A Standardized Review of Bat Names Across Multiple Taxonomic Authorities

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The taxonomic boundaries of species and higher-level taxa change relatively frequently as knowledge of population structure and evolutionary relationships improves, and older hypotheses are reframed. For the order Chiroptera (bats), valid names have long been assessed by multiple authorities, but differences among the resulting classifications largely remain unharmonized amongst authorities. We collected and aligned treatments across three primary taxonomic authorities for Chiroptera to create a single dynamic and versioned name translation tool. The resulting Bat Taxonomy Alignment will expedite future taxonomic assessments. The complexities uncovered in this alignment suggest the need for more explicit tracking of taxonomic concepts and usage of names in the future, particularly since biodiversity data (including hosts of zoonotic diseases) are cataloged and tracked using taxonomic names. Find user friendly links and more analyses here; https://jhpoelen.nl/bat-taxonomic-alignment/ The CTAF DISSCO Covid-19 Taskforce started in 2019, but has evolved into the Biodiversity Exchange on Host and Pathogen Interactions (Bi HaPI). This group formed with the goal of creating narratives framed to ready the scientific community for potential future zoonotic spillover events involving bat species. Bats play a crucial role in ecosystems as pollinators and insect population control. However, they are also known to carry and transmit zoonotic diseases to humans and other animals. Bats are unique among mammals due to their ability to fly. This ability requires a significant amount of energy, so bats have increased metabolism and body temperature - similar to the fever response in other mammals. This regular spike in body temperature could, theoretically, create an environment that is more challenging for viruses to survive in. Some studies also suggest that bats have evolved mechanisms to limit inflammation, reducing the damage to their own cells from their immune response. This could be another factor that allows them to coexist with viruses without developing severe disease responses. Correct species identification is crucial not just for monitoring disease transmission on a wide scale, but also because viruses tend to invade cells more readily from taxonomically similar species. However, the taxonomic boundaries of bat species and higher-level taxa are subject to frequent changes as our knowledge of their evolutionary relationships improves. These changes often result in discrepancies among taxonomic authorities, where different classifications coexist without being harmonized. Bats are unique among mammals due to their ability to fly. This ability requires a significant amount of energy, so bats have increased metabolism and body temperature - similar to the fever response in other mammals. This regular spike in body temperature could, theoretically, create an environment that is more challenging for viruses to survive in. Some studies also suggest that bats have evolved mechanisms to limit inflammation, reducing the damage to their own cells from their immune response. This could be another factor that allows them to coexist with viruses without developing a severe disease responses We want to know if a bat sneezes, who could be on the receiving end of that spray. Then a network of potential pathogen transmission can be constructed. Co-roosting in bats has not been thoroughly examined since their roosting behavior is elusive, their survival can be adversely impacted as they are highly susceptible to disturbances, it is difficult to identify bat species when they are active at night, and their behaviors often change seasonally. Following open access and FAIR (Findable, Accessible, Interoperable, and Reusable) principles for extracting data and choosing methodologies to liberate ecological knowledge from dark data, we aim to achieve a long-term semantic foundation for evolutionary knowledge by reconciling taxonomic names. The evolution of name-to-meaning relationships in taxonomy presents a challenge for maintaining consistent communication and integration of information over time. However, information about organismal traits, genomes, and geographic distributions continuously lead to changes in taxonomic classifications, causing discrepancies in the meaning of taxonomic names over time and across different taxonomic reference material. One approach to resolving this issue involves creating methods for monitoring taxonomic alterations that facilitate straightforward comparisons of taxonomic name treatments from one reference to another that can be shared in a fast and dynamic way. Unharmonized taxonomic treatments refer to situations where different taxonomic authorities or sources have divergent or conflicting approaches in classifying or naming taxa. It occurs when there are discrepancies in the taxonomic concepts, classifications, or naming conventions applied to the same group of organisms across different references or databases. Unharmonized treatments can include variations in species delimitation, assignment of subspecies, synonymies, elevations of taxa to higher taxonomic levels, splits, merges, or other taxonomic decisions. Resolving unharmonized taxonomic treatments involves reconciling these differences and establishing a consistent and agreed-upon taxonomy for the taxa in question For co-roost occurrence data mining, we are extracting roosting interaction evidence from published works that span 160 years and 137 countries, so we face a specific challenge with taxonomic names. Once we resolve for taxonomic names by integrating current names and sorting out disparate taxonomic treatments, our network model becomes more representative of the frequency interactions occur between species. For example, since Tadarida cynocephala is now considered a subspecies of Tadarida brasiliensis, it drastically changes the frequency of interactions associated between this species and others. Resolving taxonomic names also allowed the software to identify links to species unidentified in our data. There are multiple taxonomic authorities that researchers and research facilities may follow depending on their specific specimen collections, research interests, and historical traditions. For example, some museums follow the American Society of Mammalogists, while others may use the European Mammal Assessment or the Mammals of South-East Asia (MOSE) project. The leading authorities for the order Chiroptera include Simmons (2005) chapter in Mammal Species of the World, Bat Species of the World: A taxonomic and geographic database or batbase.org, Arizona State University housed Mammal Diversity Database, and the Handbook Mammals of the World Volume 9 Bats, edited by Wilson and Mittermeier. We present this alignment of bat taxonomic treatments and extraction of those name strings in disunity. Our results reveal ~15% of the name strings do not match across these references. Our team bought the HMW2019 printed text, outsourced digitizing this hefty text to Picturae, a company specialized in digitizing objects. This cost about $4500 for 5000 species treatments, so about $1 dollar per species record. To convert the OCR’ed (Optical Character Recognition), PDF into a structured XML format, we utilized Plazi's specialized GoldenGate mark-up editor. Plazi's workflow was specifically designed to adhere to Swiss copyright protection laws. Plazi, an association with the primary objective of transforming scientific literature, both in print and digital formats, into semantically enabled and enhanced documents, plays a crucial role in this process. The conversion involves transforming taxonomic literature into XML documents that are semantically enriched, allowing for both human and machine readability. Utilizing a specific version of Plazi's Treatment-XML, we converted the HMW2019 texts into a table schema specific to our needs. The resulting data was stored in JSON format, as provided

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