Museum Genomics.

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

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

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.

Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance.

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data.

AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.

The diversity of social complexity in termites.

Sociality underpins major evolutionary transitions and significantly influences the structure and function of complex ecosystems. Social insects, seen as the pinnacle of sociality, have traits like obligate sterility that are considered 'master traits', used as single phenotypic measures of this complexity. However, evidence is mounting that completely aligning both phenotypic and evolutionary social complexity, and having obligate sterility central to both, is erroneous. We hypothesize that obligate and functional sterility are insufficient in explaining the diversity of phenotypic social complexity in social insects. To test this, we explore the relative importance of these sterility traits in an understudied but diverse taxon: the termites. We compile the largest termite social complexity dataset to date, using specimen and literature data. We find that although functional and obligate sterility explain a significant proportion of variance, neither trait is an adequate singular proxy for the phenotypic social complexity of termites. Further, we show both traits have only a weak association with the other social complexity traits within termites. These findings have ramifications for our general comprehension of the frameworks of phenotypic and evolutionary social complexity, and their relationship with sterility.

Mass spectrometry in art conservation-With focus on paintings.

Conservation of historic artifacts has been a multidisciplinary field from its very beginning. Traditionally, it has been and still is associated with the history of art. It applies knowledge from technical and basic sciences, adapting their solutions to its goals. At present, however, a new tendency is clearly emerging-scientific research is starting to play an increasingly important role not only as a service, but also by proposing new solutions both in the traditional conservation areas and in new areas of conservation activities. The above trend opens up new perspectives for the field of preservation of our heritage but may also create new threats. Therefore, the conservators' caution in introducing new technologies should always be justified; after all, they are responsible for the effects of any activities on the historic objects. This, quite selective review, discusses application of mass spectrometry techniques for the detection of various components that are important to the conservators of our heritage with particular focus on paintings. The text also contains some basic knowledge of technical details to introduce the methodology to a broader group of professionals.

An island 'endemic' born out of hybridization between introduced lineages.

Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human-mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human-mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human-mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human-mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.

Differential performance of aqueous- and ethylic-Lugol's iodine stain to visualize anatomy in µCT-scanned vertebrates.

Museum specimens are an increasingly important tool for studying global biodiversity. With the advent of diffusible iodine-based contrast-enhanced computed tomography (diceCT), researchers can now visualize an organism's internal soft tissue anatomy without the need for physical dissection or other highly destructive sampling methods. However, there are many considerations when deciding which method of staining to use for diceCT to produce the best gray-scale contrast for facilitating downstream anatomical analyses. The general lack of direct comparisons among staining methodologies can make it difficult for researchers to determine which approaches are most appropriate for their study. Here, we compare the performance of ethylic-Lugol's iodine solution with aqueous-Lugol's staining solution across several vertebrate orders to assess differential imaging outcomes. We found that ethylic-Lugol's is better for visualizing muscle attachment to bone but provides overall lower contrast between soft tissue types. Comparatively, aqueous-based Lugol's provides high-contrast imaging among soft tissue types, although bone is more difficult to discern. We conclude that the choice of staining methodology largely depends on the type of anatomical data the researcher wishes to collect, and we provide a decision-based framework for assessing which staining methodology (ethylic or aqueous) is most appropriate for desired imaging results.

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird.

Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.

Bee species richness through time in an urbanizing landscape of the southeastern United States.

Compared to non-urban environments, cities host ecological communities with altered taxonomic diversity and functional trait composition. However, we know little about how these urban changes take shape over time. Using historical bee (Apoidea: Anthophila) museum specimens supplemented with online repositories and researcher collections, we investigated whether bee species richness tracked urban and human population growth over the past 118 years. We also determined which species were no longer collected, whether those species shared certain traits, and if collector behavior changed over time. We focused on Wake County, North Carolina, United States where human population size has increased over 16 times over the last century along with the urban area within its largest city, Raleigh, which has increased over four times. We estimated bee species richness with occupancy models, and rarefaction and extrapolation curves to account for imperfect detection and sample coverage. To determine if bee traits correlated with when species were collected, we compiled information on native status, nesting habits, diet breadth, and sociality. We used non-metric multidimensional scaling to determine if individual collectors contributed different bee assemblages over time. In total, there were 328 species collected in Wake County. We found that although bee species richness varied, there was no clear trend in bee species richness over time. However, recent collections (since 2003) were missing 195 species, and there was a shift in trait composition, particularly lost species were below-ground nesters. The top collectors in the dataset differed in how often they collected bee species, but this was not consistent between historic and contemporary time periods; some contemporary collectors grouped closer together than others, potentially due to focusing on urban habitats. Use of historical collections and complimentary analyses can fill knowledge gaps to help understand temporal patterns of species richness in taxonomic groups that may not have planned long-term data.

Historical museum samples reveal signals of selection and drift in response to changing insecticide use in an agricultural pest moth.

In response to environmental and human-imposed selective pressures, agroecosystem pests frequently undergo rapid evolution, with some species having a remarkable capacity to rapidly develop pesticide resistance. Temporal sampling of genomic data can comprehensively capture such adaptive changes over time, for example, by elucidating allele frequency shifts in pesticide resistance loci in response to different pesticides. Here, we leveraged museum specimens spanning over a century of collections to generate temporal contrasts between pre- and post-insecticide populations of an agricultural pest moth, Helicoverpa armigera. We used targeted exon sequencing of 254 samples collected across Australia from the pre-1950s (prior to insecticide introduction) to the 1990s, encompassing decades of changing insecticide use. Our sequencing approach focused on genes that are known to be involved in insecticide resistance, environmental sensation, and stress tolerance. We found an overall lack of spatial and temporal population structure change across Australia. In some decades (e.g., 1960s and 1970s), we found a moderate reduction of genetic diversity, implying stochasticity in evolutionary trajectories due to genetic drift. Temporal genome scans showed extensive evidence of selection following insecticide use, although the majority of selected variants were low impact. Finally, alternating trajectories of allele frequency change were suggestive of potential antagonistic pleiotropy. Our results provide new insights into recent evolutionary responses in an agricultural pest and show how temporal contrasts using museum specimens can improve mechanistic understanding of rapid evolution.

Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: Multiple pathways for wildlife and human exposure.

Per- and polyfluoroalkyl substances (PFAS) in the environment pose persistent and complex threats to human and wildlife health. Around the world, PFAS point sources such as military bases expose thousands of populations of wildlife and game species, with potentially far-reaching implications for population and ecosystem health. But few studies shed light on the extent to which PFAS permeate food webs, particularly ecologically and taxonomically diverse communities of primary and secondary consumers. Here we conducted >2000 assays to measure tissue-concentrations of 17 PFAS in 23 species of mammals and migratory birds at Holloman Air Force Base (AFB), New Mexico, USA, where wastewater catchment lakes form biodiverse oases. PFAS concentrations were among the highest reported in animal tissues, and high levels have persisted for at least three decades. Twenty of 23 species sampled at Holloman AFB were heavily contaminated, representing middle trophic levels and wetland to desert microhabitats, implicating pathways for PFAS uptake: ingestion of surface water, sediments, and soil; foraging on aquatic invertebrates and plants; and preying upon birds or mammals. The hazardous long carbon-chain form, perfluorooctanosulfonic acid (PFOS), was most abundant, with liver concentrations averaging >10,000 ng/g wet weight (ww) in birds and mammals, respectively, and reaching as high 97,000 ng/g ww in a 1994 specimen. Perfluorohexanesulfonic acid (PFHxS) averaged thousands of ng/g ww in the livers of aquatic birds and littoral-zone house mice, but one order of magnitude lower in the livers of upland desert rodent species. Piscivores and upland desert songbirds were relatively uncontaminated. At control sites, PFAS levels were strikingly lower on average and different in composition. In sum, legacy PFAS at this desert oasis have permeated local aquatic and terrestrial food webs across decades, severely contaminating populations of resident and migrant animals, and exposing people via game meat consumption and outdoor recreation.

Reduction of genetic diversity in 'Alala (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s.

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alala, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alala had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alala were more numerous, to samples taken between 1973 and 1998, when 'Alala population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines.

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution. Here, we investigated the macroevolution of Pinus, the largest conifer genus and characteristic of northern temperate coniferous forests, based on nearly complete species sampling. Using 1,662 genes from transcriptome sequences, we reconstructed a robust species phylogeny and reestimated divergence times of global pines. We found that ∼90% of extant pine species originated in the Miocene in sharp contrast to the ancient origin of Pinus, indicating a Neogene rediversification. Surprisingly, species at middle latitudes are much older than those at other latitudes. This finding, coupled with net diversification rate analysis, indicates that the midlatitude region has provided an evolutionary museum for global pines. Analyses of 31 environmental variables, together with a comparison of evolutionary rates of niche and phenotypic traits with a net diversification rate, found that topography played a primary role in pine diversification, and the aridity index was decisive for the niche rate shift. Moreover, fire has forced diversification and adaptive evolution of Pinus Our study highlights the importance of integrating phylogenomic and ecological approaches to address evolution of biological groups at the global scale.

Evaluation of effectiveness of an art-based museum intervention in reducing loneliness among older adults (ArtGran): a quasi-experimental study.

OBJECTIVES: Loneliness is a public health issue among older adults. We designed an intervention offering 10 sessions with diverse artistic methods (ArtGran). This study assessed the effectiveness of ArtGran in reducing loneliness and its negative effects on health in community-dwelling older adults in 2022 in Barcelona. STUDY DESIGN: Quasi-experimental study, with an intervention group (IG) and a comparison group (CG). METHODS: The sample included residents aged ≥70 years from 6 selected neighbourhoods of Barcelona. In each neighbourhood, an IG and a CG was formed with participants who reported loneliness and without special mobility needs. The participants were referred from primary care centres, social services, and community health centres. We included 138 participants (IG = 63, CG = 75). We collected data on loneliness, quality of life (QoL-5D), mood, and self-perceived health before and after the intervention through validated questionnaires. To assess the effect of the intervention, we built Poisson models with robust variance and linear regression models. RESULTS: At the end of the intervention, participants in the IG were more likely than those in the CG to be able to perform their usual activities without problems (adjusted prevalence ratio [aPR] = 1.22; 95% confidence interval [CI]: 1.02-1.45). Compared with the CG, participants in the IG attending more than half of the sessions had lower levels of loneliness (aPR = 1.36; 95%CI: 1.07-1.73), a better ability to perform their usual activities (aPR [95%CI] = 1.24 [1.05-1.48]), and higher happiness scores (ß = 0.73; P = 0.01). CONCLUSIONS: The effectiveness of the intervention was more pronounced when participants had high attendance. Our results suggest that high attendance of the ArtGran program was helpful in shielding older individuals from loneliness, fostering positive moods, and preserving their functional status.

A Holistic Approach for Enhancing Museum Performance and Visitor Experience.

Managing modern museum content and visitor data analytics to achieve higher levels of visitor experience and overall museum performance is a complex and multidimensional issue involving several scientific aspects, such as exhibits' metadata management, visitor movement tracking and modelling, location/context-aware content provision, etc. In related prior research, most of the efforts have focused individually on some of these aspects and do not provide holistic approaches enhancing both museum performance and visitor experience. This paper proposes an integrated conceptualisation for improving these two aspects, involving four technological components. First, the adoption and parameterisation of four ontologies for the digital documentation and presentation of exhibits and their conservation methods, spatial management, and evaluation. Second, a tool for capturing visitor movement in near real-time, both anonymously (default) and eponymously (upon visitor consent). Third, a mobile application delivers personalised content to eponymous visitors based on static (e.g., demographic) and dynamic (e.g., visitor movement) data. Lastly, a platform assists museum administrators in managing visitor statistics and evaluating exhibits, collections, and routes based on visitors' behaviour and interactions. Preliminary results from a pilot implementation of this holistic approach in a multi-space high-traffic museum (MELTOPENLAB project) indicate that a cost-efficient, fully functional solution is feasible, and achieving an optimal trade-off between technical performance and cost efficiency is possible for museum administrators seeking unfragmented approaches that add value to their cultural heritage organisations.

Vibration Analysis at Castello Ursino Picture Gallery (Sicily, Italy) for the Implementation of Self-Generating AlN-MEMS Sensors.

This work explores the potential of self-powered MEMS devices for application in the preventive conservation of cultural heritage. The main objective is to evaluate the effectiveness of piezoelectric aluminum nitride MEMS (AlN-MEMS) for monitoring vibrations and to investigate its potential for harvesting energy from vibrations, including those induced by visitors. A preliminary laboratory comparison was conducted between AlN-MEMS and the commercial device Tromino®. The study was then extended to the Picture Gallery of Ursino Castle, where joint measurements with the two devices were carried out. The analysis focused on identifying natural frequencies and vibrational energy levels by key metrics, including spectral peaks and the Power Spectral Density (PSD). The results indicated that the response of the AlN-MEMS aligned well with the data collected by the commercial device, especially observing high vibrational energy around 100 Hz. Such results validate the potential of AlN-MEMS for effective vibration measurement and for converting kinetic energy into electrical power, thereby eliminating the need for external power sources. Additionally, the vibrational analysis highlighted specific locations, such as the measurement point Cu4, as exhibiting the highest vibrational energy levels. These points could be used for placing MEMS sensors to ensure efficient vibration monitoring and energy harvesting.

Functionalization of Artwork Packaging Materials Utilizing Ag-Doped TiO2 and ZnO Nanoparticles.

Most of the artworks stored in museums are often kept in inappropriate climatic and environmental conditions that facilitate the formation and growth of microorganisms, such as fungi, which are responsible for many types of biodegradation phenomena. To mitigate and prevent these deteriorative processes, functionalized packaging materials can be used for the storage and handling of artworks. The aim of this study was to develop a potential anti-biodeterioration coating suitable for packaging purposes. TiO2 and ZnO doped with different amounts of Ag (0.5 wt%, 1 wt%, and 3 wt%) were synthesized and dispersed in polyvinyl alcohol (PVA) and acrylic resin (Paraloid B72), then applied on different types of packaging materials (cellulose and the high-density spunbound polyethylene fiber Tyvek®, materials that are frequently used as packaging in museums). Analytical investigations (SEM/EDS, Raman, FTIR, and XRD) were employed to assess dispersion on the packaging material. Furthermore, resistance against biodeteriogens was assessed using Cladosporium sp., a bioluminometer, to define the biocidal efficacy.

Looted artifacts and museums' perpetuation of imperialism and racism: Implications for the importance of preserving cultural heritage.

In the midst of recent protests and antiracism movements following the death of George Floyd in May of 2020 and other Black, Indigenous, and people of Color (BIPOC) murdered in the United States by police violence, protestors and advocates around the world recognized the need for Western governments and other institutions to reckon with their own imperial history-to acknowledge the linkage between the slave trade, colonialism, and racism in their countries. This recognition led to the tearing down of statues depicting racist colonial leaders and calling for museums who have perpetuated imperialism and racism through their acceptance and display of looted artifacts to return them. This article sought to answer the question posed in the call for papers, can the many manifestations of racism be effectively dealt with in our society if the status quo is unwilling to engage with the issues, address them, and relinquish power. Further the author argues that cultural looting has its roots in colonialism and racism and discusses implications of the linkage between one's stolen cultural heritage and individual and community well-being. Answers to the question include both yes, manifestations of racism can be addressed, and no, they cannot be addressed when institutions and governments refuse to engage, address the issue and do not relinquish power. The article also includes the author's thoughts on using a living heritage approach to preserve cultural heritage and offers suggestions that community psychologists, advocates and activists can help to decolonize museums as part of the broader social and racial justice movement.

The Showcases of Dental History - A Time Machine in Miniature at the University of Puerto Rico: Part I.

The evolution of 20-year-old dental museum-like showcases located in the lobby and the main hallway of the School of Dental Medicine, Puerto Rico (PR) are described along with important professionals who impacted on this development.