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1. Urban streams in Latin America: Current conditions and research needs

   https://doi.org/10.15517/RBT.V68IS2.44330  

   Walteros, Jeymmy M. ; Ramírez, Alonso ( October 2020 , Revista de Biología Tropical)

   null (Ed.)

   Introduction: Latin America is a highly urbanized region, with most of its population living in cities and urban centers. While information about urban streams in Latin America is rather limited, streams are expected to experience similar environmental impacts and conservation issues as urban streams in parts of the globe, including habitat loss, channelization, sewage discharge, trash, and loss of riparian habitats. Objective: We surveyed a network of researchers from approximately 80% of the countries in Latin America to obtain information on the condition, state of knowledge, and threats to urban streams in the region. Methods: Most participants were reached via the Macrolatinos@ network (www.macrolatinos.net). Results: We obtained 104 responses from researchers in 18 of the 23 Latin American countries. Most urban streams are impacted or degraded, and inputs of contaminants and wastewater discharges were considered major drivers of stream degradation. Most respondents indicated that stream channelization is common, with some streams completely channelized or buried. Sewage and rainfall runoff management were identified as a major factor degrading streams, with most respondents suggesting that streams are a primary destination for wastewater discharge, much of which is untreated. Major limitations to urban stream conservation in Latin America are the result of limited ecological knowledge, lack of citizen interest or political will to protect them. There are isolated efforts to restore urban streams and riparian zones, but these are initial steps that need further development. Conclusions: Our research network of Latin American scientists proved to be a valuable tool to assess a large number of urban rivers in a relatively understudied region.  Urban streams in Latin America face a diversity of stressors and management challenges, and we propose three areas that would benefit from further research to improve our understanding and management of these systems: (1) Studies should focus on the watershed, rather than isolated reaches, (2) researchers should strive to attain a better understanding of ecosystem function and the services provided by urban streams to justify management and restoration efforts, and (3) studies that integrate economic models where downstream users pay for upstream protection and restoration could prove beneficial for many Latin American cities in attempting to address water conservation issues. 

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2. Activating social change together: A qualitative synthesis of collaborative change research, evaluation and design literature

   https://doi.org/http:dx.doi.org/10.5130/ijcre.v12i1.6693  

   Busch, Melida D ; Jean-Baptiste, Elizabeth ; Person, Pamela F ; Vaughn, Lisa M. ( December 2019 , Gateways)

   Researchers, evaluators and designers from an array of academic disciplines and industry sectors are turning to participatory approaches as they seek to understand and address complex social problems. We refer to participatory approaches that collaboratively engage/ partner with stakeholders in knowledge creation/problem solving for action/social change outcomes as collaborative change research, evaluation and design (CCRED). We further frame CCRED practitioners by their desire to move beyond knowledge creation for its own sake to implementation of new knowledge as a tool for social change. In March and May of 2018, we conducted a literature search of multiple discipline-specific databases seeking collaborative, change-oriented scholarly publications. The search was limited to include peerreviewed journal articles, with English language abstracts available, published in the last five years. The search resulted in 526 citations, 236 of which met inclusion criteria. Though the search was limited to English abstracts, all major geographic regions (North America, Europe, Latin America/Caribbean, APAC, Africa and the Middle East) were represented within the results, although many articles did not state a specific region. Of those identified, most studies were located in North America, with the Middle East having only one identified study. We followed a qualitative thematic synthesis process to examine the abstracts of peer-reviewed articles to identify practices that transcend individual disciplines, sectors and contexts to achieve collaborative change. We surveyed the terminology used to describe CCRED, setting, content/topic of study, type of collaboration, and related benefits/outcomes in order to discern the words used to designate collaboration, the frameworks, tools and methods employed, and the presence of action, evaluation or outcomes. Forty-three percent of the reviewed articles fell broadly within the social sciences, followed by 26 percent in education and 25 percent in health/medicine. In terms of participants and/ or collaborators in the articles reviewed, the vast majority of the 236 articles (86%) described participants, that is, those who the research was about or from whom data was collected. In contrast to participants, partners/collaborators (n=32; 14%) were individuals or groups who participated in the design or implementation of the collaborative change effort described. In terms of the goal for collaboration and/or for doing the work, the most frequently used terminology related to some aspect of engagement and empowerment. Common descriptors for the work itself were ‘social change’ (n=74; 31%), ‘action’ (n=33; 14%), ‘collaborative or participatory research/practice’ (n=13; 6%), ‘transformation’ (n=13; 6%) and ‘community engagement’ (n=10; 4%). Of the 236 articles that mentioned a specific framework or approach, the three most common were some variation of Participatory Action Research (n=30; 50%), Action Research (n=40; 16.9%) or Community-Based Participatory Research (n=17; 7.2%). Approximately a third of the 236 articles did not mention a specific method or tool in the abstract. The most commonly cited method/tool (n=30; 12.7%) was some variation of an arts-based method followed by interviews (n=18; 7.6%), case study (n=16; 6.7%), or an ethnographic-related method (n=14; 5.9%). While some articles implied action or change, only 14 of the 236 articles (6%) stated a specific action or outcome. Most often, the changes described were: the creation or modification of a model, method, process, framework or protocol (n=9; 4%), quality improvement, policy change and social change (n=8; 3%), or modifications to education/training methods and materials (n=5; 2%). The infrequent use of collaboration as a descriptor of partner engagement, coupled with few reported findings of measurable change, raises questions about the nature of CCRED. It appears that conducting CCRED is as complex an undertaking as the problems that the work is attempting to address. 

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3. Extending Our Scientific Reach in Arboreal Ecosystems for Research and Management

   https://doi.org/10.3389/ffgc.2021.712165  

   Cannon, Charles H. ; Borchetta, Colby ; Anderson, David L. ; Arellano, Gabriel ; Barker, Martin ; Charron, Guillaume ; LaMontagne, Jalene M. ; Richards, Jeannine H. ; Abercrombie, Ethan ; Banin, Lindsay F. ; et al ( November 2021 , Frontiers in Forests and Global Change)

   The arboreal ecosystem is vitally important to global and local biogeochemical processes, the maintenance of biodiversity in natural systems, and human health in urban environments. The ability to collect samples, observations, and data to conduct meaningful scientific research is similarly vital. The primary methods and modes of access remain limited and difficult. In an online survey, canopy researchers ( n = 219) reported a range of challenges in obtaining adequate samples, including ∼10% who found it impossible to procure what they needed. Currently, these samples are collected using a combination of four primary methods: (1) sampling from the ground; (2) tree climbing; (3) constructing fixed infrastructure; and (4) using mobile aerial platforms, primarily rotorcraft drones. An important distinction between instantaneous and continuous sampling was identified, allowing more targeted engineering and development strategies. The combination of methods for sampling the arboreal ecosystem provides a range of possibilities and opportunities, particularly in the context of the rapid development of robotics and other engineering advances. In this study, we aim to identify the strategies that would provide the benefits to a broad range of scientists, arborists, and professional climbers and facilitate basic discovery and applied management. Priorities for advancing these efforts are (1) to expand participation, both geographically and professionally; (2) to define 2–3 common needs across the community; (3) to form and motivate focal teams of biologists, tree professionals, and engineers in the development of solutions to these needs; and (4) to establish multidisciplinary communication platforms to share information about innovations and opportunities for studying arboreal ecosystems. 

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4. How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging

   https://doi.org/10.3389/fphys.2022.917976  

   Czapanskiy, Max F. ; Beltran, Roxanne S. ( July 2022 , Frontiers in Physiology)

   What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology’s informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from “data as a noun” (e.g., traits, counts) to “data as a sentence”, where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure , 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally. 

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5. Linking Biodiversity Data Using Evolutionary History

   https://doi.org/10.3897/biss.3.36207  

   McTavish, Emily Jane ( June 2019 , Biodiversity Information Science and Standards)

   All life on earth is linked by a shared evolutionary history. Even before Darwin developed the theory of evolution, Linnaeus categorized types of organisms based on their shared traits. We now know these traits derived from these species’ shared ancestry. This evolutionary history provides a natural framework to harness the enormous quantities of biological data being generated today. The Open Tree of Life project is a collaboration developing tools to curate and share evolutionary estimates (phylogenies) covering the entire tree of life (Hinchliff et al. 2015, McTavish et al. 2017). The tree is viewable at https://tree.opentreeoflife.org, and the data is all freely available online. The taxon identifiers used in the Open Tree unified taxonomy (Rees and Cranston 2017) are mapped to identifiers across biological informatics databases, including the Global Biodiversity Information Facility (GBIF), NCBI, and others. Linking these identifiers allows researchers to easily unify data from across these different resources (Fig. 1). Leveraging a unified evolutionary framework across the diversity of life provides new avenues for integrative wide scale research. Downstream tools, such as R packages developed by the R OpenSci foundation (rotl, rgbif) (Michonneau et al. 2016, Chamberlain 2017) and others tools (Revell 2012), make accessing and combining this information straightforward for students as well as researchers (e.g. https://mctavishlab.github.io/BIO144/labs/rotl-rgbif.html). Figure 1. Example linking phylogenetic relationships accessed from the Open Tree of Life with specimen location data from Global Biodiversity Information Facility. For example, a recent publication by Santorelli et al. 2018 linked evolutionary information from Open Tree with species locality data gathered from a local field study as well as GBIF species location records to test a river-barrier hypothesis in the Amazon. By combining these data, the authors were able test a widely held biogeographic hypothesis across 1952 species in 14 taxonomic groups, and found that a river that had been postulated to drive endemism, was in fact not a barrier to gene flow. However, data provenance and taxonomic name reconciliation remain key hurdles to applying data from these large digital biodiversity and evolution community resources to answering biological questions. In the Amazonian river analysis, while they leveraged use of GBIF records as a secondary check on their species records, they relied on their an intensive local field study for their major conclusions, and preferred taxon specific phylogenetic resources over Open Tree where they were available (Santorelli et al. 2018). When Li et al. 2018 assessed large scale phylogenetic approaches, including Open Tree, for measuring community diversity, they found that synthesis phylogenies were less resolved than purpose-built phylogenies, but also found that these synthetic phylogenies were sufficient for community level phylogenetic diversity analyses. Nonetheless, data quality concerns have limited adoption of analyses data from centralized resources (McTavish et al. 2017). Taxonomic name recognition and reconciliation across databases also remains a hurdle for large scale analyses, despite several ongoing efforts to improve taxonomic interoperability and unify taxonomies, such at Catalogue of Life + (Bánki et al. 2018). In order to support innovative science, large scale digital data resources need to facilitate data linkage between resources, and address researchers' data quality and provenance concerns. I will present the model that the Open Tree of Life is using to provide evolutionary data at the scale of the entire tree of life, while maintaining traceable provenance to the publications and taxonomies these evolutionary relationships are inferred from. I will discuss the hurdles to adoption of these large scale resources by researchers, as well as the opportunities for new research avenues provided by the connections between evolutionary inferences and biodiversity digital databases. 

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