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。     

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。     

中国陆生脊椎动物野外调查的发展现状与文献分析

新中国成立以来,我国已开展了大量陆生脊椎动物的本底调查和多样性研究项目,取得了一系列成果,并有学者针对兽类、鸟类和两栖爬行类的野外调查监测进行了总结和展望,但尚缺乏对所有陆生脊椎动物类群的调查历史和现状的分析及基于文献收集的研究,特别是对调查方法和技术手段的对比与总结。因此,本文通过文献收集的方法,基于中国知网、Web of Science核心合集和以图书检索为主的读秀学术搜索,以“兽类”“鸟类”“爬行类”“两栖类”“动物资源”“调查”“监测”“新种”“新记录”和“物种多样性”作为检索词,检索并筛选了与兽类、鸟类、爬行类及两栖类陆生脊椎动物调查相关的文献资料共3,504篇,对陆生脊椎动物调查的研究文献在全国各省级行政区、生物多样性热点地区的分布,及其运用的调查方法和技术手段进行了系统的分析和比较。结果表明:相较兽类和两栖爬行类的调查,我国鸟类多样性的调查最多,发表文献占所有文献的70.26%。四川、云南的陆生脊椎动物调查最多,分别发表285篇、260篇文献。分布于我国的4个全球生物多样性热点地区的调查强度存在显著差异,印缅生物多样性热点地区和中国西南山地的研究文献较多,分别为348篇、...     

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。     

中国濒危兽类保护遗传学研究进展与展望

我国是全球生物多样性大国,拥有包括大熊猫、金丝猴、华南虎、麋鹿、白鱀豚等特有物种和旗舰物种在内的丰富兽类资源。近几十年来,土地利用模式转变、盗猎、环境污染、气候变化等因素使许多兽类物种面临生存威胁,导致物种遗传多样性丧失。而遗传多样性是生物多样性的基本组成部分,决定了物种和种群能否长期生存。保护遗传学作为保护生物学的一大分支学科,旨在通过遗传学分析探明种群遗传变异和物种濒危的遗传学机制。近40年来,随着研究手段和技术的不断发展,我国兽类保护遗传学在遗传多样性和近交水平评估、景观遗传学、生态遗传学和圈养种群遗传管理等方面都取得了重要成果。然而,未来人类社会发展可能为濒危兽类带来的威胁依然存在,高通量测序等新技术的进一步发展则能够帮助我们更加深入地了解濒危物种和种群遗传适应与濒危机制,从而实现对濒危兽类的有效管理与保护。     

青海省东部地区喜马拉雅旱獭种群遗传结构

本研究利用11个微卫星标记对采自青海省东部地区的13个喜马拉雅旱獭（Marmota himalayana）种群149个个体进行了基因分型,并运用种群遗传学方法对其遗传多样性和遗传结构进行分析。结果显示,11个微卫星标记位点共计检测到97个等位基因,各种群的平均观测杂合度和期望杂合度范围分别为0.58~0.82和0.60~0.79,种群遗传多样性水平相对较高;遗传结构分析表明,青海省东部地区的喜马拉雅旱獭种群具有显著的遗传结构,13个地理种群形成了3个遗传聚类群,且3个遗传聚类群与湟水河和黄河上游干流所划分出的地理单元完全一致,因此我们认为湟水河和黄河上游干流是阻碍该地区喜马拉雅旱獭种群进行迁移扩散和基因交流的天然屏障。同时,STRUCTURE分析结果还显示3个遗传聚类群间仍有明显的基因流,AMOVA分析也显示3个聚类群间变异百分比为6.60%,仅略高于聚类群内种群间的变异（4.51%）,而远低于种群内变异水平（88.90%）,表明三个聚类群间的分化程度并不是很深。这说明喜马拉雅旱獭可能通过桥梁或在枯水期等穿越河流进行基因交流。以上结果为该地区的旱獭种群监控和鼠疫防控提供了科学的理论基础。     

不仅仅是遗传多样性:植物保护遗传学进展

保护遗传学研究的是影响物种灭绝的遗传因素以及濒危物种的遗传管理, 以降低物种的灭绝风险。本文从遗传多样性本身及其对生态系统的影响两个方面介绍了植物保护遗传学的最新进展。根据遗传标记的功能, 保护遗传学研究可分为选择中性遗传变异研究和适应性遗传变异两个方面。对于目前主要采用的选择中性遗传标记研究, 本文着重介绍了以下方面的最新进展: (1)利用遗传标记进行个体、物种或遗传单元的鉴定, 从而有效地设计保护策略, 避免在迁地保护中混淆物种, 提高保护效率; (2)应重视由于物种自身生殖、扩散等原因造成的隐性瓶颈效应。由于选择中性遗传标记并不能准确反映物种的适应性遗传基础, 从适应性遗传变异角度研究濒危物种的进化潜力已成为保护遗传学的研究前沿。大部分相关研究还集中在利用基因组扫描检测受选择的位点, 而对功能基因的适应性研究还比较少。景观遗传学旨在解释景观和生境影响下的种群间基因流和遗传多样性格局, 这方面研究将会促进我们更多了解种群基因流的地理限制因子和不同景观基质下的种群遗传差异。遗传多样性作为物种的一种属性亦可在一定程度上反馈, 并影响生态系统。这提示我们不仅仅是濒危物种, 常见物种的遗传多样性及其保护亦很重要。最后, 我们从4个方面对保护遗传学研究进行了展望, 包括应加强将生态系统各环节联系起来研究遗传多样性, 在技术手段上利用多态性更丰富的分子标记, 同时强调了对常见物种保护遗传学研究的重要性, 并初步分析了我国保护遗传学研究与国际水平的差距, 建议加强种群遗传学和进化生物学基础理论的学习。     

一个新的泥鳅雄性特异DNA片段（简报）

世界上现存鱼类多达24000余种．是脊椎动物中分布最广,种类最多的类群．具有多种多样的生物学特性和重大的经济价值。与高等脊椎动物相比．其性别决定具有多样性和可塑性。大多数鱼类的性别决定机制很原始。性染色体的分化处于萌芽状态。在已进行细胞遗传学研究的1700多种鱼类中．大约有176种（占10．4％）发现有明显的异型性染色体。     

景观生态学与生物多样性保护

景观生态学的发展为生物多样性保护提供了新理论,方法和技术手段,从景观多样性与遗传多样性,物种多样性,生态系统多样性各层次生物多样性之间的相互关系及生物多样性保护的景观规划等方面评述近年来景观生态学应用于生物多样性保护的主要内容及研究进展,阐述了生物多样性动态及反馈,生物多样性保护的地理途径（ＧＡＰ分析）,景观生态安全格局,区域和大陆尺度的生态网络等一些新的概念和方法。     

植物保护遗传学研究进展

保护遗传学是过用遗传学的原理和研究手段,以生物多样性尤其是遗传多样性的研究和保护为核心的一门新兴学科,近几十年来,遗传学研究在生物多样性保护的理论和实践中发挥着越来越重要的作用。本文简要回顾了保护遗传学的发展历史,研究方向和涉及的概念,着重介绍了植物保护遗传学研究所取得的一些进展,包括植物系统发育重建和保护单元的确定,遗传多样性与物种和群体适应性之间的关系,群体遗传结构与保护策略的制定以及植物遗传资源的鉴定和利用等方面的内容,并强调保护遗传学研究是未来生物多样性和保护生物学研究中一个亟待加强的研究领域。     

High‐throughput SNPs for all: genotyping‐in‐thousands

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. 2010 ) to complete species panmixia (Côté et al. 2013 ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. 2011 ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. 2015 ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.     

Evaluating methods to visualize patterns of genetic differentiation on a landscape

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model‐based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long‐distance migration, EEMS’ model is more sensitive to short‐distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un‐intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un‐PC), a fast, model‐free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un‐PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape‐scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un‐PC, SpaceMix and EEMS.     

The role of genetic structure in the adaptive divergence of populations experiencing saltwater intrusion due to relative sea‐level rise

Saltwater intrusion into estuaries creates stressful conditions for nektonic species. Previous studies have shown that Gambusia affinis populations with exposure to saline environments develop genetic adaptations for increased survival during salinity stress. Here, we evaluate the genetic structure of G. affinis populations, previously shown to have adaptations for increased salinity tolerance, and determine the impact of selection and gene flow on structure of these populations. We found that gene flow was higher between populations experiencing different salinity regimes within an estuary than between similar marsh types in different estuaries, suggesting the development of saline‐tolerant phenotypes due to local adaptation. There was limited evidence of genetic structure along a salinity gradient, and only some of the genetic variation among sites was correlated with salinity. Our results suggest limited structure, combined with selection to saltwater intrusion, results in phenotypic divergence in spite of a lack of physical barriers to gene flow.     

Development and characterization of 29 microsatellite markers for Ligumia nasuta (Bivalvia: Unionidae) using an Illumina sequencing approach

Ligumia nasuta (Say, 1817; Eastern Pondmussel) is an imperiled freshwater mussel (Unionidae) in eastern North America. Population declines in the Laurentian Great Lakes resulting from the introduction of dreissenid mussels and habitat destruction in the 20th Century have greatly reduced and limited its distribution. To properly inform restoration and management efforts for L. nasuta, fine-scale genetic analyses must be performed on the remnant populations. This study used Illumina paired-end shotgun sequencing to identify potential microsatellite loci for L. nasuta, utilizing two samples to develop the Illumina paired-end shotgun library. Forty-eight primer pairs were tested on the remaining 24 samples. Twenty-nine of the 48 microsatellite primer sets screened were successfully amplified using 24 L. nasuta samples collected from the Great Lakes watershed. The estimated fragment size ranged from 167 to 445 base-pairs (bp) and the number of alleles per locus varied between 5 and 16 (mean = 9.7). Only five of the loci deviated significantly from Hardy–Weinberg expectations after Bonferroni corrections. The development of these new microsatellite loci will greatly facilitate future genetic studies on L. nasuta.     

A C++ Template Library for Efficient Forward-Time Population Genetic Simulation of Large Populations

fwdpp is a C++ library of routines intended to facilitate the development of forward-time simulations under arbitrary mutation and fitness models. The library design provides a combination of speed, low memory overhead, and modeling flexibility not currently available from other forward simulation tools. The library is particularly useful when the simulation of large populations is required, as programs implemented using the library are much more efficient than other available forward simulation programs.     

Size differentiation in Finnish house sparrows follows Bergmann's rule with evidence of local adaptation

Bergmann's rule predicts that individuals are larger in more poleward populations and that this size gradient has an adaptive basis. Hence, phenotypic divergence in size traits between populations (P_ST) is expected to exceed the level of divergence by drift alone (F_ST). We measured 16 skeletal traits, body mass and wing length in 409 male and 296 female house sparrows Passer domesticus sampled in 12 populations throughout Finland, where the species has its northernmost European distributional margin. Morphometric differentiation across populations (P_ST) was compared with differentiation in 13 microsatellites (F_ST). We find that twelve traits phenotypically diverged more than F_ST in both sexes, and an additional two traits diverged in males. The phenotypic divergence exceeded F_ST in several traits to such a degree that findings were robust also to strong between‐population environmental effects. Divergence was particularly strong in dimensions of the bill, making it a strong candidate for the study of adaptive molecular genetic divergence. Divergent traits increased in size in more northern populations. We conclude that house sparrows show evidence of an adaptive latitudinal size gradient consistent with Bergmann's rule on the modest spatial scale of ca. 600 km.     

Amylase activity is associated with AMY2B copy numbers in dog: implications for dog domestication,diet and diabetes

High amylase activity in dogs is associated with a drastic increase in copy numbers of the gene coding for pancreatic amylase, AMY2B, that likely allowed dogs to thrive on a relatively starch‐rich diet during early dog domestication. Although most dogs thus probably digest starch more efficiently than do wolves, AMY2B copy numbers vary widely within the dog population, and it is not clear how this variation affects the individual ability to handle starch nor how it affects dog health. In humans, copy numbers of the gene coding for salivary amylase, AMY1, correlate with both salivary amylase levels and enzyme activity, and high amylase activity is related to improved glycemic homeostasis and lower frequencies of metabolic syndrome. Here, we investigate the relationship between AMY2B copy numbers and serum amylase activity in dogs and show that amylase activity correlates with AMY2B copy numbers. We then describe how AMY2B copy numbers vary in individuals from 20 dog breeds and find strong breed‐dependent patterns, indicating that the ability to digest starch varies both at the breed and individual level. Finally, to test whether AMY2B copy number is strongly associated with the risk of developing diabetes mellitus, we compare copy numbers in cases and controls as well as in breeds with varying diabetes susceptibility. Although we see no such association here, future studies using larger cohorts are needed before excluding a possible link between AMY2B and diabetes mellitus.     

Genes,environment and responsibility for violent behavior: “Whatever genes one has it is preferable that you are prevented from going around stabbing people”

For the legal system to function effectively people are generally viewed as autonomous actors able to exercise choice and responsible for their actions. It is conceivable that genetic traits associated with violent and antisocial behavior could call into question an affected individual's responsibility for acts of criminal violence. Evidence concerning genes associated with violent and antisocial behavior has been introduced in criminal courts in the USA and Italy, either alone or with associated environmental factors. One example of a “genetic defense” is based on low levels of monoamine oxidase A (MAOA) activity, with a prevalence of around 30% in Caucasian males. In countries with trial by jury it is particularly relevant to consider the views of publics on criminal liability and the significance they assign to evidence citing genetic influences on behavior. This article draws on largely qualitative research looking at participants' explanations of, and assigning of responsibility for, violent and antisocial behavior where environmental or genetic influences are claimed. Genetic factors were not viewed deterministically by participants but were considered by most to be irrelevant to personal responsibility. Notions of human agency, free will and choice were crucial to explanations of problem behaviors and ensured that offenders could be held responsible despite evidence on environmental and genetic factors.     

Is there such a thing as landscape genetics?

For a scientific discipline to be interdisciplinary, it must satisfy two conditions; it must consist of contributions from at least two existing disciplines, and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this study, I examine the complete body of peer‐reviewed literature self‐identified as landscape genetics (LG) using the statistical approaches of text mining and natural language processing. The goal here was to quantify the kinds of questions being addressed in LG studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published LG studies examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual‐ and population‐based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if LGs is to serve as a real bridge connecting evolution and ecology sensu lato.     

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as F_ST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses.