Keitt TH,Viral BS.Using circuit theory to model connectivity in ecology,evolution and conservation[J].Ecology,2008,89(10):2712-2724.
[13]McRae BH,Beier P.Circuit theory predicts gene flow in plant and animal populations[J].Proc Natl Acad Sci USA,2007,104(50):19885-19890.
[14]McRae BH.Isolation by resistance[J].Evolution,2006,60(8):1551-1561.
[15]Urban D,Keitt T.Landscape connectivity:a graph-theoretic perspective[J].Ecology,2001,82(5):1205-1218.
[16]刘佳,尹海伟,孔繁花,李沐寒.基于电路理论的南京城市绿色基础设施格局优化[J].生态学报,2018,38(12):4363-4372.Liu J,Yin HW,Kong FH,Li MH.Structure optimization of circuit theory-based green infrastructure in Nanjing,China[J].Acta Ecologica Sinica,2018,38(12):4363-4372.
[17]宋利利,秦明周.整合电路理论的生态廊道及其重要性识别[J].应用生态学报,2016,27(10):3344-3352.Song LL,Qin MZ.Identification of ecological corridors and its importance by integrating circuit theory[J].Chinese Journal of Applied Ecology,2016,27(10):3344-3352.
[18]Saeki I,Hirao AS,Kenta T,Nagamitsu T,Hiura T.Landscape genetics of a threatened maple,Acer miyabei:implications for restoring riparian forest connectivity[J].Biol Conserv,2018,220:299-307.
[19]Gharehaghaji M,Minor ES,Ashley MV,Abraham ST,Koenig WD.Effects of landscape features on gene flow of valley oaks(Quercus lobata)[J].Plant Ecol,2017,218(4):487-499.
[20]Ortego J,Gugger PF,Sork VL.Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak[J].J Biogeogr,2015,42(2):328-338.
[21]Yu HB,Zhang YL,Liu LS,Qi W,Li SC,et al.Combining the least cost path method with population genetic data and species distribution models to identify landscape connectivity during the late Quaternary in Himalayan hemlock[J].Ecol Evol,2015,5(24):S781-S791.
[22]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[J].Am J Bot,2017,104(3):439-450.
[23]Lee SR,Jo YS,Park CH,Friedman JM,Olson MS.Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States[J].Mol Ecol,2018,27(3):636-646.
[24]Tumas HR,Shamblin BM,Woodrey M,Nibbelink NP,Chandler R,et al.Landscape genetics of the foundational salt marsh plant species black needlerush(Juncus roemerianus Scheele)across the northeastern Gulf of Mexico[J].Landscape Ecol,2018,33(9):1585-1601.
[25]Fant JB,Havens K,Keller JM,Radosavljevic A,Yates ED.The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic,Cirsium pitcheri(Asteraceae)[J].Heredity,2014,112(5):519-523.
[26]李小白,向林,罗洁,胡标林,田胜平,等.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J].中国细胞生物学学报,2013,35(5):720-726.Li XB,Xiang L,Luo J,Hu BL,Tian SP,et al.The strategy of RNA-seq,application and development of molecular marker derived from RNA-seq[J].Chinese Journal of Cell Biology,2013,35(5):720-726.
[27]Helyar SJ,Hemmerhansen J,Bekkevold D,Taylor M,Ogden R,et al.Application of SNPs for population genetics of nonmodel organisms:new opportunities and challenges[J].Mol Ecol Res,2011,11(s1):123-129.
[28]Zeller KA,McGarigal K,Whiteley AR.Estimating landscape resistance to movement:a review[J].Landscape Ecol,2012,27(6):777-797.
[29]Andrew RL,Ostevik KL,Ebert DP,Rieseberg LH.Adaptation with gene flow across the landscape in a dune sunflower[J].Mol Ecol,2012,21(9):2078-2091.
[30]Cruickshank TE,Hahn MW.Reanalysis suggests that genomic islands of speciation are due to reduced diversity,not reduced gene flow[J].Mol Ecol,2014,23(13):3133-3157.
[31]Thiele J,Buchholz S,Schirmel J.Using resistance distance from circuit theory to model dispersal through habitat corridors[J].J Plant Ecol,2018,11(3):385-393.
[32]Grafius DR,Corstanje R,Siriwardena GM,Plummer KE,Harris JA.A bird's eye view:using circuit theory to study urban landscape connectivity for birds[J].Landscape Ecol,2017,32(9):1771-1787.
[33]Simpkins CE,Dennis TE,Etherington TR,Perry GLW.Assessing the performance of common landscape connectivity metrics using a virtual ecologist approach[J].Ecol Model,2018,367:13-23.
[34]Mcclure ML,Hansen AJ,Inman RM.Connecting models to movements:testing connectivity model predictions against empirical migration and dispersal data[J].Landscape Ecol,2016,31(7):1419-1432.
[35]Poor EE,Loucks C,Jakes A,Urban DL.Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations[J].PLo S One,2012,7(11):e49390.
[36]Anderson CD,Epperson BK,Fortin MJ,Holderegger R,James PMA.Considering spatial and temporal scale in landscape-genetic studies of gene flow[J].Mol Ecol,2010,19(17):3565-3575.
[37]Bezanson J,Edelman A,Karpinski S,Shah VB.Julia:Afresh approach to numerical computing[J].Siam Rev,2017,59(1):65-98.
[38]Creech TG,Epps CW,Landguth EL,Wehausen JD,Crowhurst RS,et al.Simulating the spread of selectiondriven genotypes using landscape resistance models for desert bighorn sheep[J].PLo S One,2017,12(5):e176960.