景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

植物景观遗传学研究进展

植物景观遗传学是新兴的景观遗传学交叉学科的一个重要研究方向。目前植物景观遗传学的研究虽落后于动物,但其在生物多样性保护方面具有的巨大潜力不可忽视。从景观特征对遗传结构、环境因素对适应性遗传变异影响两个方面,系统综述了近十年来国际上植物景观遗传学的研究焦点和研究进展,比较了植物景观遗传学与动物景观遗传学研究在研究设计和研究方法上的异同,并基于将来植物景观遗传学由对空间遗传结构的描述发展为对景观遗传效应的量化分析及预测的发展框架,具体针对目前景观特征与遗传结构研究设计的系统性差、遗传结构与景观格局在时间上的误配、适应性位点与环境变量的模糊匹配、中性遗传变异与适应性遗传变异研究的分隔、景观与遗传关系分析方法的局限等五个方面提出了研究对策。     

山地景观生态学研究进展

山地环境对全球变化的高度敏感性及其在陆地淡水资源与生物资源方面的巨大影响,推动山地景观生态学迅猛发展。在系统分析2000年以来山地景观生态学文献计量基础上,针对山地景观生态学主要学科方向与科学问题,以山地垂直带谱结构分布模式与形成机制,山地景观生态功能的分布格局与驱动因素,山地景观生态结构与格局对全球变化的响应等三大领域为重点,综述了自2000年以来的主要研究进展和取得的新认识,归纳了每个领域现阶段存在的主要前沿问题。围绕上述山地景观生态学重点领域,提出了山地景观生态学未来重点发展的6个研究方向:全球山地环境变化综合观测网络与方法、山地多维景观生态格局与时空变化规律及其驱动机制、整合景观生态学方法的林线动态与机制研究、山地生物生产力和物种多样性变化与模拟、景观生态水碳耦合循环变化与影响、山地垂直带谱结构理论与模式等,为进一步推动山地景观生态学发展、准确理解山地环境对全球变化的响应规律及其影响提供理论参考。     

景观生态学:两栖动物生态学研究的新途径

全球两栖动物正以远超过自然灭绝的高速率灭绝,这与生境丧失和景观破碎化有着直接关系。生境丧失导致两栖动物的生存空间减少,使局部种群消失,而景观破碎化则导致两栖动物种群之间的隔离度增加,不利于动物的繁殖和扩散。但两者往往是同时出现,相互作用。复合种群、景观连接度、景观遗传学及景观模型模拟等理论和方法的发展,为在生境丧失与破碎化景观下两栖动物的种群结构、组成和动态变化研究提供了理论基础和技术方法。同时景观生态学中特别重视研究的尺度,生境破碎化是发生在景观尺度下的生境变化过程,因此对生境破碎化的影响应该从现有的主要集中在斑块尺度和斑块-景观尺度转变到景观尺度上来。     

异质种群动态模型:破碎化景观动态模拟的新途径

景观破碎化导致物种以异质种群方式存活,使得基于异质种群动态模拟破碎化景观动态成为可能。异质种群动态模型的发展为景观动态模拟奠定了良好基础。根据空间处理方式的不同,异质种群模型可分为三大类,可不同程度地用于描述破碎化景观动态。(1)空间不确定异质种群模型,假定所有局域种群间均等互联,模型中不包含空间信息,仅能用于景观斑块动态描述;(2)空间确定异质种群模型,假设局域种群在二维空间上以规则格子形式排列,是一种准现实的空间处理方式,可用于景观动态的简单描述;(3)空间现实异质种群模型,包含了破碎化景观中局域种群的几何特征,可直接用于真实景观动态的模拟研究。空间现实的和基于个体的异质种群模型不但是未来异质种群模型发展的主流,也将成为未来破碎化景观动态研究的重要工具。为了更加准确完整地描述破碎化景观动态,不但应该综合运用已有的各种异质种群模型方法,更要引进新模型来刎画多物种、多变量、高维度、复杂连接的破碎化景观格局与过程。     

景观破碎化对植物种群的影响

景观破碎化是目前存在的一种普遍现象,是由于人为因素或其它非人为因素的干扰所导致的景观破碎分离并由简单趋向复杂的过程。它直接或间接影响着景观的结构、功能及其动态。本文首先简要介绍景观破碎化的成因和不同研究角度与水平上景观破碎化影响的表现;然后着重分析景观破碎化对植物种群的大小和灭绝速率、扩散和迁入、遗传和变异以及存活力等的影响;同时归纳现阶段研究景观破碎化对植物种群影响的主要方法和模型;最后提出目前景观破碎化对植物种群影响研究中存在的三个主要问题：缺乏原始的资料、成熟的模型和破碎化与其他因素,如污染、气候变化等,交互作用的识别。     

动物种群遗传异质性研究进展

生境破碎和种群隔离在野生动物管理中倍受关注,种群遗传异质性结合种群统计学和生境资料,可解释和推测种群经历的种群统计学随机事件,分析异质生境对种群遗传组成的影响,估计地理种群之间的基因交流和遗传分化,对物种保护具有重要指导意义。     

2000-2015年丹顶鹤重要繁殖地景观格局变化研究

以18个自然保护区为研究对象,全面系统地研究了我国丹顶鹤大陆种群重要繁殖地景观格局变化,结果表明：2000-2015年丹顶鹤重要繁殖地土地利用变化明显,突出表现为沼泽湿地面积急剧减少了1400.5 km²,主要转化为耕地、水体和草地,耕地面积大幅增加了1085.4 km²,主要由沼泽湿地、草地和林地转化而来;丹顶鹤重要繁殖地2000-2015年景观连通性保持稳定,但吉林莫莫格、黑龙江七星河、挠力河等自然保护区景观破碎化程度明显增加;东部种群重要繁殖地沼泽湿地缩减面积和不适宜生境增加面积均大于西部种群,表明东部种群繁殖地的恶化程度更为严重,需引起高度关注。首次基于长时间序列对丹顶鹤大陆种群繁殖地的变化开展了较为全面的研究,为有针对性地开展栖息地保护管理工作、促进丹顶鹤野生种群健康可持续发展提供了依据。     

广西黑叶猴栖息地景观格局破碎化分析及其对种群的影响

黑叶猴(Trachypithecus francoisi)是仅分布于喀斯特石山生境的珍稀濒危灵长类动物。由于非法捕杀和人类活动干扰,其种群数量正在急剧减少。同时,随着森林砍伐和土地开垦的加速,其栖息地严重破碎化。因此,了解栖息地破碎化对黑叶猴种群的影响对于保护这一珍稀濒危物种具有重要意义。基于遥感影像、土地利用数据以及黑叶猴种群调查数据,通过Fragstats软件开展广西黑叶猴栖息地景观破碎化分析,并通过相关性和多元逐步回归分析,探讨了景观格局对广西黑叶猴种群数量的影响。结果表明：(1)广西黑叶猴栖息地呈现破碎化严峻、斑块形状复杂化、斑块团聚程度较弱且分散化的现象;栖息地以林地景观占据重要优势,但人为景观的干扰十分强烈;在不同地区中,生境破碎化程度、人为干扰强度以及景观配置均呈现不同的特征,其中扶绥地区人为干扰最为强烈,德保地区的景观块数破碎化程度较为严重,而龙州地区的人为干扰程度最小,其森林景观最为聚集。(2)蔓延度指数、平均斑块分维指数、林地面积、林地斑块大小、裸岩面积和裸岩面积比重等景观指数与黑叶猴种群数量有显著正向关系,Shannon多样性指数则是显著负向关系;而耕地面积、耕地...     

澳门地区鸟类生境的景观格局

以2006年澳门地区TM遥感图像为主要数据源,在RS、GIS技术支持下,根据与鸟类活动密切相关的生境特征,利用Fragstats 3.3分析生境格局的基本特征和地区差异,讨论了景观的破碎化程度、连通性、景观异质性等对鸟类有重要影响的生境因素。结果显示：澳门的鸟类生境格局在澳门半岛和路氹离岛差异较大,与其城市化的程度有较高的相关性;澳门半岛以建设用地为基底,绿地数量少且破碎,景观多样性和异质性较低;路氹离岛以林地为基底,中部填海区的建设用地和裸地以大斑块存在,生境类型分布较澳门半岛均匀,连通性较佳,总体鸟类生境格局优于澳门半岛。澳门半岛有鸟类72种,其中陆生鸟类48种、水鸟24种;路氹离岛有鸟类146种,其中陆生鸟类94种、水鸟52种。对鸟类调查数据分析发现,生境格局对于鸟类物种数、多样性和均匀度方面均有一定影响。澳门在珠江口地区候鸟迁徙和湿地保护方面的重要性较高,在城市发展过程中应重视提高景观多样性和异质性,保护重要鸟类生境,以适应不同鸟类对各种生境的需求。     

Effects of landscape structure on genetic diversity of Geum urbanum L. populations in agricultural landscapes

Plant species in fragmented populations are affected by landscape structure because persistence within and migration among inhabited patches may be influenced by the identity and configuration of surrounding habitat elements. This may also be true for species of the semi-natural vegetation in agricultural landscapes. To determine the effect of landscape elements we analyzed Wood Avens (Geum urbanum L.) populations within three 4×4 km² agricultural landscapes in Germany, Switzerland and Estonia, which differ in levels of land use intensity and habitat fragmentation. Genetic variation was determined in 15 randomly selected populations in each landscape using 10 microsatellite loci. The landscape structure was assessed at two circles around each population, with radii defined by the range limits of spatial genetic autocorrelation. Multiple regression analysis was used to determine the influence of landscape structure variables for inter- and intrapopulation genetic diversity. Gene diversity was equally high in Germany (H_e=0.27) and Switzerland (H_e=0.26) but lower in Estonia (H_e=0.16). A high overall inbreeding coefficient (F_IS=0.89) was found, as expected for a selfing breeding system in G. urbanum. Genetic differentiation among populations was high (overall F_ST=0.43, 0.48, and 0.45 in Estonia, Switzerland and Germany, respectively), and did not differ among the three landscapes. Only a moderate influence of individual land use types on genetic diversity within and among populations was found with some idiosyncratic relationships. Genetic variation within populations was correlated to the amount of hedgerows positively in Estonia but negatively in Switzerland. The study demonstrates that the distribution of individual land use types affects the genetic pattern of a common plant species. However, different variables were identified to influence the genetic structure in three different landscapes. This indicates a major influence of landscape-specific land use history and stochastic processes determining gene flow and plant population structure.     

Perspectives and challenges in landscape genetics

A recent workshop held at the University of Grenoble gathered the leading experts in the field of landscape genetics and spatial statistics. Landscape genetics was only recently defined as an independent research field. It aims to understand the processes of gene flow and local adaptation by studying the interactions between genetic and spatial or environmental variation. This workshop discussed the perspectives and challenges of combining emerging molecular, spatial and statistical tools to unravel how landscape and environmental variables affect genetic variation.     

Genetic structure of expanding wolf (Canis lupus) populations in Italy and Croatia,and the early steps of the recolonization of the Eastern Alps

After centuries of range contraction and demographic declines wolves are now expanding in Europe, colonizing regions from where they have been absent for centuries. Wolf colonizing the western Alps originate by the expansion of the Italian population. Vagrant wolves of Italian and Dinaric-Balkan origins have been recently observed in the Eastern Alps. In this study we compared the genetic structure of wolf populations in Italy and Croatia, aiming to identify the sources of the ongoing recolonization of the Eastern Alps. DNA samples, extracted from 282 Italian and 152 Croatian wolves, were genotyped at 12 autosomal microsatellites (STR), four Y-linked STR and at the hypervariable part of the mitochondrial DNA control-region (mtDNA CR1). Wolves in Croatia and Italy underwent recent demographic bottlenecks, but they differ in genetic diversity and population structure. Wolves in Croatia were more variable at STR loci (N_A = 7.4, H_O = 0.66, H_E = 0.72; n = 152) than wolves in Italy (N_A = 5.3, H_O = 0.57, H_E = 0.58; n = 282). We found four mitochondrial DNA (mtDNA CR1) and 11 Y-STR haplotypes in Croatian wolves, but only one mtDNA CR1 and three Y-STR haplotypes in Italy. Wolves in Croatia were subdivided into three genetically distinct subpopulations (in Dalmatia, Gorski kotar and Lika regions), while Italian wolves were not sub-structured. Assignment testing shows that the eastern and central Alps are recolonized by wolves dispersing from both the Italian and Dinaric populations. The recolonization of the Alps will predictably continue in the future and the new population will be genetically admixed and very variable with greater opportunities for local adaptations and survival.     

Why replication is important in landscape genetics: American black bear in the Rocky Mountains

We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation, altitude, variation in elevation and road coverage. In all but one of the study areas, isolation by landscape resistance was more supported than IBD suggesting gene flow is likely influenced by elevation, forest cover, and roads. However, the landscape features influencing gene flow varied among study areas. Using subsets of loci usually gave models with the very similar landscape features influencing gene flow as with all loci, suggesting the landscape features influencing gene flow were correctly identified. To test if the cause of the variability of supported landscape features in study areas resulted from landscape differences among study areas, we conducted a limiting factor analysis. We found that features were supported in landscape models only when the features were highly variable. This is perhaps not surprising but suggests an important cautionary note - that if landscape features are not found to influence gene flow, researchers should not automatically conclude that the features are unimportant to the species' movement and gene flow. Failure to investigate multiple study areas that have a range of variability in landscape features could cause misleading inferences about which landscape features generally limit gene flow. This could lead to potentially erroneous identification of corridors and barriers if models are transferred between areas with different landscape characteristics.     

Landscape genetics of the widespread ground-beetle Carabus auratus in an agricultural region

The brachypterous carabid beetle Carabus auratus was chosen as an indicator organism for analysing the relationship between landscape composition and population genetic structure (AFLP) in an agricultural region. We selected eight landscape sections with different landscape composition. The landscapes were analysed in 7 radii ranging from 500 to 2000 m (step size: 250 m). It is shown that the population as a whole exhibits a moderate genetic differentiation with geographically restricted genetic exchange. Genetic diversity of local populations is high. It is positively associated with increasing numbers of migrants estimated from the molecular data. This indicates that even widespread species with a presumed low dispersal capacity may exhibit high levels of genetic exchange at larger spatial scales. The availability of grassland within the landscape sections enhanced genetic diversity of local populations at larger spatial scales and explained over 50% of the observed genetic diversity. Thus, the unexpectedly high genetic exchange of C. auratus critically depends on the availability of suitable landscape features. Our results emphasise the need to take into account the adverse effects of ongoing changes in landscape composition on the genetic diversity even of widespread species when aiming at conserving genetic and functional diversity in agricultural landscapes.     

景观遗传学：概念与方法

全球变化下的物种栖息地丧失和破碎化给生物多样性保护带来了新的问题和挑战,生物多样性保护必须由单纯的物种保护上升到栖息地景观的保护。景观遗传学是定量确定栖息地景观特征对种群遗传结构影响的一门交叉学科,在生物保护及自然保护区管理方面有巨大的潜力。从生物多样性保护的角度评述了景观结构与遗传多样性的关系,介绍了景观遗传学的基本概念,研究尺度和方法,并对景观遗传学当前的研究焦点及面临的挑战做了总结。     

不同分离源植物乳杆菌的群体基因组分析

【背景】植物乳杆菌(Lactobacillus plantarum)广泛存在于植物、乳制品、肉制品、哺乳动物和昆虫的肠道等多种生态环境中。【目的】探究不同分离源L. plantarum基因组与其所在环境是否存在潜在的联系。【方法】利用比较基因组学对126株分离自植物、乳制品、肉制品、果蝇及哺乳动物肠道和口腔等部位的L. plantarum菌株基因组进行系统发育分析和功能基因组分析,解析不同分离源菌株间的亲缘关系和进化历程。【结果】果蝇分离株的基因组大小显著高于植物、哺乳动物肠道、肉制品和乳制品分离株(P0.05),植物和哺乳动物肠道、口腔等部位与肉制品分离株的基因组大小和编码基因数量无显著差异(P0.05)。基于单拷贝基因串联和核心基因系统发育树分析均发现,果蝇分离株和乳制品分离株分别集中聚集分布在某一分支中,其余分离源均匀分布在各个分支中。附属基因分析结果与系统发育树分析结果一致。功能基因注释结果发现,果蝇分离株的环境特异性基因参与低聚果糖和几丁质代谢,乳制品分离株的环境特异性基因参与mazEF毒素-抗毒素系统和CRISPR系统。【结论】植物乳杆菌分离株为适应较为独特的果蝇和乳制品生境而发生了适应性进化。本研究为植物乳杆菌适应性进化提供了新见解,同时为解析菌株的进化历程提供了理论基础。