Modelling spatial patterns of biodiversity for conservation prioritization in North-eastern Mexico

Relationships between spatial patterns of bird and mammal species richness in north‐eastern Mexico were analysed in relation to the location of three biosphere reserves (El Abra‐Tanchipa, El Cielo, and Sierra Gorda) and 13 priority areas recently identified for conservation. Ecological niches were modelled and potential distributions delimited for 285 bird and 114 mammal species using a genetic algorithm based on locality information from museum specimens and 15 selected environmental attributes. Potential distributions were transformed into hypothesized current distributions based on species–habitat associations as reflected in a recent land‐use map. Although species richness was lower when distributions were reduced from potential to current, spatial patterns of potential and current richness were similar. Heuristic, complementarity‐based prioritization procedures were used to identify combinations of areas and sites with maximal species representation: the biosphere reserves included 79% of birds and 74% of mammal species; eight priority areas provided an additional 11% of birds and 13% of mammals; the remaining 10% of birds and 13% of mammals were concentrated in new sites across the study area.     

Efficient rescue of threatened biodiversity data using reBiND workflows

Abstract

Biodiversity data generated in the context of research projects often lack a strategy for long-term preservation and availability, and are therefore at risk of becoming outdated and finally lost. The reBiND project aims to develop an efficient and well-documented workflow for rescuing such data sets. The workflow consists of phases for data transformation into contemporary standards, data validation, storage in a native XML database, and data publishing in international biodiversity networks. It has been developed and tested using the example of collection and observational data but is flexible enough to be transferred to other data types and domains.     

Data requirements and data sources for biodiversity priority area selection

The data needed to prioritize areas for biodiversity protection are records of biodiversity features — species, species assemblages, environmental classes — for each candidate area. Prioritizing areas means comparing candidate areas, so the data used to make such comparisons should be comparable in quality and quantity. Potential sources of suitable data include museums, herbariums and natural resource management agencies. Issues of data precision, accuracy and sampling bias in data sets from such sources are discussed and methods for treating data to minimize bias are reviewed.     

大数据时代的整合生物信息学

随着生物数据测量技术的不断发展,生物数据的类型、内容、复杂度不断增加,生物信息学已迈入大数据时代。面对大数据时代多模态、多层次、高维度、非线性的复杂生物数据,生物信息学需要发展相应的方法和技术进行有效整合生物信息学研究与应用。本文对大数据时代整合生物信息学所涉及的数据整合、方法整合、系统整合及相关问题进行梳理和探讨。     

关于组学大数据背景下《微生物学》教材框架的思考

微生物学是生物学的重要内容,是全国高等院校生物学专业或相关专业的本科生必修的一门核心基础课,其主要任务是给学生提供基础的、系统的、前沿的微生物学知识和理论。随着高通量测序、质谱、芯片等高通量技术的快速发展,生命科学领域快速进入了以海量多元组学(基因组学、转录组学、蛋白质组学、免疫组学、代谢组学等)数据为特征的大数据时代,而这势必会对微生物学教材已有的内容产生冲击和补充。本文对如何在组学大数据背景下对国内经典的微生物学教材进行改革,将目前最具突破性的组学成果整合到已有的教材框架中或革新现有教材框架进行了初步探讨。     

High resolution satellite imagery for tropical biodiversity studies: the devil is in the detail

While high resolution satellite remote sensing has been hailed as a very useful source of data for biodiversity assessment and monitoring, applications have been more developed in temperate areas. The biodiverse tropics offer a challenge of an altogether different magnitude for hyperspatial and hyperspectral remote sensing. This paper examines issues related to hyperspatial and hyperspectral remotely sensed imagery, which constitutes one of the most potentially powerful yet underutilized sources of for tropical research on biodiversity. Hyperspatial data with their increased pixel resolution are possibly best suited at facilitating the accurate location of features such as tree canopies, but less suited to the identification of aspects such as species identity, particularly when spatial resolution becomes too fine and pixels are smaller than the size of the object (e.g., tree canopy) being identified. Hyperspectral data on the other hand, with their high spectral resolution, can be used to record information pertaining to a range of critical plant properties related to species identity, and can be very effective used for discriminating tree species in tropical forests, despite the greater complexity of such environments. There remains a glaring gap in the easy availability of hyperspectral and hyperspatial satellite data in the tropics due to reasons of cost, data coverage, and security restrictions. Stimulating discussion on the applications of this powerful, but underutilized tool by ecologists, is the first step in promoting a more extensive use of such data for ecological studies in tropical biodiversity rich areas.     

黄淮海湿地生态系统服务与生物多样性保护格局的耦合性

研究生物多样性格局与生态系统服务格局之间的空间耦合效应,探讨以生物多样性保育为核心目标的自然保护体系同时能多大程度满足对生态系统服务功能的维护和支撑,已成为自然保护领域新的热点关注问题。目前研究多限于陆域生态系统,其方法难以适用于湿地生态系统。以黄淮海湿地——这一高强度人类活动的区域为研究区,基于湿地生态系统的横向连接度、纵向连接度(2D)以及结合地下水的垂向连接度(3D),对黄淮海地区湿地具有的生态系统服务功能进行了空间评估和分析,识别出具有重要意义的生态系统服务功能区域,结合现有保护区分布情况进行空间分析,评价现有保护区对生态系统服务功能的支持程度,即生物多样性保护与生态系统服务功能重点区域的空间耦合性。研究结果表明:目前湿地保护区并未有效覆盖湿地生态系统关键区域,湿地生态系统服务关键格局也存在大量明显的保护空缺。同时,随着2D到3D延伸,保护区对生态系统服务功能的支持程度也稍有提高,这与系统保护规划中选择不同保护目标后保护规划格局发生变化的情况类似,而生态系统服务功能的"热点地区"(重要区域)与保护生物学中所指的物种保护的热点地区类似,这表明生态系统服务功能的规划和保护也可以借鉴保护生物学中系统保护规划的理论和方法,为后续研究提供参照。     

噬藻体生物多样性的研究动态

噬藻体(Cyanophage)是感染原核生物蓝藻(Cyanobacteria)的病毒,广泛分布于各种水生态系统中,对调控初级生产力、蓝藻种群密度及结构演替、微生物间基因转移以及全球生物地理化学循环等方面有重大影响。关注噬藻体的生物多样性,发现其感染相关基因,阐明噬藻体与宿主蓝藻的相互作用,将为藻华控制及认识病毒在复杂水环境中的功能提供重要信息。本文就噬藻体生物多样性,包括生态系统多样性、物种多样性及遗传多样性研究动态做一综述。     

Amazonian lowland, white sand areas as ancestral regions for South American biodiversity: Biogeographic and phylogenetic patterns in Potalia (Angiospermae: Gentianaceae)

Present-day white sand areas in South America are thought to be relictual areas of earlier, widespread habitats now covered by more recent sediments mainly from the Andean orogeny. These ancient, nutrient-poor areas have been suggested to be possible ancestral regions for neotropical plant diversity. Members of the genus Potalia of the Gentianaceae grow in the New World tropics from Costa Rica in the north to southern Bolivia. Until recently, only one Potalia species was accepted, but a new revision identifies eight others. Three species are endemic to lowland, white sand areas in the Amazon and Orinoco basins and share morphological characteristics with Anthocleista, the African – Malagasy sister group to Potalia. To resolve phylogenetic and biogeographic patterns in Potalia, morphological characters and sequences of the internal transcribed spacer (ITS) and the 5S non-transcribed spacer (5S-NTS) of the ribosomal nuclear DNA were collected and used for phylogenetic reconstruction using Bayesian and parsimony-based methods. Potalia species restricted to ancient, nutrient-poor white sand areas of the Amazon Basin and Guayana Shield were placed basal to other Potalia taxa from finer, lateritic, and younger soils, further suggesting that lowland white sand areas may be ancestral seats of neotropical diversity.     

In silico environmental sampling of emerging fungal pathogens via big data analysis

Yeast species in the Candida haemulonii complex (C. haemulonii, C. haemulonii var. vulnera, C. duobushaemulonii, C. pseudohaemulonii, and C. vulturna) and closely related species (C. auris, C. heveicola, and C. ruelliae) are of significant public health concern worldwide. Little is known about their natural habitat. To understand the worldwide emergence of new fungal pathogens, it is important to identify key environmental habitats. Showing the effectiveness of the primary fungal DNA barcode and leveraging big data archived in the Sequence Read Archive (SRA) database enabled the identification of novel reservoirs over a wide range of geographical areas for those yeasts. We identified 1209 datasets corresponding to species in the C. haemulonii complex and three closely related species. Our results imply that climate change is not the main driver for the emergence of pathogenic multidrug-resistant yeast species. This approach opens the door for further big data analysis using the accessible resources of such databases.     

BitTorious: global controlled genomics data publication,research and archiving via BitTorrent extensions

Background

Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the interoperability of those deployments in a manner embracing the heterogeneous needs, terms and infrastructure of collaborating parties. This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent.

Results

The BitTorious portal was sucessfully used to manage many concurrent domestic Bittorrent clients across the United States: exchanging genomics data payloads in excess of 500GiB using the uTorrent client software on Linux, OSX and Windows platforms. Individual nodes were sporadically interrupted to verify the resilience of the system to outages of a single client node as well as recovery of nodes resuming operation on intermittent Internet connections.

Conclusions

The authorization-based extension of Bittorrent and accompanying BitTorious reference tracker and user management web portal provide a free, standards-based, general purpose and extensible data distribution system for large ‘omics collaborations.     

Examination of the 'founder effect' in biodiversity research: patterns and imbalances in the published literature

We reviewed 2524 articles published from 1987 to 1995 in five international journals, Conservation Biology , Biological Conservation , Biodiversity and Conservation , Ecological Applications , and the Journal of Applied Ecology , to assess patterns and imbalances in biodiversity research in the following subject areas: locations where research was conducted, types of organisms studied, types of ecosystems studied, types of methodologies used, and types of stresses investigated. Biodiversity research was found to be narrowly focused with little deviation from its initial course set of being a discipline concerned largely with the implications of forest habitat loss on charismatic terrestrial megafauna; i.e. the 'founder effect' is very much in evidence. The 'sleeping dragon' of ignored marine biodiversity is really symptomatic of a wider problem, and can perhaps be referred to as a 'hibernating hydra' of many imbalances due to, for example, under-representations of research from developing nations, or on amphibians and invertebrates, alpine and arctic systems, sociological components and chemical stresses etc. It is time to take steps to actively awaken the creature so that conservation biology/applied ecology can become more pluralistic in scope.     

Present patterns and future prospects for biodiversity in the Western Hemisphere

Creating networks of nature reserves to protect areas rich in biodiversity from the adverse impacts of anthropogenic change is a critical and urgent task. We illustrate the skewed geographical and size distributions of protected areas in the Western Hemisphere. For instance, 811 of 1413 reserves in the Western Hemisphere are smaller than 10 km², and 35% of the total area of these reserves is in Alaska. We compile ranges for all bats in the continental Western Hemisphere and find that 82% of threatened and small‐range species are not protected adequately. Many of the most vulnerable species occur in the areas of highest human density. We provide maps delineating areas where conservation investments may have the greatest impact in preventing biodiversity losses.     

Distribution patterns of biodiversity and the design of a representative reserve network in Portugal

Representativeness is a desirable property of conservation networks. In this paper an attempt is made to assess the efficiency of current conservation networks in Portugal in representing vertebrates (reptiles and amphibians) and plants (gymnosperms, pteridophytes and bryophytes). It was found that whilst the protected areas do not sample all species in the database they provide a better result than choosing areas at random. For the goal of maximizing representation of taxa per unit area hotspots and complementarity performed better. A pattern of over-representation of vertebrates in relation to lower plants was discovered among selected conservation areas in Portugal suggesting that charismatic organisms with large home ranges may not always be the most appropriate surrogates for biodiversity when representativeness is sought. When trying to fill the gaps in current protected areas with additional areas only complementarity performed better than choosing areas at random. Both rarity and richness hotspots gave worse results. Opportunistic administrative criteria such as supplementing the PAS with other conservation areas (CORINE Biotopes) without taking into account their contribution to a representation goal was nearly half as good as choosing areas at random. The results recall for the need of explicit goals and accountable methods in area selection for conservation and reinforce the role of complementarity for finding additional areas to protected areas when limited resources are available for ‘in situ’ conservation.     

Modelling relationships between species spatial abundance patterns and climate

Aim To move towards modelling spatial abundance patterns and to evaluate the relative impacts of climatic change upon species abundances as opposed to range extents. Location Southern Africa, including Lesotho, Namibia, South Africa, Swaziland and Zimbabwe. Methods Quantitative response surface models were fitted for 78 bird species, mostly endemic (68) or near‐endemic to the region, to model relationships between species reporting rates (i.e. the proportion of checklists reporting a species for a particular grid cell), as recorded by the Southern African Bird Atlas Project, and four bioclimatic variables derived from climatic data for the period 1961–90. With caution, reporting rates can be used as a proxy for abundance. Models were used to project potential impacts of a series of projected climatic change scenarios upon species abundance patterns and range extents. Results Most models obtained were robust with good predictive power. Projections of potential future abundance patterns indicate that the magnitude of impacts upon a proxy for abundance are greater than those upon range extent for the majority of species (82% by 2071–2100). For most species (74%) both abundance and range extent are projected to decrease by 2100. Impacts are especially severe if species are unable to realize projected range changes; when only the area of a species' simulated present range is considered, overall abundance decreases of more than 80% are projected for 19 (24%) of species examined. Main conclusions Our results indicate that projected climatic changes are likely to elicit greater relative changes in species abundances than range extents. For most species examined changes were decreases, suggesting the impacts upon biodiversity are likely generally to be negative. These results also suggest that previous estimates of the proportion of species at increased risk of extinction as a result of climatic change may, in some cases, be under‐estimates.     

A collaborative GIS method for integrating local and technical knowledge in establishing biodiversity conservation priorities

Methods for establishing biodiversity conservation priorities are urgently required, as the number of species and habitats that are threatened increases relative to the material resources available for their conservation. The identification of priority areas demands the integration of biophysical data on ecosystems together with social data on human pressures and planning opportunities. But comprehensive and reliable data are rarely available to demarcate where the need for action is most urgent and where the benefits of conservation strategies can be maximized. Strategic conservation initiatives cannot wait for the creation of comprehensive databases. In order to fill the missing data gaps, the combined knowledge of local and technical experts can be used. This study presents a collaborative geographic information system (GIS) method for integrating the knowledge of local and technical experts with existing spatial environmental data to establish priority areas for biodiversity conservation. Procedures for structuring and framing the discussions, establishing assessment criteria, integrating knowledge with data, and building consensus are incorporated into the method. The method provides a novel cooperative mechanism to aid spatial knowledge management and inclusive biodiversity planning.     

Environmental gradients and community attributes underlying biodiversity patterns of semi-arid Mediterranean grasslands

Protection and/or establishment of forest plantation have been used as a management strategy to conserve and stop the deterioration of semi-arid Mediterranean grasslands ecosystems, producing a mosaic of vegetation types. This study was intended to investigate the changes in grassland community in response to protection and forest tree plantation practice as well as to explore the underlying environmental gradients responsible for the observed differences or similarities among these vegetation types. Two multivariate analysis methods including discriminate analysis and non-metric multi-dimensional scaling were used to quantify changes in community composition and attributes following different management practices (free grazing, protection with open grassland, sparse and dense forest tree plantations). This was investigated using species frequency, species abundance, or habitat characteristics. The study results showed that habitat types differed significantly between each other and were significantly separated using multivariate approaches. Discrimination based on habitat characteristics and species composition indicated that protection (or grazing) and light (or shade) explained more than 90% of the observed variability in community changes in response to the protection and forest tree plantation. Also, results indicated that shade effect can be attributed to tree canopy cover and/or litter accumulation on the ground. It could be hypothesized that protection from grazing and afforestation resulted in complex environmental gradients of which shade, litter accumulation as well as protection from grazing disturbance are major constituents. A careful manipulation of protection and afforestation can be used to create a spatially different environmental gradients leading to greater habitat diversity as well as a greater species diversity, and better conservation means of grassland in semi-arid areas.     

Freshwater fish biodiversity in the Yangtze River basin of China: patterns, threats and conservation

We synthesized information on freshwater fish biodiversity in the Yangtze River basin. We documented 361 species and subspecies that had been recorded and described from the basin. Of these, 177 species are endemic. The basin is usually divided into three parts, i.e. the upper reaches, the middle reaches and the lower reaches. This study indicated that the three reaches approach was not supported by fish distribution patterns. Hydrological alterations are perhaps the largest threat to fish biodiversity in the basin. Fishes in the upper reaches will be seriously affected by the construction of the Three Gorges Dam and other dams, and action should be taken for priority conservation. The most immediate restoration need is reconnection of the Yangtze River with its lakes. The cluster of lakes in the Central Yangtze should be protected to maintain habitats for spawning, feeding and migration of migratory fishes. Our study indicates a need to identify areas of high fish biodiversity and to select nature reserves to mitigate the loss of fish biodiversity in the Yangtze River basin.     

Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains

Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues. However, most previous studies have focused on the entire Qinghai-Tibet Plateau, leaving independent physical geographic subunits in the region less well understood. We studied the current plant diversity of the Kunlun Mountains, an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and community phylogenetic structure of the current plant diversity in the area. The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains. The taxonomic richness, phylogenetic diversity, and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation, particularly the southeastern regions. The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization. The Hengduan Mountains, a biodiversity hotspot, is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary. The net relatedness index indicated that 20 of the 28 communities examined were phylogenetically dispersed, while the remaining communities were phylogenetically clustered. The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered. These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes, and habitat filtering may play an important role in this ecological process.