Cultured fish: integrative biology and management of domestication and interactions with wild fish

Fish aquaculture for commodity production, fisheries enhancement and conservation is expanding rapidly, with many cultured species undergoing inadvertent or controlled domestication. Cultured fish are frequently released, accidentally and deliberately, into natural environments where they may survive well and impact on wild fish populations through ecological, genetic, and technical interactions. Impacts of fish released accidentally or for fisheries enhancement tend to be negative for the wild populations involved, particularly where wild populations are small, and/or highly adapted to local conditions, and/or declining. Captive breeding and supplementation can play a positive role in restoring threatened populations, but the biology of threatened populations and the potential of culture approaches for conserving them remain poorly understood. Approaches to the management of domestication and cultured‐wild fish interactions are often ad hoc, fragmented and poorly informed by current science. We develop an integrative biological framework for understanding and managing domestication and cultured‐wild fish interactions. The framework sets out how management practices in culture and for cultured fish in natural environments affect domestication processes, interactions between cultured and wild fish, and outcomes in terms of commodity production, fisheries yield, and conservation. We also develop a typology of management systems (specific combinations of management practices in culture and in natural environments) that are likely to provide positive outcomes for particular management objectives and situations. We close by setting out avenues for further research that will simultaneously improve fish domestication and management of cultured‐wild fish interactions and provide key insights into fundamental biology.     

东北森林区生态保护及生物资源开发利用技术及示范

由中央财政专项资助的项目(2016YFC0500300),面向东北林区天然林保护与经济绿色转型发展等重大需求,针对关键技术瓶颈开展技术研发和集成,建立森林生态系统与生物资源监测平台,突破重要生物资源允收量控制、关键种保护和群落定向分类等天然林保护关键技术,基于品种创新、原生境生态培育和高附加值产品工艺研发,建立全产业链技术体系与标准,支持东北林区天然林有效保护和林区经济的可持续发展。本项目预期建立天然林保护与生物资源利用全产业链技术体系与规程29套以上,育成新品种15个以上,开发生态产品16项以上,申请发明专利25项以上,生态产品全部产业转化,项目形成的技术体系将在龙江森工的伊春林区、牡丹江林区和吉林森工的长白山林区建立三大规模化示范基地,结合周边生态脆弱地区示范推广,总面积达10万hm2以上,示范区非林经济总量提高50%、人均收入平均增长1.5倍。     

Next-generation sequencing for understanding and accelerating crop domestication

Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associated with domestication. Species-specific data can be obtained from related wild species by whole-genome shot-gun sequencing. This sequence data can be used to design species specific polymerase chain reaction (PCR) primers. Sequencing of the products of PCR amplification of target genes can be used to explore genetic variation in large numbers of genes and gene families. Novel allelic variation in close or distant relatives can be characterized by NGS. Examples of recent applications of NGS to capture of genetic diversity for crop improvement include rice, sugarcane and Eucalypts. Populations of large numbers of individuals can be screened rapidly. NGS supports the rapid domestication of new plant species and the efficient identification and capture of novel genetic variation from related species.     

High-throughput DNA barcoding for ecological network studies

The network theoretical framework of ecological community studies is expected to promote not only the basic understanding of ecological and coevolutionary dynamics but also the application of those scientific insights into ecosystem management. However, our knowledge of ecological network architecture in the wild largely stems from empirical studies on macro-organismal systems such as those of plant–pollinator, plant–seed disperser, and prey–predator interactions. In this sense, we have remained ignorant of the diversity of ecological network architecture, its underlying assembly processes, and its consequences on ecological and coevolutionary dynamics. In this paper, I discuss how the high-throughput DNA barcoding of microbes, especially that based on next-generation sequencing, potentially expands the target of ecological network studies. I review the methodological platforms of next-generation sequencing-based analyses of microbe–host animal/plant networks and then introduce some case studies on the networks of plants and their hyper-diverse fungal symbionts. As those preliminary studies are uncovering the unexpected diversity of ecological network architecture, further application of such next-generation sequencing-based analyses to a diverse array of microbial systems will significantly improve our views on community ecological and coevolutionary processes.     

Toward the domestication of lignocellulosic energy crops: learning from food crop domestication

Domestication of cereal crops has provided a stable source of food for thousands of years. The extent to which lignocellulosic crops will contribute to the world's renewable energy depends largely on how the new crops will be domesticated. Growing miscanthus as biofuel feedstocks on marginal and degraded land in northern and northwestern China offers an example for developing theoretical framework and practical strategies for energy crop domestication. The domestication should incorporate the highest possible genetic diversity from wild species, focus on the improvement of drought and cold tolerance especially in the stage of crop establishment, increase the efficiencies of water and nutrient uses and photosynthesis, adjust vegetative growing season according to local temperature and precipitation, and reduce or prevent seed production. Positive ecological effects on soil conservation, landscape restoration, carbon sequestration, and hydrological cycles should be maximized, while negative impact on biodiversity needs to be minimized. With the development of other sources of renewable energy, the role of lignocellulosic crops may evolve from primarily energy production to increasingly ecological restoration and biomaterial development. The integration of this new cropping system into the existing agriculture may open a new avenue to the long-term sustainability of our society.     

Biodiversity as a source for synthetic domestication of useful specific traits

Plant and animal domestication form the foundation of agriculture. Currently, there are considerable efforts and hypotheses to understand adaptation and regulatory processes involving domestication and biodiversity organisms. Here, we propose the use of recombinant DNA as a foundation for the synthetic domestication of biodiversity traits. For example, we commented on current studies involving synthetic spider‐like fibres production in bacteria and mimicking oil seed species in genetically manipulated soybean. We suggest that this approach constitutes a sustainable and viable option for conservation and development of value‐added processes and products from biodiversity.     

Moving beyond abundance distributions: neutral theory and spatial patterns in a tropical forest

Assessing the relative importance of different processes that determine the spatial distribution of species and the dynamics in highly diverse plant communities remains a challenging question in ecology. Previous modelling approaches often focused on single aggregated forest diversity patterns that convey limited information on the underlying dynamic processes. Here, we use recent advances in inference for stochastic simulation models to evaluate the ability of a spatially explicit and spatially continuous neutral model to quantitatively predict six spatial and non-spatial patterns observed at the 50 ha tropical forest plot on Barro Colorado Island, Panama. The patterns capture different aspects of forest dynamics and biodiversity structure, such as annual mortality rate, species richness, species abundance distribution, beta-diversity and the species–area relationship (SAR). The model correctly predicted each pattern independently and up to five patterns simultaneously. However, the model was unable to match the SAR and beta-diversity simultaneously. Our study moves previous theory towards a dynamic spatial theory of biodiversity and demonstrates the value of spatial data to identify ecological processes. This opens up new avenues to evaluate the consequences of additional process for community assembly and dynamics.     

Whole-genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin

Shifting from a livestock-based protein diet to a plant-based protein diet has been proposed as an essential requirement to maintain global food sustainability, which requires the increased production of protein-rich crops for direct human consumption. Meanwhile, the lack of sufficient genetic diversity in crop varieties is an increasing concern for sustainable food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics. Narrow-leafed lupin (Lupinus angustifolius L.) has experienced rapid domestication and has become a new legume crop over the past century, with the potential to provide protein-rich seeds. Here, using long-read whole-genome sequencing, we assembled the third-generation reference genome for the narrow-leafed lupin cultivar Tanjil, comprising 20 chromosomes with a total genome size of 615.8 Mb and contig N50 = 5.65 Mb. We characterized the original mutation and putative biological pathway resulting in low seed alkaloid level that initiated the recent domestication of narrow-leafed lupin. We identified a 1133-bp insertion in the cis-regulatory region of a putative gene that may be associated with reduced pod shattering (lentus). A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as precisely predicted by the original model of the bottleneck effect on genetic variability in populations. Our results identify the key domestication genetic loci and provide direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.     

Divergent responses of flagship,keystone and resource-limited bio-indicators to forest structure

Bio-indicators are often proposed to set conservation priorities in forest habitat owing to the difficulties of determining forest intrinsic ecological value. Here, we tested the efficacy of a number of potential bird indicator groups in monitoring beech Fagus sylvatica forest status by analyzing their associations with the spatial and structural variables of forest vegetation that indicate key ecological patterns and processes. The density of cavity nesting birds, indicating the presence of limited forest resources (resource-limited indicators), was influenced by tree species diversity, vertical species mingling and diameter, parameters reflecting maturity, gap-dynamic processes, as well as resource and shelter availability. Heterogeneity in shrub species composition, another parameter depending on forest dynamics, was positively associated with the occurrence of Capercaillie, a “flagship” species for forest conservation. The presence of woodpeckers, a “keystone” group that provides shelter and foraging substrate to other organisms, was positively affected by the basal area of standing dead trees that is indirectly associated with natural nutrient availability. These findings suggest that single indicators fail to provide a complete assessment of forest status, and their use in monitoring or managing forest ecosystem need to be contextualized to specific ecological patterns. The combined use of several indicators, representing various taxa, functions and life histories, appears to be preferable, and is logistically feasible if these can be surveyed together. Several indicators would likely display a wider range of sensitivities to the modification of natural processes and permit more comprehensive tracking of forest dynamics than single flagship, keystone or resource-limited indicators.     

Domestication of cereal crops in the old world: in search of a new approach to solving old problem

N.I. Vavilov's theory of the centres of origin of cultivated plants is still as a methodological base for studying processes of domestication. This theory, along with archaeological, botanical, and molecular genetic data, helped to determine the most probable regions where the principal cultivated species were introduced into culture. The search for the mechanisms of origins of morphological changes in the course of domestication is one of evolutionary biology's oldest problems. Employing novd molecular biological data for solving this problem provides a key to the understanding of these mechanisms and helps to reconstruct a possible scenario of how the traits that distinguish domesticated plants from their wild relatives got involved into selection. It is hypothesized that distinct physiological and morphological differences important to ancient agrarians originated from quantitative and/or qualitative changes in the loci regulating the programmes of plant ontogeny. This hypothesis helps to reveal the mechanisms of origin of certain traits in the course of domestication, to study the connection between the direction of selection and how such traits are genetically controlled, and to outline particular ways for further detailed studies of the evolutionary aspect of domestication processes.     

Dual invasion analysis: a general model of novel ecological dynamics due to Bt product and resistant pests in wild settings

Transgenic Bt crops have been integrated as a central component of the agricultural policies of many nations across the globe due to their insecticidal properties. While focus on increased yield resulting from the use of Bt crops has overshadowed the concerns of pest populations developing resistance, resistance has been recently discovered in even highly managed fields. One issue that has received less attention is the resulting set of ecological dynamics from escaped Bt products into wild settings. I present a differential equation model of the ecological interaction between a wild plant–pest community and an invading Bt toxin-producing plant and the ensuing evolution of pest resistance. Key to this model investigation is the assumption of energy costs with both the production of Bt toxin by Bt plants and the resistance to Bt toxin exhibited by resistant pest individuals. Results show that persistence of the initial invading Bt plant population is possible through an intransitive loop dynamic. Furthermore, coexistence of wild-type plants and pests as well as Bt-producing plants and resistant pests is possible through the dynamics resultant from energy trade-offs.     

Evolutionary dynamics of transposable elements during silkworm domestication

Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.     

Production of edible mushrooms in forests: trends in development of a mycosilviculture

Developing the production of ectomycorrhizal (ECM) mushrooms in forest has become a challenge. Only a few ECM species are currently cultivable. Controlled mycorrhization practices offer promising advance to produce currently uncultivable ECM mushrooms. The persistence of the production of edible species, either cultivated or wild, depends on both the tree and the ecological environment (fungal communities, climate, soil, tree development). Developing adapted forest management practices appears to be means to improve production of edible ECM mushrooms. This review summarises current knowledge on the development of a science-based mycosilviculture for the production of edible ECM mushrooms.     

退化森林生态系统恢复评价研究综述

森林退化是一个世界性的问题,对退化的森林进行恢复评价是合理地进行森林生态系统管理的基础。介绍了森林退化的概念,综述了退化森林生态系统恢复评价的一般程序,主要包括恢复目标的确定、参照系的选择、评价指标体系的构建及定量评价等几个方面。目前,大多数退化森林恢复评价主要包括物种多样性、植被结构和生态学过程3个方面。其中,物种多样性包括物种丰富度和多度等;植被结构包括植被盖度、乔木密度、高度、胸高断面积、生物量和凋落物结构等;生态学过程包括养分库、土壤有机质以及生物间的相互关系等。不同的研究者或管理者由于对恢复其生态系统服务功能的需求存在差异,评价退化生态系统恢复的角度也不一样。恢复评价可以从特殊种群到整个生态系统的不同层次进行。在深刻理解森林退化定义的基础上,建立现实的目标和正确地选择参照系是恢复评价的前提。     

Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification

The evolution of the polyploid Triticum wheats is distinctive in that domestication, natural hybridization and allopolyploid speciation have all had significant impacts on their diversification. In this review, I outline the phylogenetic relationships of cultivated wheats and their wild relatives and provide an overview of the recent progress and remaining issues in understanding the genetic and ecological factors that favored their evolution. An attempt is made to view the evolution of the polyploid Triticum wheats as a continuous process of diversification that was initiated by domestication of tetraploid emmer wheat and driven by various natural events ranging from interploidy introgression via hybridization to allopolyploid speciation of hexaploid common wheat, instead of viewing it as a group of discrete evolutionary processes that separately proceeded at the tetraploid and hexaploid levels. This standpoint underscores the important role of natural hybridization in the reticulate diversification of the tetraploid-hexaploid Triticum wheat complex and highlights critical, but underappreciated, issues that concern the allopolyploid speciation of common wheat.     

片段化森林群落构建的生态过程及其检验方法

鉴于全球森林均呈现片段化(破碎化)的分布状态, 理解片段化森林群落构建的过程很有必要。该文通过综述群落构建的主要生态过程如生态漂变、扩散、选择和物种形成等在片段化森林群落构建中的相对作用, 发现因片段化森林形成方式的不同, 重构群落(片段化生境中通过次生演替重新形成的森林群落)和解构群落(原有森林被片段化后形成的森林群落)在不同演替阶段所受到的主要生态过程的相对作用有所不同。虽然利用基于群落内物种分布格局推测构建过程(如物种多度分布、零模型结合β多样性的方法、功能特征的收敛和发散等)、人工控制实验、群落结构动态分析等方法对片段化森林中群落构建的过程进行了有效的检验, 但是针对片段化森林群落构建过程的实验性研究仍然不足。未来有待在理论模型、群落构建过程的检验以及理论与物种保护相结合等方面继续开展深入的研究。     

Domestication Shapes Recombination Patterns in Tomato

Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.     

Habitat features and genetic integrity of wild grapevine Vitis vinifera L. subsp. sylvestris (C.C. Gmel.) Hegi populations: A case study from Sicily

Wild grapevine represents a valuable genetic resource for both future breeding programmes of cultivated grape and conservation of biological diversity in natural environments. In Sicily, the knowledge of this species is quite scarce and fragmentary. Therefore, in order to assess the presence and the genetic quality of wild grapevine in the island, eight populations from different locations were investigated. Their habitats were characterized and the genetic diversity was measured by microsatellite markers in order to evaluate possible relationships between genetic features and the ecological behaviour of populations.With the exception of one population found in a scree-type habitat, all the others were present in flooded areas. Grapevine populations growing in riparian habitats were characterized by low inter- and intra-population variability. Conversely, the scree-type population proved to be the most compact and distinctive, as well as the most genetically isolated. Interestingly, together with other two populations from the northern mountain range of the island, this scree-type grapevine population was genetically rather distant from local domestic accessions, suggesting a weak gene exchange with the cultivated grapevines in Sicily. On the contrary, the other populations showed evidences of probable introgression events, as a result of either gene flow between domestic and wild plants, or of possible secondary domestication/genetic improving processes, based on the use of native wild material.