Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network.

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment.

More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882‒6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.

Investigating the free-roaming dog population and gastrointestinal parasite diversity in Tulúm, México.

Free-roaming domestic dogs (Canis lupus familiaris) pose major conservation and public health risks worldwide. To better understand the threat of domestic dogs to wildlife and people and add to the growing literature on free-roaming dog ecology, a study was conducted to estimate the dog population in Tulúm, México. A modified mark-recapture technique and program MARK were used to obtain dog population estimates along six different transects dividing the city. Population estimates ranged from 19.75 dogs in one transect to 101.841 dogs in another, with 150 total dogs identified throughout the study and an estimated minimum population density of 48.57 dogs/km2. Fecal samples were also opportunistically collected for parasite identification through fecal flotation analysis using the McMaster technique. Out of 25 samples collected, 19 tested positive for gastrointestinal parasites with the most common species found being Ancylostoma caninum, followed by Toxocara canis, Dipylidium caninum, and Cystoisospora spp. Parasite loads ranged from 50 to 10,700 ova per gram of feces. The large population of free-roaming dogs and the prevalence of three zoonotic parasites highlight the importance of understanding free-roaming dog ecology and educating the public on the health risks free-roaming dogs pose. Los perros callejeros (Canis lupus familiaris) representan un gran riesgo para la conservación de animales y la salud pública mundialmente. Para comprender mejor la amenaza que significan los perros domésticos para la fauna silvestre y los humanos y aportar a la creciente bibliografía sobre la ecología de los perros callejeros, se realizó una investigación para estimar la población de los perros en Tulúm, México. Se utilizó una técnica modificada de marcado y recaptura junto con el programa MARK para estimar la población canina en seis transectos de la ciudad. Los estimados varían desde 19.75 perros en un transecto hasta 101,841 en otro, con un total de 150 perros identificados en el transcurso de la investigación y una densidad mínima estimada de 48,57 perros/km2. Además, se hizo una recolección oportunista de muestras de heces para la identificación de parásitos por medio del análisis de flotacíon fecal, con el método McMaster. De las 25 muestras recolectadas, 19 resultaron positivas para parásitos gastrointestinales, de las cuales las especies más comunes fueron Ancylostomoa caninum, seguida por Toxocara canis, Dipylidium caninum, y Cystoisospora spp. Las cargas parasitarias variaron desde 50 hasta 10.700 óvulos por gramo de heces. La alta población de perros callejeros y la prevalencia de tres enfermedades zoonóticas resaltan la importancia de entender la ecología de los perros callejeros y educar al público sobre los riesgos que significan los perros callejeros para la salud.

Two new species of Peromyscus (Cricetidae: Neotominae) from the Transverse Volcanic Belt of Mexico.

Specimens of the Peromyscus boylii species group distributed in the western and northeastern montane regions of Michoacán, México, historically have been assigned to P. levipes. Previous studies indicated that these specimens possessed mitochondrial DNA haplotypes that were distinct from both P. levipes and P. kilpatricki, a recently named species in the P. boylii species group from northeastern Michoacán and western Morelos. Herein karyotypic, DNA sequence, and morphological data were analyzed from those populations to evaluate their taxonomic affinity. Karyotypic data indicated that individuals from western Michoacán (Dos Aguas and Aguililla) and from a newly discovered population in northeastern Michoacán (Zinapécuaro) were chromosomally similar to P. carletoni (FN = 68) but distinct from other taxa assigned to the P. boylii species group. Analyses of cranial characteristics indicated that, relative to other species in the P. boylii species group, two morphologically distinct groups were present that corresponded to the Dos Aguas/Aguililla and Zinapécuaro populations, respectively. The latter population, although represented by a small sample size (n = 5 specimens), appeared to exhibit some trenchant morphological distinctions compared with other cryptic species in the P. boylii group. Phylogenetic analyses (parsimony, Bayesian, and likelihood) of DNA sequences obtained from the mitochondrial cytochrome-b gene indicated that although the individuals from Dos Aguas/Aguililla and Zinapécuaro formed a sister group relationship, they formed monophyletic clades that differed genetically (2.54%)-a level approaching that seen between other sister species of Peromyscus. Further, the Dos Aguas/Aguililla and Zinapécuaro clade was more closely aligned with a clade containing representatives of P. carletoni and P. levipes instead of with those from closer geographic proximities (P. kilpatricki) located in eastern Michoacán. Together, these results indicated that these two populations seemingly represent two undescribed species in the P. boylii species group for which we propose the names Peromyscus greenbaumi for populations in western Michoacán (circa Dos Aguas and Aguililla) and Peromyscus ensinki for populations in northeastern Michoacán (circa Zinapécuaro).

Los especímenes del grupo de especies de Peromyscus boylii distribuidos en las regiones montañosas occidentales y el noreste de Michoacán, México, históricamente fueron asignados a P. levipes. Sin embargo, estudios previos han indicado que estos especímenes poseen haplotipos de ADN mitocondrial que son distintos de P. levipes y P. kilpatricki, una especie recientemente nombrada en el grupo de especies P. boylii del noreste de Michoacán y el oeste de Morelos. Los datos cariotípicos indicaron que los individuos del oeste de Michoacán (Dos Aguas y Aguililla) y de una población recién descubierta en el noreste de Michoacán (Zinapécuaro) eran cromosómicamente similares a P. carletoni (FN = 68), pero distintos de otros taxones asignados al grupo de especies P. boylii. Los análisis de las características craneales indicaron que en relación con otras especies del grupo de especies P. boylii, dos grupos morfológicamente distintos estaban presentes, y que correspondían a las poblaciones de Dos Aguas/Aguililla y Zinapécuaro, respectivamente. Aunque representada por un tamaño de muestra pequeño (n = 5 especímenes), esta última población pareció exhibir algunas diferencias morfológicas en comparación con las otras especies crípticas en el grupo P. boylii. Los análisis filogenéticos (parsimonia, inferencia bayesiana y verosimilitud) de secuencias de ADN obtenidas del gen mitocondrial citocromo-b, indicaron que, aunque los individuos de Dos Aguas/Aguililla y Zinapécuaro tienen una relación de grupo hermano, estos forman clados monofiléticos que difieren genéticamente (2.54%), nivel que se acerca al observado entre otras especies hermanas de Peromyscus. Además, el clado de Dos Aguas/Aguililla y Zinapécuaro está más estrechamente alineado con un clado que contenía representantes de P. carletoni y P. levipes en lugar de aquellos de proximidades geográficas más cercanas (P. kilpatricki) ubicados en el este de Michoacán. Estos resultados indicaron que estas dos poblaciones aparentemente representan dos especies no descritas en el grupo de especies P. boylii para las cuales proponemos los nombres Peromyscus greenbaumi para poblaciones en el oeste de Michoacán (hacia Dos Aguas y Aguililla) y Peromyscus ensinki para poblaciones en el noreste de Michoacán (circa Zinapécuaro).

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.

Genetic diversity of chemokine XCL1 and its receptor XCR1 in murine rodents.

The chemokine ligand XCL1 plays critical roles in immune responses with diverse physiological and pathological implications through interactions with a cognate G protein-coupled receptor XCR1. To shed insight into their versatile nature, we analyzed genetic variations of XCL1 and XCR1 in murine rodents, including commonly-used model organisms Mus musculus (house mouse) and Rattus norvegicus (Norway rat). Our results showed that adaptive selection has contributed to the genetic diversification of these proteins in murine lineage. Moreover, in both M. musculus and R. norvegicus, the chemokine and its receptor exhibit similar signs of selective sweeps resulting from positive selection. In light of currently available structural and interaction information for chemokines and their receptors, the similarity of XCL1/XCR1 evolutionary patterns among murine species and the parallels of their evolutionary footprints within individual species suggest that interplay could exist between the adaptively selected changes, or between the domains on which the identified changes are located, and consequently preserve the physiological interaction of XCL1 and XCR1.

What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification.

The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

Multilocus analyses indicate a mosaic distribution of hybrid populations in ground squirrels (genus Ictidomys).

DNA sequence data from mitochondrial cytochrome-b (Cytb) and Y-linked structural maintenance of chromosomes (SmcY) genes were combined with 478 nuclear loci obtained from amplified fragment length polymorphisms (AFLP) to assess the extent of hybridization and genetic spatial structure of populations in two hybridizing species of ground squirrel (Ictidomys parvidens and Ictidomys tridecemlineatus). Based on AFLP analyses of 134 individuals from 28 populations, 10 populations were identified that possessed hybrid individuals. Overall estimates of F ST values revealed strong support for population structure in the Cytb data set; however, analyses of the SmcY gene and the AFLP data indicated ongoing gene flow between species. Pairwise F ST comparisons of populations were not significant for the SmcY gene; although they were significant for the Cytb gene, indicating that these populations were structured and that gene flow was minimal. Therefore, gene flow between I. parvidens and I. tridecemlineatus appeared to be restricted to populations that exhibited hybridization. In addition, the fragmented nature of the geographic landscape suggested limited gene flow between populations. As a result, the distributional pattern of interspersed parental and hybrid populations were compatible with a mosaic hybrid zone model. Because ground squirrels display female philopatry and male-biased dispersal, the ecology of these species is compatible with this hypothesis.