CWRML: representing crop wild relative conservation and use data in XML

Background Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Results Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. Conclusion CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data

Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review

Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts

Bridging the biodiversity data gaps: Recommendations to meet users’ data needs

A strong case has been made for freely available, high quality data on species occurrence, in order to track changes in biodiversity. However, one of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Therefore publishers of such data must face the challenge of maximizing quality, utility and breadth of data coverage, in order to make such data useful to users. Here, we report a number of recommendations that stem from a content need assessment survey conducted by the Global Biodiversity Information Facility (GBIF). Through this survey, we aimed to distil the main user needs regarding biodiversity data. We find a broad range of recommendations from the survey respondents, principally concerning issues such as data quality, bias, and coverage, and extending ease of access. We recommend a candidate set of actions for the GBIF that fall into three classes: 1) addressing data gaps, data volume, and data quality, 2) aggregating new kinds of data for new applications, and 3) promoting ease-of-use and providing incentives for wider use. Addressing the challenge of providing high quality primary biodiversity data can potentially serve the needs of many international biodiversity initiatives, including the new 2020 biodiversity targets of the Convention on Biological Diversity, the emerging global biodiversity observation network (GEO BON), and the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES)

Use of habitat suitability modeling in the integrated urban water system modeling of the Drava River (Varazdin, Croatia)

The development of practical tools for providing accurate ecological assessment of rivers and species conditions is necessary to preserve habitats and species, stop degradation and restore water quality. An understanding of the causal mechanisms and processes that affect the ecological water quality and shape macroinvertebrate communities at a local scale has important implications for conservation management and river restoration. This study used the integration of wastewater treatment, river water quality and ecological assessment models to study the effect of upgrading a wastewater treatment plant (WWTP) and their ecological effects for the receiving river. The WWTP and the water quality and quantity of the Drava river in Croatia were modelled in the software WEST. For the ecological modeling, the approach followed was to build habitat suitability and ecological assessment models based on classification trees. This technique allows predicting the biological water quality in terms of the occurrence of macroinvertebrates and the river status according to ecological water quality indices. The ecological models developed were satisfactory, and showed a good predictive performance and good discrimination capacity. Using the integrated ecological model for the Drava river, three scenarios were run and evaluated. The scenario assessment showed that it is necessary an integrated approach for the water management of the Drava river, which considers an upgrading of the WWTP with Nitrogen and Phosphorous removal and the treatment of other diffuse pollution and point sources (including the overflow of the WWTP). Additionally, if an increase in the minimum instream flow after the dams is considered, a higher dilution capacity and a higher self-cleaning capability could be obtained. The results proved that integrated models like the one presented here have an added value for decision support in water management. This kind of integrated approach is useful to get insight in aquatic ecosystems, for assessing investments in sanitation infrastructure of urban wastewater systems considering both, the fulfilling of legal physical chemical emission limits and the ecological state of the receiving waters

Species distribution models

Species distribution models are a group of methods often used to estimate consequences of global change, to assess ecological status and for other ecological applications. The main idea behind species distribution models is that the geographical distributions of species can, to a large part, be explained by environmental factors and that species distributions therefore can be predicted in time or space. For robust and reliable applications, models need to be based on sound ecological principles, predictions need to be as accurate as possible, and model uncertainties need to be understood. Two approaches are available for modelling entire species communities: (1) each species can be modelled individually and independently of other species or (2) community information can be incorporated into the models. The first study in this thesis compares these two modelling approaches for predicting phytoplankton assemblages in lakes. The results showed that predictive accuracy was higher when species were modelled individually. The results also showed that phytoplankton can be used for model-based assessment of ecological status. This finding is important because phytoplankton is required for assessing the ecological status of European water bodies according to the European Water Framework Directive. Dispersal barriers in the landscape or limited dispersal ability of species might be a reason for species being absent from suitable habitats, and these factors might therefore affect model accuracy. The second study in this thesis examines the influence of dispersal and the spatial configuration of ecosystems on prediction accuracy of benthic invertebrate and phytoplankton distribution and assemblage composition. The results showed only a minor influence of spatial configuration and no effect of flight ability of invertebrates on model accuracy. However, the models used may partly account for dispersal constraints, since dispersal-related factors, such as lake surface area, are included as predictor variables. The result also showed that composition of littoral invertebrate assemblages was easier to predict at sites located in well-connected lake systems, possibly because the relatively unstable littoral zone necessitates a need for species to re-colonize disturbed habitats from source populations

Hawaiian Picture‐Winged Drosophila Exhibit Adaptive Population Divergence along a Narrow Climatic Gradient on Hawaii Island

1. Anthropogenic influences on global processes and climatic conditions are increasingly affecting ecosystems throughout the world. 2. Hawaii Island’s native ecosystems are well studied and local long‐term climatic trends well documented, making these ecosystems ideal for evaluating how native taxa may respond to a warming environment. 3.This study documents adaptive divergence of populations of a Hawaiian picture‐winged Drosophila, D. sproati, that are separated by only 7 km and 365 m in elevation. 4.Representative laboratory populations show divergent behavioral and physiological responses to an experimental low‐intensity increase in ambient temperature during maturation. The significant interaction of source population by temperature treatment for behavioral and physiological measurements indicates differential adaptation to temperature for the two populations. 5.Significant differences in gene expression among males were mostly explained by the source population, with eleven genes in males also showing a significant interaction of source population by temperature treatment. 6.The combined behavior, physiology, and gene expression differences between populations illustrate the potential for local adaptation to occur over a fine spatial scale and exemplify nuanced response to climate change