Mammal collections of the Western Hemisphere: a survey and directory of collections

Mass production of unvouchered records fails to represent global biodiversity patterns

The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.

Temporal rate of postmortem DNA degradation in archived tissue samples: evidence from liver and muscle

Guidelines identifying best practices for harvesting tissues that lead to optimal DNA preservation are few but are important curatorial concerns for genetic resource collections. We conducted a temporal study to establish rate of DNA degradation of tissue samples extracted from field-caught museum specimens. Five individuals of Sigmodon hispidus were collected and their liver and muscle tissues were harvested. Each tissue type was sectioned into 15 subsamples, and each was preserved in liquid nitrogen at different time intervals (2, 4, 8, 16, and 32 min; 1, 2, 4, 8, and 16 h; and 1, 2, 4, 8, and 16 days) following death. DNA was extracted using an automated robotic instrument and molecular mass profiles were determined fluorometrically. Postmortem DNA degradation was continuous and dependent on time, but also was significantly affected by differences among individual cotton rats. DNA fragments of ≥10,000 base pairs in length were present in muscle samples across all time intervals, whereas DNA fragments of this size in liver samples were no longer present after 8–16 h postmortem. DNA molecular mass profiles showed that muscle samples retained 80% of their longest fragments (≥10,000 base pairs) until 1 day postmortem, whereas liver samples retained the same percentage only until 8 min after death. Although rates of decay were measured from samples in a laboratory (not field) setting, rates of decay presented here can guide field and museum workers in best practices. Results suggest that opportunistic samples, such as those from roadkill specimens, are more likely to be of use for a variety of molecular methods when muscle is preserved. Considerations of differences in rates of degradation may also guide selection of tissue types housed in genetic resource collections, especially under space-limited circumstances.

Temporal-dependent effects of DNA degradation on frozen tissues archived at −80°C

Frozen tissues, associated with natural history and biological collections, historically have been archived at temperatures between −20°C and −80°C. More recently, the availability of liquid nitrogen systems has enabled the storage of tissue samples (biobanking) at temperatures as low as −196°C. Currently, it is not known how the degree of coldness (e.g., −80°C or −196°C) or longevity (time in storage) impacts preservation of tissue samples. To examine the effects of long-term storage (−80°C and −196°C) on DNA degradation, tissue samples (muscle and liver) archived for 30, 20, 10, or 1 years were obtained from the Natural Science Research Laboratory at Texas Tech University. The integrity of DNA (measured as molecular weight and fragment length) extracted from samples was determined using automated DNA isolation methods followed by microfluidic distribution measurement. DNA distributions were compared using measures of central tendency, a regression-based molecular mass profile, and as a latent variable in a structural equation model. Muscle samples consistently outperformed liver samples in terms of quality of DNA yield. Also, muscle samples exhibited a significant linear relationship with time in which older samples were more degraded than were recent samples. The signal for a temporal effect on DNA was strongest when considering a latent variable of DNA quality based on mode and kurtosis; 37% of the variation in the latent variable was explained by variation in units of time. More recent time points tended to be more similar, but the temporal effect on the latent variable remained strong even when the oldest samples were removed from the analysis. In contrast, integrity of DNA from liver samples did not have a significant linear relationship with time; however, in some years they exhibited non-normally distributed DNA quality metrics that may have reflected sensitivity of liver tissue to degradation during specimen preparation, DNA extraction, or archive parameters. Results indicated that tissue type and temporal effects influenced rates of DNA degradation, with the latter emphasizing the long-term value of biobanking at the coldest temperatures possible (liquid nitrogen storage) to mitigate degradation of biological samples of ever-increasing scientific value.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

The Open-Specimen Movement

The open-science movement seeks to increase transparency, reproducibility, and access to scientific data. As primary data, preserved biological specimens represent records of global biodiversity critical to research, conservation, national security, and public health. However, a recent decrease in specimen preservation in public biorepositories is a major barrier to open biological science. As such, there is an urgent need for a cultural shift in the life sciences that normalizes specimen deposition in museum collections. Museums embody an open-science ethos and provide long-term research infrastructure through curation, data management and security, and community-wide access to samples and data, thereby ensuring scientific reproducibility and extension. We propose that a paradigm shift from specimen ownership to specimen stewardship can be achieved through increased open-data requirements among scientific journals and institutional requirements for specimen deposition by funding and permitting agencies, and through explicit integration of specimens into existing data management plan guidelines and annual reporting.

A new species and three subspecies of the desert shrew (Notiosorex) from the Baja California peninsula and California

Desert shrews of the genus Notiosorex comprise four species with morphological characteristics that are difficult to distinguish among the species. Indeed, N. cockrumi was described using only genetic markers. Based on molecular divergence documented in N. crawfordi, we hypothesize that a fifth species is present in the Baja California peninsula. Genetic variation at the species level was analyzed using individuals from locations west of the Colorado River in the Baja California peninsula, Mexico, and California, United States. Molecular markers of mitochondrial origin (cytochrome b, 1,140 bp; cytochrome c oxidase subunit I, 542 bp; and cytochrome c oxidase subunit III, 672 bp), as well as the nuclear intron 7 of the beta fibrinogen gene (385 bp) were used to construct a phylogeny for species of the genus Notiosorex. Genetic distances of 12.46–15.58% between west and east of the Colorado River were obtained using p-distance models. Our phylogenetic analyses showed almost identical topologies, placing populations from west of the Colorado River in three monophyletic clades with high bootstrap support values. Results of molecular phylogenetic identity among shrews of the genus Notiosorex support the existence of an undescribed, polytypic species of Notiosorex west of the Colorado River.

A revision of Neusticomys peruviensis (Rodentia: Cricetidae) with the description of a new subspecies

Neusticomys peruviensis is a poorly known sigmodontine rodent of the tribe Ichthyomyini, represented in collections by only five specimens collected in five localities from lowland forests of central and southern Peru. Recent expeditions in Llanchama, in northern Peru, north of the Río Amazonas, and near Allpahuayo Mishana Natural Reserve (Loreto, Peru), were successful in obtaining three specimens of Neusticomys. Based on morphological and meristic data, we found the population at Llanchama is distinct from the allopatric populations of N. peruviensis, and other species of Neusticomys. A species distribution model also shows the population at Llanchama is not highly predicted by the set of variables of the known localities of N. peruviensis. However, sequence data from the mitochondrial cytochrome-b gene indicate that genetic distinctiveness is low. Because intraspecific variability is important to understand evolutionary and biogeographic processes, and in concordance with the polytypic species concept, we interpret the population at Llanchama to represent a new subspecies of N. peruviensis that we describe in this paper.

Patterns in research and data sharing for the study of form and function in caviomorph rodents

The combination of morphometrics, phylogenetic comparative methods, and open data sets has renewed interest in relating morphology to adaptation and ecological opportunities. Focusing on the Caviomorpha, a well-studied mammalian group, we evaluated patterns in research and data sharing in studies relating form and function. Caviomorpha encompasses a radiation of rodents that is diverse both taxonomically and ecologically. We reviewed 41 publications investigating ecomorphology in this group. We recorded the type of data used in each study and whether these data were made available, and we re-digitized all provided data. We tracked two major lines of information: collections material examined and trait data for morphological and ecological traits. Collectively, the studies considered 63% of extant caviomorph species; all extant families and genera were represented. We found that species-level trait data rarely were provided. Specimen-level data were even less common. Morphological and ecological data were too heterogeneous and sparse to aggregate into a single data set, so we created relational tables with the data. Additionally, we concatenated all specimen lists into a single data set and standardized all relevant data for phylogenetic hypotheses and gene sequence accessions to facilitate future morphometric and phylogenetic comparative research. This work highlights the importance and ongoing use of scientific collections, and it allows for the integration of specimen information with species trait data. Recientemente ha resurgido el interés por estudiar la relación entre morfología, ecología, y adaptación. Esto se debe al desarrollo de nuevas herramientas morfométricas y filogenéticas, y al acceso a grandes bases de datos para estudios comparados. Revisamos 41 publicaciones sobre ecomorfología de roedores caviomorfos, un grupo diverso y bien estudiado, para evaluar los patrones de investigación y la transparencia para la liberación de datos. Registramos los tipos de datos que se utilizaron para cada estudio y si los datos están disponibles. Cuando estos datos se compartieron, los redigitalizamos. Nos enfocamos en los ejemplares consultados, y en datos que describen rasgos ecológicos y morfológicos para las especies estudiadas. Los estudios que revisamos abarcan el 63% de las especies de caviomorfos que actualmente existen. Encontramos que raramente fueron compartidos los datos que se tomaron para especies, y menos aún para ejemplares. Los datos morfológicos y ecológicos eran demasiado heterogéneos e exiguos para consolidar en un solo banco de datos; debido a esta circunstancia, creamos tablas relacionales con los datos. Además, enlazamos todas las listas individuales de especímenes para crear un solo banco de datos y estandarizamos todos los datos pertinentes a hipótesis filogenéticas, así como los números de acceso de secuencias genéticas, para así facilitar eventuales estudios comparados de morfometría y filogenia. Este trabajo resalta la importancia de las colecciones científicas y documenta su uso, además permitiendo la futura integración de datos derivados de ejemplares con datos sobre rasgos ecomorfológicos a nivel de especie.

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

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.

Curatorial guidelines and standards of the American Society of Mammalogists for collections of genetic resources

The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial standards for managing a collection-accreditation program under the auspices of the American Society of Mammalogists. To date, the Systematic Collections Committee has provided guidance for the more traditional specimen collections (skin, skeletal, fluid, etc.) and specimen data management. Given the rapidly expanding role of genetic resources in biological research, the Systematic Collections Committee herein presents a series of formal guidelines and standards designed to assist collections professionals in the current best practices for curation and maintenance of collections of genetic resources, to ensure long-term integrity of the archived material, and to address personnel safety and guidelines for researchers and curatorial staff. These guidelines and standards are intended to provide constructive guidance and a mechanism of accreditation for collections that vary in scale and infrastructure.

El Comité de Colecciones Sistemáticas de la Sociedad Americana de Mastozoólogos asesora a curadores y demás personal afiliado a colecciones de historia natural en asuntos relacionados a la administración, curación y acreditación de especímenes de mamíferos y su información pertinente. El Comité de Colecciones Sistemáticas mantiene también una lista de normas curatoriales para la gestión de un programa de acreditación de colecciones auspiciados por la Sociedad Americana de Mastozoólogos. A la fecha, el Comité de Colecciones Sistemáticas ha proporcionado una guía para las colecciones de muestras tradicionales (piel, esqueleto, líquido, etc.) y el manejo de datos asociados a estos especímenes. Dado el rápido crecimiento del papel que desempeñan los recursos genéticos en investigaciones biológicas, el Comité de Colecciones Sistemáticas presenta en esta publicación una serie de pautas y estándares formales diseñados para ayudar a los profesionales de colecciones científicas en las mejores prácticas actuales para la conservación y mantenimiento de colecciones de recursos genéticos, a modo de garantizar la integridad a largo plazo del material archivado, y tratar sobre la seguridad del personal y directrices para investigadores y personal curatorial. Estas pautas y estándares tienen como objetivo proporcionar una orientación constructiva y un mecanismo de acreditación para colecciones que varían en escala e infraestructura.

Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites

Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.