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1. Wanted: Standards for FAIR taxonomic concept representations and relationships 

   https://doi.org/10.3897/biss.5.75587  

   Sterner, Beckett; Upham, Nathan; Gupta, Prashant; Powell, Caleb; Franz, Nico (September 2021, Biodiversity Information Science and Standards)

   Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption of one-to-one relationships between names and biological entities breaks down (Remsen 2016, Franz and Sterner 2018). Taxonomic treatments and checklists provide authoritative information about the correct usage of names for species, including operational representations of the meanings of those names in the form of range maps, reference genetic sequences, or diagnostic traits. They increasingly provide taxonomic intelligence in the form of precise description of the semantic relationships between different published names in the literature. Making this authoritative information Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al. 2016) would be a transformative advance for biodiversity data sharing and help drive adoption and novel extensions of existing standards such as the Taxonomic Concept Schema and the OpenBiodiv Ontology (Kennedy et al. 2006, Senderov et al. 2018). We call for the greater, global Biodiversity Information Standards (TDWG) and taxonomy community to commit to extending and expanding on how FAIR applies to biodiversity data and include practical targets and criteria for the publication and digitization of taxonomic concept representations and alignments in taxonomic treatments, checklists, and backbones. As a motivating case, consider the abundantly sampled North American deer mouse— Peromyscus maniculatus (Wagner 1845)—which was recently split from one continental species into five more narrowly defined forms, so that the name P. maniculatus is now only applied east of the Mississippi River (Bradley et al. 2019, Greenbaum et al. 2019). That single change instantly rendered ambiguous ~7% of North American mammal records in the Global Biodiversity Information Facility (n=242,663, downloaded 2021-06-04; GBIF.org 2021) and ⅓ of all National Ecological Observatory Network (NEON) small mammal samples (n=10,256, downloaded 2021-06-27). While this type of ambiguity is common in name-based databases when species are split, the example of P. maniculatus is particularly striking for its impact upon biological questions ranging from hantavirus surveillance in North America to studies of climate change impacts upon rodent life-history traits. Of special relevance to NEON sampling is recent evidence suggesting deer mice potentially transmit SARS-CoV-2 (Griffin et al. 2021). Automating the updating of occurrence records in such cases and others will require operational representations of taxonomic concepts—e.g., range maps, reference sequences, and diagnostic traits—that are FAIR in addition to taxonomic concept alignment information (Franz and Peet 2009). Despite steady progress, it remains difficult to find, access, and reuse authoritative information about how to apply taxonomic names even when it is already digitized. It can also be difficult to tell without manual inspection whether similar types of concept representations derived from multiple sources, such as range maps or reference sequences selected from different research articles or checklists, are in fact interoperable for a particular application. The issue is therefore different from important ongoing efforts to digitize trait information in species circumscriptions, for example, and focuses on how already digitized knowledge can best be packaged to inform human experts and artifical intelligence applications (Sterner and Franz 2017). We therefore propose developing community guidelines and criteria for FAIR taxonomic concept representations as "semantic artefacts" of general relevance to linked open data and life sciences research (Le Franc et al. 2020). 

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2. Distributed, but Global in Reach: Outline of a de-centralized paradigm for biodiversity data intelligence

   https://doi.org/10.3897/biss.3.37749  

   Franz, Nico; Gilbert, Edward; Sterner, Beckett (July 2019, Biodiversity Information Science and Standards)

   We provide an overview and update on initiatives and approaches to add taxonomic data intelligence to distributed biodiversity knowledge networks. "Taxonomic intelligence" for biodiversity data is defined here as the ability to identify and renconcile source-contextualized taxonomic name-to-meaning relationships (Remsen 2016). We review the scientific opportunities, as well as information-technological and socio-economic pathways - both existing and envisioned - to embed de-centralized taxonomic data intelligence into the biodiversity data publication and knowledge intedgration processes. We predict that the success of this project will ultimately rest on our ability to up-value the roles and recognition of systematic expertise and experts in large, aggregated data environments. We will argue that these environments will need to adhere to criteria for responsible data science and interests of coherent communities of practice (Wenger 2000, Stoyanovich et al. 2017). This means allowing for fair, accountable, and transparent representation and propagation of evolving systematic knowledge and enduring or newly apparent conflict in systematic perspective (Sterner and Franz 2017, Franz and Sterner 2018, Sterner et al. 2019). We will demonstrate in principle and through concrete use cases, how to de-centralize systematic knowledge while maintaining alignments between congruent or concflicting taxonomic concept labels (Franz et al. 2016a, Franz et al. 2016b, Franz et al. 2019). The suggested approach uses custom-configured logic representation and reasoning methods, based on the Region Connection Calculus (RCC-5) alignment language. The approach offers syntactic consistency and semantic applicability or scalability across a wide range of biodiversity data products, ranging from occurrence records to phylogenomic trees. We will also illustrate how this kind of taxonomic data intelligence can be captured and propagated through existing or envisioned metadata conventions and standards (e.g., Senderov et al. 2018). Having established an intellectual opportunity, as well as a technical solution pathway, we turn to the issue of developing an implementation and adoption strategy. Which biodiversity data environments are currently the most taxonomically intelligent, and why? How is this level of taxonomic data intelligence created, maintained, and propagated outward? How are taxonomic data intelligence services motivated or incentivized, both at the level of individuals and organizations? Which "concerned entities" within the greater biodiversity data publication enterprise are best positioned to promote such services? Are the most valuable lessons for biodiversity data science "hidden" in successful social media applications? What are good, feasible, incremental steps towards improving taxonomic data intelligence for a diversity of data publishers? 

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3. Biosystematic studies on the status of Solanum chilense

   https://doi.org/10.1002/ajb2.1621  

   Raduski, Andrew_R; Igić, Boris (March 2021, American Journal of Botany)

   PremiseCommon taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members ofSolanumsect.Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self‐incompatibility, which determines individual propensity for outcrossing MethodsHere, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced‐representation sequencing (RAD‐seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data. ResultsOverall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently describedSolanum chilenserepresent separately evolving populations, and conceal at least one undescribed cryptic species. ConclusionsDespite its vast economic importance,Solanumsect.Lycopersiconstill exhibits considerable taxonomic instability. A pattern of under‐recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference. 

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4. Effect of topographic complexity on species richness in the Galápagos Islands

   https://doi.org/10.1111/jbi.14230  

   Roell, Yannik E.; Phillips, John G.; Parent, Christine E. (August 2021, Journal of Biogeography)

   Abstract AimThe accumulation of species through time has been proposed to have a hump‐shaped relationship on volcanic islands (highest species richness during intermediate stages of an island's lifespan). Change in topographic complexity (TC) of islands over time is assumed to follow the same relationship. However, TC can be measured in different ways and may not have the same impact across taxonomic groups. Here, we quantify TC across the Galápagos Islands and test the assumption that TC follows a predictable trajectory with island age. Subsequently, we ask whether including TC improves statistical models seeking to explain variation in species richness across islands. LocationGalápagos Archipelago, Ecuador. TaxonNative and endemic terrestrial animals and plants. MethodsFor each island, we generated eight TC indices from a 30‐m resolution digital elevation model. We tested for a relationship between each index and island age, and whether it significantly contributes to observed variation in species richness, using 11 different models for 12 taxonomic groups across the Galápagos Islands. ResultsFour TC indices were significantly negatively correlated with either island age or ontogenetic age and only one index followed the hump‐shaped relationship with age. No index consistently contributed to the variation in species richness for all taxonomic groups. However, for all 12 taxonomic groups, incorporating at least one TC index in modelling species richness improved one or more models. The most common TC index improving models was standard deviation of slope, although each index improved at least five models across all taxa. Different factors predicted taxon‐specific richness, and habitat diversity was significant for all taxa. Main conclusionsTopographic complexity is an important component influencing species richness, but its impact likely differs among taxonomic groups and different scales. Therefore, future studies should incorporate broad, multi‐dimensional measures of TC to understand the biological importance of TC. 

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5. Development and characterization of microsatellite markers for Antennaria corymbosa (Asteraceae) and close relatives

   https://doi.org/10.1002/aps3.11268  

   Thapa, Ramhari; Bayer, Randall_J; Mandel, Jennifer_R (June 2019, Applications in Plant Sciences)

   PremiseThe genusAntennariahas a complex evolutionary history due to dioecism, excessive polyploidy, and the evolution of polyploid agamic complexes. We developed microsatellite markers fromA. corymbosato investigate genetic diversity and population genetic structure inAntennariaspecies. Methods and ResultsTwenty‐four novel microsatellite markers (16 nuclear and eight chloroplast) were developed fromA. corymbosausing an enriched genomic library. Ten polymorphic nuclear markers were used to characterize genetic variation in five populations ofA. corymbosa. One to four alleles were found per locus, and the expected heterozygosity and fixation index ranged from 0.00 to 0.675 and −0.033 to 0.610, respectively. We were also able to successfully amplify these markers in five additionalAntennariaspecies. ConclusionsThese markers are promising tools to study the population genetics of sexualAntennariaspecies and to investigate interspecific gene flow, clonal diversity, and parentage ofAntennariapolyploid agamic complexes. 

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