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1. Fluid preservation causes minimal reduction of parasite detectability in fish specimens: A new approach for reconstructing parasite communities of the past?

   https://doi.org/10.1002/ece3.6379  

   Fiorenza, Evan A.; Leslie, Katie L.; Torchin, Mark E.; Maslenikov, Katherine P.; Tornabene, Luke; Wood, Chelsea L. (June 2020, Ecology and Evolution)

   Abstract Long‐term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid‐preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artifacts that are introduced by the preservation process. Here, we experimentally address whether the preservation process alters the degree to which metazoan parasites are detectable in fluid‐preserved fish specimens when using visual parasite detection techniques. We randomly assigned fish of three species (Gadus chalcogrammus, Thaleichthys pacificus, and Parophrys vetulus) to two treatments. In the first treatment, fish were preserved according to the standard procedures used in ichthyological collections. Immediately after the fluid‐preservation process was complete, we performed parasitological dissection on those specimens. The second treatment was a control, in which fish were dissected without being subjected to the fluid‐preservation process. We compared parasite abundance between the two treatments. Across 298 fish individuals and 59 host–parasite pairs, we found few differences between treatments, with 24 of 27 host–parasite pairs equally abundant between the two treatments. Of these, one pair was significantly more abundant in the preservation treatment than in the control group, and two pairs were significantly less abundant in the preservation treatment than in the control group. Our data suggest that the fluid‐preservation process does not have a substantial effect on the detectability of metazoan parasites. This study addresses only the effects of the fixation and preservation process; long‐term experiments are needed to address whether parasite detectability remains unchanged in the months, years, and decades of storage following preservation. If so, ecologists will be able to reconstruct novel, long‐term datasets on parasite diversity and abundance over the past century or more using fluid‐preserved specimens from natural history collections. 

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2. A reconstruction of parasite burden reveals one century of climate-associated parasite decline

   https://doi.org/10.1073/pnas.2211903120  

   Wood, Chelsea L.; Welicky, Rachel L.; Preisser, Whitney C.; Leslie, Katie L.; Mastick, Natalie; Greene, Correigh; Maslenikov, Katherine P.; Tornabene, Luke; Kinsella, John M.; Essington, Timothy E. (January 2023, Proceedings of the National Academy of Sciences)

   Long-term data allow ecologists to assess trajectories of population abundance. Without this context, it is impossible to know whether a taxon is thriving or declining to extinction. For parasites of wildlife, there are few long-term data—a gap that creates an impediment to managing parasite biodiversity and infectious threats in a changing world. We produced a century-scale time series of metazoan parasite abundance and used it to test whether parasitism is changing in Puget Sound, United States, and, if so, why. We performed parasitological dissection of fluid-preserved specimens held in natural history collections for eight fish species collected between 1880 and 2019. We found that parasite taxa using three or more obligately required host species—a group that comprised 52% of the parasite taxa we detected—declined in abundance at a rate of 10.9% per decade, whereas no change in abundance was detected for parasites using one or two obligately required host species. We tested several potential mechanisms for the decline in 3+-host parasites and found that parasite abundance was negatively correlated with sea surface temperature, diminishing at a rate of 38% for every 1 °C increase. Although the temperature effect was strong, it did not explain all variability in parasite burden, suggesting that other factors may also have contributed to the long-term declines we observed. These data document one century of climate-associated parasite decline in Puget Sound—a massive loss of biodiversity, undetected until now. 

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3. Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

   https://doi.org/10.7717/peerj.8086  

   Cobb, Neil S.; Gall, Lawrence F.; Zaspel, Jennifer M.; Dowdy, Nicolas J.; McCabe, Lindsie M.; Kawahara, Akito Y. (January 2019, PeerJ)

   Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research. 

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4. Who is that?! Using Genetic and Morphological Data to Identify Cryptic African Tree Frog Specimens in Natural History Collections

   Vargas, Arlene; Bell, Rayna (October 2023, Society for the Advancement of Chicanos/Hispanics and Native Americans in Science - 2023 NDiSTEM)

   Natural history collections are important resources for research and conservation. Unfortunately, sometimes certain taxa can be hard to identify to the species level or can be misidentified, impacting how those specimens and their accompanying data are used for future research and conservation. African tree frogs (Family Arthroleptidae, Genus Leptopelis) are a group of big-eyed tree frogs found across Sub-Saharan Africa. While they have morphological differences that can help tell members of the genus apart, when in the field species can look similar to each other which gives rise to them being misidentified or unidentified in collections. In particular, Leptopelis exhibit extensive intraspecific variation in coloration and pattern that makes identification based solely on morphology challenging. The goal of this project is to use DNA barcoding of the 16s mtDNA gene and morphological characteristics to update the identification of “Leptopelis sp.” specimens that are part of the California Academy of Science’s Herpetology collection to the species level. By comparing the genetic and morphological data collected to identified reference specimens in the Academy’s collection we can confirm species identification and update the Academy’s database. Having the opportunity to identify species in natural history collections using both genetic and morphological analysis helps us better understand what species are found in an area, and can reveal new localities and range expansions of poorly known species. These data serve as an important baseline for monitoring how species are adapting to global change and enable future research on these poorly known, charismatic frogs. 

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5. Collections do not have to Remain Ambiguous Forever: Seven steps to getting the correct people into your data

   https://doi.org/10.3897/biss.6.91194  

   Groom, Quentin; Bräuchler, Christian; Cubey, Robert; Dillen, Mathias; Huybrechts, Pieter; Kearney, Nicole; Leachman, Siobhan; Paul, Deborah L; Rogers, Heather; Santos, Joaquim; et al (August 2022, Biodiversity Information Science and Standards)

   People are involved with the collection and curation of all biodiversity data, whether they are researchers, members of the public, taxonomists, conservationists, collection managers or wildlife managers. Knowing who those people are and connecting their biographical information to the biodiversity data they collect helps us contextualise their scientific work. We are particularly concerned with those people and communities involved in the collection and identification of biological specimens. People from herbaria and natural science museums have been collecting and preserving specimens from all over the world for more than 200 years. The problem is that many of these people are only known by unstandardized names written on specimen labels, often with only initials and without any biographical information. The process of identifying and linking individuals to their biographies enables us to improve the quality of the data held by collections while also quantifying the contributions of the often underappreciated people who collected and identified these specimens. This process improves our understanding of the history of collecting, and addresses current and future needs for maintaining the provenance of specimens so as to comply with national and international practices and regulations. In this talk we will outline the steps that collection managers, data scientists, curators, software engineers, and collectors can take to work towards fully disambiguated collections. With examples, we can show how they can use these data to help them in their work, in the evaluation of their collections, and in measuring the impact of individuals and organisations, local to global. 

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