Tailoring evidence into action: using a codesign approach for biodiversity information in the Tropical Andes / Toma de decisiones basadas en la evidencia: un enfoque de codiseño para la información sobre biodiversidad en los Andes tropicales / Tomada de decisão baseada em evidências: uma abordagem de co-design para informações sobre biodiversidade nos Andes tropicais

Biodiversity conservation is a complex and transdisciplinary problem that requires engagement and cooperation among scientific, societal, economic, and political institutions. However, historical approaches have often failed to bring together and address the needs of all relevant stakeholders in decision­making processes. The Tropical Andes, a biodiversity hotspot where conservation efforts often conflict with socioeconomic issues and policies that prioritize economic development, provides an ideal model to develop and implement more effective approaches. In this study, we present a co­design approach that mainstreams and improves the flow of biodiversity information in the Tropical Andes, while creating tailored outputs that meet the needs of economic and societal stakeholders. We employed a consultative process that brought together biodiversity information users and producers at the local, national, and regional levels through a combination of surveys and workshops. This approach identified priority needs and limitations of the flow of biodiversity information in the region, which led to the co­design of user­relevant biodiversity indicators. By leveraging the existing capacities of biodiversity information users and producers, we were able to co­design multiple biodiversity indicators and prioritize two for full implementation ensuring that the data was findable, accessible, interoperable, and reusable based on the FAIR principles. This approach helped address limitations that were identified in the stakeholder engagement process, including gaps in data availability and the need for more accessible biodiversity information. Additionally, capacity­building workshops were incorporated for all producers of biodiversity information involved, which aimed to not only improve the current flow of biodiversity information in the region but also facilitate its future sustainability. Our approach can serve as a valuable blueprint for mainstreaming biodiversity information and making it more inclusive in the future, especially considering the diverse worldviews, values, and knowledge systems between science, policy, and practice.

La conservación de la biodiversidad es un problema complejo y transdisciplinario que requiere el compromiso y la cooperación entre instituciones científicas, sociales, económicas y políticas. Sin embargo, los enfoques tradicionales/convencionales  a menudo no logran  reunir y abordar las necesidades de todos los actores relevantes en los procesos de toma de decisiones. Los Andes tropicales, un área clave  de biodiversidad donde los esfuerzos de conservación a menudo entran en conflicto con cuestiones socioeconómicas y políticas que priorizan el desarrollo económico, proporcionan un modelo ideal para desarrollar e implementar enfoques más efectivos. En este estudio, presentamos un enfoque co-diseño que integra y mejora el flujo de información sobre biodiversidad en los Andes tropicales, creando resultados personalizados que satisfacen las necesidades, tanto económicas como sociales, de las partes interesadas. Empleamos un proceso de consulta que reunió a usuarios y productores de información sobre biodiversidad a nivel local, nacional y regional, a través de encuestas y talleres. Este enfoque ha permitido identificar necesidades prioritarias y limitaciones del flujo de información sobre biodiversidad en la región; lo cual llevó al codiseño de indicadores de biodiversidad relevantes para los usuarios. Aprovechando las capacidades existentes de los usuarios y productores de información sobre biodiversidad, pudimos co-diseñar múltiples indicadores de biodiversidad y priorizar dos de estos para su implementación completa, asegurando que los datos sean localizables, accesibles, interoperables y reutilizables, según los principios FAIR. Este enfoque ayudó a abordar las limitaciones que se identificaron en el proceso de participación de las partes interesadas; incluidas las brechas en la disponibilidad de datos y la necesidad de información sobre biodiversidad más accesible. Además, se incorporaron talleres de desarrollo de capacidades para todos los productores de información sobre biodiversidad involucrados, los cuales apuntaron no sólo a mejorar el flujo actual de información sobre biodiversidad en la región, sino también facilitar su sostenibilidad futura. Nuestro enfoque puede servir como un modelo valioso para incorporar la información sobre biodiversidad y hacerla más inclusiva en el futuro; especialmente si consideramos las diversas perspectivas globales, valores y sistemas de conocimiento implicados en las interacciones entre  la ciencia, la política y su aplicación práctica.

A conservação da biodiversidade é um problema complexo e transdisciplinar que requer compromisso e cooperação entre instituições científicas, sociais, económicas e políticas. No entanto, as abordagens tradicionais/convencionais muitas vezes não conseguem reunir e responder às necessidades de todos os intervenientes relevantes nos processos de tomada de decisão. Os Andes tropicais, uma área chave para a biodiversidade onde os esforços de conservação entram frequentemente em conflito com questões socioeconómicas e políticas que dão prioridade ao desenvolvimento económico, fornecem um modelo ideal para desenvolver e implementar abordagens mais eficazes. Neste estudo, apresentamos uma abordagem de co-design que integra e melhora o fluxo de informações sobre biodiversidade nos Andes tropicais, criando resultados personalizados que atendem às necessidades, tanto econômicas quanto sociais, das partes interessadas. Empregamos um processo de consulta que reuniu usuários e produtores de informações sobre biodiversidade nos níveis local, nacional e regional, por meio de pesquisas e workshops. Esta abordagem permitiu identificar necessidades prioritárias e limitações do fluxo de informação sobre a biodiversidade na região; o que levou à concepção conjunta de indicadores de biodiversidade relevantes para os utilizadores. Aproveitando as capacidades existentes dos utilizadores e produtores de informação sobre biodiversidade, fomos capazes de conceber em conjunto vários indicadores de biodiversidade e priorizar dois deles para implementação total, garantindo que os dados sejam localizáveis, acessíveis, interoperáveis ​​e reutilizáveis, de acordo com os princípios FAIR. Esta abordagem ajudou a resolver as limitações identificadas no processo de envolvimento das partes interessadas; incluindo lacunas na disponibilidade de dados e a necessidade de informações mais acessíveis sobre biodiversidade. Além disso, foram incorporados workshops de capacitação para todos os produtores de informação sobre biodiversidade envolvidos, que visaram não só melhorar o fluxo actual de informação sobre biodiversidade na região, mas também facilitar a sua sustentabilidade futura. A nossa abordagem pode servir como um modelo valioso para incorporar informações sobre biodiversidade e torná-las mais inclusivas no futuro; especialmente se considerarmos as diversas perspectivas globais, valores e sistemas de conhecimento envolvidos nas interações entre ciência, política e sua aplicação prática.

A strategy to estimate unknown viral diversity in mammals.

UNLABELLED: The majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed "virodiversity") for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox, Pteropus giganteus) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families in P. giganteus to be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses. IMPORTANCE: Recent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever estimate of the number of viruses that exist in a mammalian host. As pathogens continue to emerge from wildlife, this estimate allows us to put preliminary bounds around the potential size of the total zoonotic pool and facilitates a better understanding of where best to allocate resources for the subsequent discovery of global viral diversity.

Bats are a major natural reservoir for hepaciviruses and pegiviruses.

Although there are over 1,150 bat species worldwide, the diversity of viruses harbored by bats has only recently come into focus as a result of expanded wildlife surveillance. Such surveys are of importance in determining the potential for novel viruses to emerge in humans, and for optimal management of bats and their habitats. To enhance our knowledge of the viral diversity present in bats, we initially surveyed 415 sera from African and Central American bats. Unbiased high-throughput sequencing revealed the presence of a highly diverse group of bat-derived viruses related to hepaciviruses and pegiviruses within the family Flaviridae. Subsequent PCR screening of 1,258 bat specimens collected worldwide indicated the presence of these viruses also in North America and Asia. A total of 83 bat-derived viruses were identified, representing an infection rate of nearly 5%. Evolutionary analyses revealed that all known hepaciviruses and pegiviruses, including those previously documented in humans and other primates, fall within the phylogenetic diversity of the bat-derived viruses described here. The prevalence, unprecedented viral biodiversity, phylogenetic divergence, and worldwide distribution of the bat-derived viruses suggest that bats are a major and ancient natural reservoir for both hepaciviruses and pegiviruses and provide insights into the evolutionary history of hepatitis C virus and the human GB viruses.

Pathogens, pests, and economics: drivers of honey bee colony declines and losses.

The Western honey bee (Apis mellifera) is responsible for ecosystem services (pollination) worth US$215 billion annually worldwide and the number of managed colonies has increased 45% since 1961. However, in Europe and the U.S., two distinct phenomena; long-term declines in colony numbers and increasing annual colony losses, have led to significant interest in their causes and environmental implications. The most important drivers of a long-term decline in colony numbers appear to be socioeconomic and political pressure on honey production. In contrast, annual colony losses seem to be driven mainly by the spread of introduced pathogens and pests, and management problems due to a long-term intensification of production and the transition from large numbers of small apiaries to fewer, larger operations. We conclude that, while other causal hypotheses have received substantial interest, the role of pests, pathogens, and management issues requires increased attention.

Plant and animal endemism in the eastern Andean slope: challenges to conservation.

BACKGROUND: The Andes-Amazon basin of Peru and Bolivia is one of the most data-poor, biologically rich, and rapidly changing areas of the world. Conservation scientists agree that this area hosts extremely high endemism, perhaps the highest in the world, yet we know little about the geographic distributions of these species and ecosystems within country boundaries. To address this need, we have developed conservation data on endemic biodiversity (~800 species of birds, mammals, amphibians, and plants) and terrestrial ecological systems (~90; groups of vegetation communities resulting from the action of ecological processes, substrates, and/or environmental gradients) with which we conduct a fine scale conservation prioritization across the Amazon watershed of Peru and Bolivia. We modelled the geographic distributions of 435 endemic plants and all 347 endemic vertebrate species, from existing museum and herbaria specimens at a regional conservation practitioner's scale (1:250,000-1:1,000,000), based on the best available tools and geographic data. We mapped ecological systems, endemic species concentrations, and irreplaceable areas with respect to national level protected areas. RESULTS: We found that sizes of endemic species distributions ranged widely (< 20 km2 to > 200,000 km2) across the study area. Bird and mammal endemic species richness was greatest within a narrow 2500-3000 m elevation band along the length of the Andes Mountains. Endemic amphibian richness was highest at 1000-1500 m elevation and concentrated in the southern half of the study area. Geographical distribution of plant endemism was highly taxon-dependent. Irreplaceable areas, defined as locations with the highest number of species with narrow ranges, overlapped slightly with areas of high endemism, yet generally exhibited unique patterns across the study area by species group. We found that many endemic species and ecological systems are lacking national-level protection; a third of endemic species have distributions completely outside of national protected areas. Protected areas cover only 20% of areas of high endemism and 20% of irreplaceable areas. Almost 40% of the 91 ecological systems are in serious need of protection (= < 2% of their ranges protected). CONCLUSIONS: We identify for the first time, areas of high endemic species concentrations and high irreplaceability that have only been roughly indicated in the past at the continental scale. We conclude that new complementary protected areas are needed to safeguard these endemics and ecosystems. An expansion in protected areas will be challenged by geographically isolated micro-endemics, varied endemic patterns among taxa, increasing deforestation, resource extraction, and changes in climate. Relying on pre-existing collections, publically accessible datasets and tools, this working framework is exportable to other regions plagued by incomplete conservation data.

A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia).

Despite their obvious utility, detailed species-level phylogenies are lacking for many groups, including several major mammalian lineages such as bats. Here we provide a cytochrome b genealogy of over 50% of bat species (648 terminal taxa). Based on prior analyzes of related mammal groups, cytb emerges as a particularly reliable phylogenetic marker, and given that our results are broadly congruent with prior knowledge, the phylogeny should be a useful tool for comparative analyzes. Nevertheless, we stress that a single-gene analysis of such a large and old group cannot be interpreted as more than a crude estimate of the bat species tree. Analysis of the full dataset supports the traditional division of bats into macro- and microchiroptera, but not the recently proposed division into Yinpterochiroptera and Yangochiroptera. However, our results only weakly reject the former and strongly support the latter group, and furthermore, a time calibrated analysis of a pruned dataset where most included taxa have the entire 1140bp cytb sequence finds monophyletic Yinpterochiroptera. Most bat families and many higher level groups are supported, however, relationships among families are in general weakly supported, as are many of the deeper nodes of the tree. The exceptions are in most cases apparently due to the misplacement of species with little available data, while in a few cases the results suggest putative problems with current classification, such as the non-monophyly of Mormoopidae. We provide this phylogenetic hypothesis, and an analysis of divergence times, as tools for evolutionary and ecological studies that will be useful until more inclusive studies using multiple loci become available.