Effectiveness of in situ and ex situ conservation of crop diversity. What a Phaseolus vulgaris L. landrace case study can tell us

The effectiveness of in situ (on-farm) and ex situ conservation strategies to maintain total genetic diversity was assessed in a threatened Phaseolus vulgaris L. landrace. Farmer seed lots (subpopulations) were sampled initially and then after in situ and ex situ multiplication (two locations). The number of plants used in the ex situ multiplications (120) was much larger than that normally used in germplasm bank procedures and the farmer seed lots were kept separate. In situ, the landrace was multiplied by each farmer with the usual population size. Eighty plants from the initial population, the in situ and the two ex situ multiplications were individually tested using 26 microsatellite markers. Most of the genetic parameters showed a consistent decline in the ex situ populations compared with the in situ population, with a notable loss of less frequent alleles. The differentiation among the farmer subpopulations increased when the multiplication took place outside of the adaptation area. Although 120 plants were multiplied in each ex situ cycle, a bottleneck effect was present. In addition, tests for neutrality detected three loci that are involved in pathogen response and are potentially under selective effects. The diversity conservation and the management practices of autogamous landrace crops are discussed.     

Biodiversity conservation in cocoa production landscapes: an overview

Cocoa agroforests that retain a floristically diverse and structurally complex shade canopy have the potential to harbour significant levels of biodiversity, yet few studies have documented the plant and animal species occurring within these systems or within landscapes dominated by cocoa production. In this special issue, we bring together nine studies from Latin America, Africa and Asia that document the contribution of cocoa agroforestry systems to biodiversity conservation, and explore how the design, management and location of these systems within the broader landscape influence their value as habitats, resources and biological corridors. Tree diversity within the cocoa production systems is variable, depending on management, cultural differences, location and farm history, among other factors. Animal diversity is typically highest in those cocoa agroforests that have high plant diversity, structurally complex canopies, and abundant surrounding forest cover. In general, both plant and animal diversity within cocoa agroforests is greater than those of other agricultural land uses, but lower than in the original forest habitat. There are several emerging threats to biodiversity conservation within cocoa production landscapes, including the loss of remaining forest cover, the simplification of cocoa shade canopies and the conversion of cocoa agroforestry systems to other agricultural land uses with lower biodiversity value. To counter these threats and conserve biodiversity over the long-term, land management should focus on conserving native forest habitat within cocoa production landscapes, maintaining or restoring floristically diverse and structurally complex shade canopies within cocoa agroforests, and retaining other types of on-farm tree cover to enhance landscape connectivity and habitat availability.     

Phytodiversity of temperate permanent grasslands: ecosystem services for agriculture and livestock management for diversity conservation

Plant diversity has been reported to increase productivity. Farming practices aiming at conserving or increasing plant diversity are, however, usually less profitable than conventional ones. In this review, we aim to find reasons for this discrepancy, discuss ecosystem services of grassland phytodiversity that are useful for farmers, and ways of livestock management most beneficial for diversity. Under agricultural conditions, a clear effect of species richness on a site’s primary or secondary production has not yet been demonstrated. Reasons could be that species numbers in permanent grassland are above the threshold of five species found effective in experimental plots or that the conditions are more in equilibrium with management than in weeded experimental plots. Other diversity effects on production stability, nutrient and water retention or product quality might convince farmers to increase diversity. However, these should be tested in agricultural situations, as most research has again been carried out in experimental plots. To enhance phytodiversity, grazing has been found superior over mowing, as selective grazing, treading and excreta deposition increase the heterogeneity of a sward and thus the niches available. Especially rotational grazing with intermediate intensity may be advantageous for phytodiversity. However, complex interactions between environmental conditions, sward composition, management and livestock behaviour make it difficult to forecast grazing effects. Thus, ecological and agricultural researchers should cooperate more, e.g. either in interdisciplinary projects or by hiring researchers from the respective other profession and thus diversifying research groups, in order to integrate agricultural management into biodiversity research and biodiversity measurements into agricultural research to advance our understanding of how to make conservation and enhancement of grassland phytodiversity both feasible and sustainable.     

中国生物多样性就地保护的研究与实践

中国是世界上生物多样性最丰富的地区之一,但面临着较大的生态衰退风险。中国生物多样性受到的威胁来自包括人口众多、经济发展模式单一落后、工业化进程加快、气候变化和外来物种入侵等多种因素。生物多样性的就地保护对于维护国家生态安全具有重要意义,同时也是中国可持续发展的需要。本文就中国生物多样性就地保护的研究成果和保护成就进行了回顾,提出了未来应该着重加强的研究领域。中国生物多样性的就地保护研究与实践主要集中在生物多样性资源调查、濒危物种管理和自然保护区建设等方面。中国政府在生物多样性就地保护领域开展了大量卓有成效的工作,发布实施了一系列的保护行动规划,不断提高了生物多样性的保护水平。中国的生物多样性就地保护经过了由数量发展到质量发展的阶段后,未来的研究重点应该集中在生物多样性形成与维持机制、生物多样性受胁原因与响应机制、生物多样性长期监测与评估、自然保护区有效管理和自然保护区立法等方面。     

Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

Understanding how natural selection generates and maintains adaptive genetic diversity in heterogeneous environments is key to predicting the evolutionary response of populations to rapid environmental change. Detecting selection in complex spatial environments remains challenging, especially for threatened species where the effects of strong genetic drift may overwhelm signatures of selection. We carried out a basinwide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High‐resolution environmental data and 5162 high‐quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated with a steep hydroclimatic gradient and with human disturbance across the naturally and anthropogenically fragmented Murray–Darling Basin (Australia). Our approach included F_ST outlier tests to define neutral loci, and a combination of spatially explicit genotype–environment association analyses to identify candidate adaptive loci while controlling for the effects of landscape structure and shared population history. We found low levels of genetic diversity and strong neutral population structure consistent with expectations based on spatial stream hierarchy and life history. In contrast, variables related to precipitation and temperature appeared as the most important environmental surrogates for putatively adaptive genetic variation at both regional and local scales. Human disturbance also influenced the variation in candidate loci for adaptation, but only at a local scale. Our study contributes to understanding of adaptive evolution along naturally and anthropogenically fragmented ecosystems. It also offers a tangible example of the potential contributions of landscape genomics for informing in situ and ex situ conservation management of biodiversity.     

中国生物多样性适应气候变化策略研究

全球气候变化不仅给人类社会可持续发展带来严峻挑战,而且严重威胁到生物多样性及生态安全。我国是生物多样性最为丰富的国家之一,气候变化已经在对动物分布、行为和迁移,植物物候、植被和群落结构等方面造成了影响,并增加了珍稀濒危物种的灭绝风险,同时对生态系统的功能方面也造成了明显影响。未来气候变化将成为生物多样性丧失的主要驱动力之一。世界很多国家都在制定生物多样性适应气候变化的策略和采取适应行动,加强生物多样性的保护。本文在分析国外适应策略的基础上,结合中国生物多样性的现状,提出了适应气候变化的策略建议,包括制定生物多样性适应气候变化的国家战略,开展气候变化对生物多样性的影响监测和评估,针对敏感物种的就地保护和迁地保护,针对气候变化将导致退化生态系统开展恢复与重建,重点关注生物多样性适应气候变化优先区的保护,通过科学研究和国际合作,促进生物多样性适应气候变化技术的提高,期望为我国生物多样性保护和应对气候变化提供支持。     

The conservation of agrobiodiversity on-farm: questioning the emerging paradigm

The genetic diversity of traditional varieties of crops is the most economically valuable part of global biodiversity and is of paramount importance for future world crop production. The Biodiversity Convention has given a clear mandate for on-farm conservation. However, very little formal research has been done and no agreed set of scientific principles yet exists for on-farm conservation of genetic resources. This lack of scientific knowledge has not prevented an explosion of recommendations on how to conserve agrobiodiversity on-farm and it is possible to identify an emerging paradigm. Through a review of some of the assumptions on which this paradigm is based, we clearly show that if attempts to conserve agrobiodiversity on-farm are based on these misconceptions, they are likely to fail. By assessing the present activities of farmers, we propose a research agenda to increase the diversity available to farmers and to enhance farmers' capacity to manage this diversity dynamically. Increasing genetic diversification, combined with farmers' experimental abilities, and underpinned by the formal system, will ensure greater on-farm conservation of more useful genetic resources.     

Contribution of genetics and genomics to seagrass biology and conservation

Genetic diversity is one of three forms of biodiversity recognized by the IUCN as deserving conservation along with species and ecosystems. Seagrasses provide all three levels in one. This review addresses the latest advances in our understanding of seagrass population genetics and genomics within the wider context of ecology and conservation. Case studies are used from the most widely studied, northern hemisphere species Zostera marina, Z. noltii, Posidonia oceanica and Cymodocea nodosa.

We begin with an analysis of the factors that have shaped population structure across a range of spatial and temporal scales including basin-level phylogeography, landscape-scale connectivity studies, and finally, local-scale analyses at the meadow level—including the effects of diversity, clonality and mating system. Genetic diversity and clonal architecture of seagrass meadows differ within and among species at virtually all scales studied. Recent experimental studies that have manipulated seagrass genetic biodiversity indicate that genotypic diversity matters in an immediate ecological context, and enhances population growth, resistance and resilience to perturbation, with positive effects on abundance and diversity of the larger community. In terms of the longer term, evolutionary consequences of genetic/genotypic diversity in seagrass beds, our knowledge remains meagre. It is here that the new tools of ecogenomics will assist in unravelling the genetic basis for adaptation to both biotic and abiotic change. Gene expression studies will further assist in the assessment of physiological performance which may provide an early warning system under complex disturbance regimes that seagrasses are at or near their tolerance thresholds.

At the most fundamental level, ecological interactions of seagrasses with their environment depends on the genetic architecture and response diversity underlying critical traits. Hence, given the rapid progress in data acquisition and analysis, we predict an increasing role of genetic and genomic tools for seagrass ecology and conservation.     

Landscape perspectives on agricultural intensification and biodiversity – ecosystem service management

Understanding the negative and positive effects of agricultural land use for the conservation of biodiversity, and its relation to ecosystem services, needs a landscape perspective. Agriculture can contribute to the conservation of high‐diversity systems, which may provide important ecosystem services such as pollination and biological control via complementarity and sampling effects. Land‐use management is often focused on few species and local processes, but in dynamic, agricultural landscapes, only a diversity of insurance species may guarantee resilience (the capacity to reorganize after disturbance). Interacting species experience their surrounding landscape at different spatial scales, which influences trophic interactions. Structurally complex landscapes enhance local diversity in agroecosystems, which may compensate for local high‐intensity management. Organisms with high‐dispersal abilities appear to drive these biodiversity patterns and ecosystem services, because of their recolonization ability and larger resources experienced. Agri‐environment schemes (incentives for farmers to benefit the environment) need to broaden their perspective and to take the different responses to schemes in simple (high impact) and complex (low impact) agricultural landscapes into account. In simple landscapes, local allocation of habitat is more important than in complex landscapes, which are in total at risk. However, little knowledge of the relative importance of local and landscape management for biodiversity and its relation to ecosystem services make reliable recommendations difficult.     

Conservation of Scops Owl Otus scops in the Alps: relationships with grassland management, predation risk and wider biodiversity

The Scops Owl Otus scops is the most endangered and least studied owl in Europe, with widespread declines reported throughout Europe. The species is qualitatively associated with two threats: changes in agricultural practices and predation by Tawny Owls Strix aluco . We investigated these two threats to a population in the Alps, where land abandonment is causing widespread woodland expansion with unknown consequences. Predation risk and environmental indicators of the degree of agricultural change both predicted Scops Owl distribution. Furthermore, agricultural change also affected broader biodiversity, as estimated by the richness and diversity of bird and diurnal butterfly species. This resulted in a strong association between Scops Owl presence and wider biodiversity, which held at different spatial scales and justified a conservation focus on a single, threatened species. The persistence of Scops Owls in the Alps could be promoted through subsidies halting land abandonment and promoting extensive grassland management practices. Such interventions would have the additional advantage of yielding broader biodiversity benefits.     

Forest biodiversity in a changing climate: which logic for conservation strategies?

Climate change has direct and indirect impacts on forest ecosystems worldwide. In this context, changing site conditions and altered disturbance regimes as well as forest management responses are challenging the conservation of biodiversity in forests. Climate-induced dynamics and uncertainties related to future forest ecosystem development are calling into question current conservation strategies and concepts. Given the longevity of trees, slow development rates of forest ecosystems and slow migration rates of many forest species, the planning of adaptation measures in response to climate change are especially difficult though highly important for forest biodiversity conservation. This paper introduces a special issue with eight contributions which deal with a variety of aspects of forest biodiversity conservation in the face of climate change. More specifically, the papers address direct impacts of climate change on forest biodiversity, adaptation measures for forest and conservation management, as well as resulting challenges for conservation strategies and concepts. In conclusion, adaptation measures that enhance diversity and provide different options for future action, thereby maintaining ecosystems’ resilience, as well as conservation management operating on a landscape level, are promoted as being beneficial for coping with uncertainties related to climate change. Adaptive management, which constantly reviews conservation goals and measures, and which takes into account both science-based and local ecological knowledge on climate change can be a valuable tool to inform decisions for forest biodiversity conservation.     

Does flooding of rice fields after cultivation contribute to wetland plant conservation in southern Brazil?

Question: Does flooding of rice fields after cultivation contribute to wetland plant conservation in southern Brazil? Location: Rice fields in the coastal plain of southern Brazil. Methods: Six rice fields with different management practices were randomly selected (three dry rice fields and three flooded rice fields). Six collections were carried out over the rice cultivation cycle. Richness and biomass were measured using the quadrat method. Results: A total of 88 macrophyte species was recorded. There was no statistical interaction between management practices and rice cultivation phases for macrophyte richness and biomass. Macrophyte species richness and biomass changed over time, but were similar between flooded and dry rice fields. The first three axes generated by detrended correspondence analysis explained 29% of the variation in species composition and the multivariate analysis of variance showed that there was a statistical interaction between management practices and agricultural periods. Conclusions: Rice fields may help to conserve an important fraction of the aquatic macrophyte diversity of wetlands of southern Brazil by providing the setting up of a greater number of species within the agricultural landscape. However, rice fields must not be viewed as surrogate systems for natural wetlands. The difference in species composition between flooded and dry rice fields is interesting in terms of biodiversity conservation. If rice producers could keep part of their agricultural land flooded during the fallow phase, this management practice could be an important strategy for the conservation of biodiversity in areas where natural wetlands have been converted to rice fields.     

Butterfly diversity at the ecotone between agricultural and semi‐natural habitats across a climatic gradient

Aim Understanding the response of species to ecotones and habitat edges is essential to designing conservation management, especially in mosaic agricultural landscapes. This study examines how species diversity and composition change with distance from semi‐natural habitats, over ecotones into agricultural fields, and how within‐site patterns of community transition change across a climatic gradient and differ between crop types. Location A total of 19 sites in Israel where semi‐natural habitats border agricultural fields (wheat fields or olive groves) distributed along a sharp climatic gradient ranging between 100 and 800 mm mean annual rainfall. Methods  We performed butterfly surveys in 2006. We analysed species richness (α‐diversity), diversity, community nestedness and species turnover (β‐diversity) within sites and between sites (γ‐diversity). We also assessed where species of conservation concern occurred. Results In wheat sites, richness and diversity declined abruptly from ecotones to fields and remained homogenously poor throughout the fields, regardless of climate. In olive sites, despite the sharp structural boundary, richness and diversity remained high from the semi‐natural habitat to the grove margins and then declined gradually into groves. Species of conservation concern occurred across all habitats at olive sites, but none were found inside wheat fields or at their ecotones. The contrast in community structure between semi‐natural habitats and fields was affected by both climate and field type. Irrigation in arid regions did not augment species diversity. Main conclusions Our results indicate that consideration of crop type, within a climatic context, should receive high priority in biodiversity conservation in agricultural areas. In ‘hostile’ crops, such as wheat, we suggest favouring a combination of high‐intensity management and wide margins over less intensive management without margins, which may merely aid generalist butterfly species. The scarcity of butterflies in arid irrigated fields suggests a need to carefully assess the effects of irrigation and agrochemicals on species’ communities.     

植物的交配系统与濒危植物的保护繁育策略

植物的交配系统在理论上被视为影响种群遗传结构最为显著的因素之一。在具体实践中,指导着遗传育种和濒危植物的保护。本文首先剖析了交配系统及其相关的概念,并简要回顾交配系统研究的历史、重要的理论模型和方法。然后说明交配系统与种群遗传结构的具体关系,进而讨论交配系统在濒危植物进化与适应中的作用。最后说明交配系统的信息在就地与迁地保护中的重要性。     

农作物遗传多样性农家保护的现状及前景

农作物地方品种的有效保护是农业生物多样性的可持续利用的基础。由于现代农业的集约化生产方式使大量农作物地方品种被少数高产改良品种所取代,造成农作物基因库的严重“基因流失”（genetic erosion)。农家保护是在农业生态系统中进行的动态保护,被保护的生物多亲性可在其生境中继续进化而产生新的遗传变异,在而是农业生物多样性就地保护的重要途径。然而,尽管人们对作物品种资源农家保护的兴趣不断增长,也有大量有关农家的保护的研究和案例分析,但目前为止还没有比较成功的农家保护实例报道。因此,对农家保护的机制及科学问题进行深入的研究,并寻求一条新的途径来充分发挥农家保护应有的作用,显得格外重要。利用生物多样性布局的水稻混合间栽的生产模式,不仅解决了病害控制的问题,而且也保护了水稻地方品种的多样性。这种混合间栽的生物多样性布局和生产方式可能成为农保护的一条新途径。     

Household Differentiation and On-farm Conservation of Biodiversity by Indigenous Households in Xishuangbanna, China

With diversification of field type among households in same eco-environment and social situation, even in the same ecosystem, merging household socio-economics with biodiversity initiative values to determine incentives and optimum strategy of on-farm conservation of biodiversity. Botany survey of agroecosystems at landscape level in Daka and Baka, Xishuangbanna, Yunnan, China, as well as household differentiation of biodiversity in agroecosystem and on-farm conservation strategy merging household socio-economic characters were studied. There were 73 families 179 species distributed in 0.1 ha of different agroecosystems in Daka, and 70 families 166 species distributed in 0.08 ha different agroecosystems of Baka respectively. The cosmopolitan families, such as Gramineae and Compositae decreased the percentage of tropical families and subtropical families. Botany survey among 12 random selected households from Daka in 46 sampling plots of different agroecosystems showed significant differentiation of the species richness indices of natural biodiversity and agrobiodiversity as there were differences of cognition and utilization of plant species besides management practices among households. Dengrogram using the Ward method of hierarchical cluster analysis based on annual questionnaire interview of 60% household from 1998 to 2001 in Daka showed disparity among different households’ socio-economics which underpins management diversity. There were significant correlation coefficients between household socio-economics and species richness indices of different agroecosystems. Fallow size had significant positive correlation coefficients with species richness index of rubber plantation. By contraries, production input had negative correlation coefficients with species richness index of upland rice field. Meanwhile, cereal crop income had significant positive correlation coefficient with agro-species richness index of rubber plantation. By contraries, other income such as off-farm income had negative correlation coefficients with agro-species richness index of rubber plantation. Innovations of the expert farmer on agrobiodiversity on farm conservation were admiration.     

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。     

When the shoe doesn’t fit: applying conservation unit concepts to western painted turtles at their northern periphery

As biodiversity continues to be lost at an alarming rate, strategies for prioritizing populations for conservation have become increasingly important. Maintaining intraspecific genetic diversity is of particular importance for preserving evolutionary history and the potential for future adaptation. In order to effectively protect this diversity, units below the species level need to be defined. However, delineation of such units is subject to many challenges, with no one strategy applying universally across taxa. In this study we carried out the first genetic assessment of the western painted turtle (Chrysemys picta bellii) at its northern periphery in British Columbia (BC), Canada, using mitochondrial DNA haplotypic and microsatellite genotypic data to examine population structure and demographic history. We compared the application of evolutionarily significant unit and management unit criteria with Canadian designatable unit guidelines to determine appropriate conservation units. Our results show that BC western painted turtles form a single evolutionarily significant unit, with each occupied site constituting a separate management unit. In contrast, there is evidence for six discrete designatable units. Patterns of genetic variation in BC western painted turtles indicate that the conservation of each region is important to maintaining regional diversity and evolutionary novelty in this widespread species.     

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。     

Impact of land-use intensity on the conservation of functional and phylogenetic diversity in temperate semi-natural plant communities

The earth is facing a worldwide decline in biodiversity, with land-use change identified as one of the most important drivers. There is evidence that the loss of diversity has a significant impact on ecosystem functioning. Earlier research focused on species richness, but more recent, functional and phylogenetic diversity came into the picture as the stronger determinants of ecosystem processes. The effects of increasing land-use intensity on functional (FD) and phylogenetic diversity (PD), however, are still poorly understood. We studied how FD and PD are affected by land-use intensity in temperate plant communities. Our results show that land-use intensity has a clear impact on species richness, but also affects functional and phylogenetic diversity. Intensive agricultural areas fail to support high and sustainable levels of functional and phylogenetic diversity. These results highlight the need for the protection of biodiversity in nature reserves and the conservation of areas with extensive agricultural practices. Because species richness may influence the measures of functional and phylogenetic diversity, we compared the observed FD and PD values with random values generated with a matrix-swap null model. The observed discrepancy between species loss and the loss of FD and PD calls for an integrated approach to biodiversity conservation, in which the different components of biodiversity are considered together.