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1. occTest : An integrated approach for quality control of species occurrence data

   https://doi.org/10.1111/geb.13847  

   Serra‐Diaz, Josep M; Borderieux, Jeremy; Maitner, Brian; Boonman, Coline_C F; Park, Daniel; Guo, Wen‐Yong; Callebaut, Arnaud; Enquist, Brian J; Svenning, Jens‐C; Merow, Cory (July 2024, Global Ecology and Biogeography)

   Abstract AimSpecies occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses. InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases(i.e. cleaning vs. testing)that encompass different testBlocksgrouping differenttestTypes(e.g.environmental outlier detection), which may use differenttestMethods(e.g.Rosner test, jacknife,etc.). Four differenttestBlockscharacterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed. Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application. 

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2. Genomic Insights Into Inbreeding and Adaptive Divergence of Trout Populations to Inform Genetic Rescue

   https://doi.org/10.1111/eva.70090  

   Bell, Donovan A; Carim, Kellie J; Kovach, Ryan; Eby, Lisa A; Barfoot, Craig; Painter, Sally; Lodmell, Angela; Amish, Stephen J; Smith, Seth; Rosenthal, Leo; et al (March 2025, Evolutionary Applications)

   ABSTRACT Genetic rescue, specifically translocation to facilitate gene flow among populations and reduce the effects of inbreeding, is an increasingly used approach in conservation. However, this approach comes with trade‐offs, wherein gene flow may reduce fitness when populations have adaptive differentiation (i.e., outbreeding depression). A better understanding of the interaction between isolation, inbreeding, and adaptive divergence in key traits, such as life history traits, will help to inform genetic rescue efforts. Stream‐dwelling salmonids, such as the westslope cutthroat trout (Oncorhynchus lewisi; WCT), are well‐suited for examining these trade‐offs because they are increasingly isolated by habitat degradation, exhibit substantial variation in life history traits among populations, and include many species of conservation concern. However, few genomic studies have examined the potential trade‐offs in inbreeding versus outbreeding depression in salmonids. We used > 150,000 SNPs to examine genomic variation and inbreeding coefficients in 565 individuals across 25 WCT populations that differed in their isolation status and demographic histories. Analyses of runs of homozygosity revealed that several isolated WCT populations had “flatlined” having extremely low genetic variation and high inbreeding coefficients. Additionally, we conducted genome scans to identify potential outlier loci that could explain life history differences among 10 isolated populations. Genome scans identified one candidate genomic region that influenced maximum length and age‐1 to age‐2 growth. However, the limited number of candidate loci suggests that the life history traits examined may be driven by many genes of small effect or phenotypic plasticity. Although adaptive differentiation should be considered, the high inbreeding coefficients in several populations suggest that genetic rescue may benefit the most genetically depauperate WCT populations. 

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3. Pitfalls and windfalls of detecting demographic declines using population genetics in long‐lived species

   https://doi.org/10.1111/eva.13754  

   Clark, Meaghan I; Fitzpatrick, Sarah W; Bradburd, Gideon S (July 2024, Evolutionary Applications)

   Abstract Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (N_e) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward‐time, individual‐based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data. 

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4. Longevity, Not Stream Flow, Explains Variation in Freshwater Mussel Growth Rates Across Four Rivers

   https://doi.org/10.1111/fwb.14373  

   Brunetz, Ian_A; Lopez, Jonathan_W; Hopper, Garrett_W; González, Irene_Sánchez; Atkinson, Carla_L (December 2024, Freshwater Biology)

   ABSTRACT Freshwater mussels (Bivalvia: Unionida) are among the most imperilled freshwater taxa. Yet, there is a lack of basic life history information for mussels, including data on their growth and longevity. These data help inform conservation efforts, as they can indicate whether species or populations may be vulnerable to decline and inform which species may be best adapted to certain habitats. We aimed to quantify growth and longevity in five mussel species from four river systems in the southeastern United States and test whether growth was related to stream flow. We also interpreted our findings in the context of life history theory.To model mussel growth and longevity, we cut radial thick sections from the shells of mussels and used high‐resolution photography to image the shells. We identified annual growth rings (annuli) and used von Bertalanffy growth models to estimate growth rate (K) and maximum age (A_max) across 13 mussel populations. We then used biochronological methods to remove age‐related variation in annual growth in each shell. We tested whether annual growth was correlated with stream flow using discharge‐based statistics.We found substantial variation inKandA_maxamong species and among populations of the same species.Kwas negatively related toA_max. We did not find consistent correlations between annual growth and stream flow.Our estimates ofKandA_maxalign with previous studies on closely related species and populations. They also match the eco‐evolutionary prediction that growth rate and longevity are negatively related. Life history theory predicts that short‐lived species with higher growth rates should be better adapted to environments with cyclical disturbance regimes, whereas longer‐lived species with low growth rates should be better adapted to stable environments. The lack of correlation between annual growth and stream flow suggests that mussel growth may be limited by other factors in our study system.While some species seem to have relatively narrow ranges for growth and longevity, other species show wide variation among populations. This highlights the need for species‐ and population‐specific conservation efforts. Fundamental life history information can be integrated with other species traits to predict how freshwater taxa may respond to ecological threats. 

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5. Securing the Chain of Custody and Integrity of Data in a Global North-South Partnership to Monitor the Quality of Essential Medicines

   https://doi.org/10.30953/bhty.v5.230  

   Hayes, Kathleen; Meyers, Natalie; Sweet, Christopher; Ashenef, Ayenew; Johann, Tim; Lieberman, Marya; Kochalko, David (March 2022, Blockchain in Healthcare Today)

   Substandard and falsified (SF) pharmaceuticals account for an estimated 10% of the pharmaceutical supply chain in low- and middle-income countries (LMICs), where a lack of regulatory and laboratory resources limits the ability to conduct effective post-market surveillance and allows SF products to penetrate the supply chain. The Distributed Pharmaceutical Analysis Laboratory (DPAL) was established in 2014 to expand testing of pharmaceutical dosage forms sourced from LMICs; DPAL is an alliance of academic institutions throughout the United States and abroad that provides high quality, validated chemical analysis of pharmaceutical dosage forms sourced from partners in LMICs. Results from analysis are reported to relevant regulatory agencies and are used to inform purchasing decisions made by in-country stakeholders. As the DPAL program has expanded to testing more than 1000 pharmaceutical dosage forms annually, challenges have surfaced regarding data management and sample tracking. Here, we describe a pilot project between DPAL and ARTiFACTs that applies blockchain to organize and manage key data generated during the DPAL workflow, including a sample’s progress through the workflow, its physical location, provenance of metadata, and lab reputability. Recording time and date stamps with this data will create a permanent and verifiable chain-of-custody for samples. This secure, distributed ledger will be linked to an easy-to-use dashboard, allowing stakeholders to view results and experimental details for each sample in real time and verify the integrity of DPAL analysis data. Introducing this blockchain-based system as a pilot will allow us to test the technology with real users analyzing real samples. Feedback from users will be recorded and necessary adjustments will be made to the system before the implementation of blockchain across all DPAL sites. Anticipated benefits of implementing blockchain for managing DPAL data include efficient management for routing work, increasing throughput, creating a chain of custody for samples and their data in alignment with the distributed nature of DPAL, and using the analysis results to detect patterns of quality within and across brands of products and develop enhanced sampling techniques and best practices. 

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