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.

A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.

Centering Microbes in the Emerging Role of Integrative Biology in Understanding Environmental Change.

The current environmental changes stressing the Earth's biological systems urgently require study from an integrated perspective to reveal unexpected, cross-scale interactions, particularly between microbes and macroscale phenomena. Such interactions are the basis of a mechanistic understanding of the important connections between deforestation and emerging infectious disease, feedback between ecosystem disturbance and the gut microbiome, and the cross-scale effects of environmental pollutants. These kinds of questions can be answered with existing techniques and data, but a concerted effort is necessary to better coordinate studies and data sets from different disciplines to fully leverage their potential.

Identifying structural connectivity priorities in eastern Paraguay's fragmented Atlantic Forest.

The Atlantic Forest of eastern Paraguay has experienced extensive recent deforestation. Less than one-third of the region is forested, and the remaining forest largely consists of isolated remnants with potentially disrupted connectivity for forest fauna. We used a graph theory approach to identify those forest remnants that are important in maintaining landscape structural connectivity for mammals in this fragmented forest. We quantified structural connectivity for forest remnants over the period 2000-2019 at three levels: the entire network of Atlantic Forest remnants in eastern Paraguay; at 10 smaller, nested spatial scales (40-10,000 m) encompassing a range of potential mammalian dispersal abilities; and at the level of individual remnants. We used 10 graph theory metrics to assess aspects of network complexity, dispersal-route efficiency, and individual remnant importance in supporting structural connectivity. We identified forest remnants that serve as important structural connectivity roles as stepping stones, hubs, or articulation points and that should be prioritized for connectivity conservation. Structural connectivity was constrained for organisms incapable of travelling at least 9-12 km (farthest distances between nearest-neighboring forest remnants depending on whether smaller remnants were included or not) and was particularly limited for area-sensitive forest-specialist mammals. With the increased forest loss and fragmentation that is occurring, the connectivity of this system will likely be further compromised, but most of the remnants that we identified as playing important roles for structural connectivity were outside of the country's proposed "green corridor," indicating additional areas where conservation action can be directed.

Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group).

BACKGROUND: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. RESULTS: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. CONCLUSION: The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Small mammal glucocorticoid concentrations vary with forest fragment size, trap type, and mammal taxa in the Interior Atlantic Forest.

Species that live in degraded habitats often show signs of physiological stress. Glucocorticoid hormones (e.g., corticosterone and cortisol) are often assessed as a proxy of the extent of physiological stress an animal has experienced. Our goal was to quantify glucocorticoids in free-ranging small mammals in fragments of Interior Atlantic Forest. We extracted glucocorticoids from fur samples of 106 small mammals (rodent genera Akodon and Oligoryzomys, and marsupial genera Gracilinanus and Marmosa) from six forest fragments (2-1200 ha) in the Reserva Natural Tapytá, Caazapá Department, Paraguay. To our knowledge, this is the first publication of corticosterone and cortisol levels for three of the four sampled genera (Akodon, Oligoryzomys, and Marmosa) in this forest system. We discovered three notable results. First, as predicted, glucocorticoid levels were higher in individuals living withing small forest fragments. Second, animals captured live using restraint trapping methods (Sherman traps) had higher glucocorticoid levels than those animals captured using kill traps (Victor traps), suggesting that hair glucocorticoid measures can reflect acute stress levels in addition to long-term glucocorticoid incorporation. These acute levels are likely due to urinary steroids diffusing into the hair shaft. This finding raises a concern about the use of certain trapping techniques in association with fur hormone analysis. Finally, as expected, we also detected genus-specific differences in glucocorticoid levels, as well as cortisol/corticosterone ratios.

Predictive sampling effort and species-area relationship models for estimating richness in fragmented landscapes.

Loss of habitat, specifically deforestation, is a major driver of biodiversity loss. Species-area relationship (SAR) models traditionally have been used for estimating species richness, species loss as a function of habitat loss, and extrapolation of richness for given areas. Sampling-species relationships (SSRs) are interrelated yet separate drivers for species richness estimates. Traditionally, however, SAR and SSR models have been used independently and not incorporated into a single approach. We developed and compared predictive models that incorporate sampling effort species-area relationships (SESARS) along the entire Atlantic Forest of South America, and then applied the best-fit model to estimate richness in forest remnants of Interior Atlantic Forest of eastern Paraguay. This framework was applied to non-volant small mammal assemblages that reflect different tolerances to forest loss and fragmentation. In order to account for differences in functionality we estimated small mammal richness of 1) the entire non-volant small mammal assemblage, including introduced species; 2) the native species forest assemblage; and 3) the forest-specialist assemblage, with the latter two assemblages being subsets of the entire assemblage. Finally, we geospatially modeled species richness for each of the three assemblages throughout eastern Paraguay to identify remnants with high species richness. We found that multiple regression power-law interaction-term models that only included area and the interactions of area and sampling as predictors, worked best for predicting species richness for the entire assemblage and the native species forest assemblage, while several traditional SAR models (logistic, power, exponential, and ratio) best described forest-specialist richness. Species richness was significantly different between assemblages. We identified obvious remnants with high species richness in eastern Paraguay, and these remnants often were geographically isolated. We also found relatively high predicted species richness (in relation to the entire range of predicted richness values) in several geographically-isolated, medium-size forest remnants that likely have not been considered as possible priority areas for conservation. These findings highlight the importance of using an empirical dataset, created using sources representing diverse sampling efforts, to develop robust predictive models. This approach is particularly important in geographic locations where field sampling is limited yet the geographic area is experiencing rapid and dramatic land cover changes. When combined, area and sampling are powerful modeling predictors for questions of biogeography, ecology, and conservation, especially when addressing habitat loss and fragmentation.

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America.

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from -5.83 to -29.75 decimal degrees of latitude and -34.82 to -56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

Description of Litomosoides ysoguazu n. sp. (Nematoda, Onchocercidae), a parasite of the tuft-toed rice rat Sooretamys angouya (Fischer) (Rodentia: Cricetidae), and a first record of L. esslingeri Bain, Petit & Berteaux, 1989 in Paraguay.

Paraguay is a small landlocked country whose mammalian fauna is among the least studied in South America, as well as their parasites. As a result of a study of the effects of habitat fragmentation on small mammal biodiversity in eastern Paraguay, we have collected some parasites of cricetid rodents. Herein, we describe a new species of Litomosoides Chandler, 1931 parasitising the body cavity of the tuft-toed rice rat Sooretamys angouya (Fischer) and Litomosoides esslingeri Bain, Petit & Diagne, 1989 parasitising Oligoryzomys nigripes (Olfers), thus expanding its geographical distribution into Paraguay. Litomosoides ysoguazu n. sp. is characterised by the large size of the females (92.2-117.6 mm long) and by having buccal capsule with an anterior widening with rounded edges on the chitinous segment and a rounded widening at the base; male tail with a single pair of adcloacal papillae, three to five pairs of asymmetrical postcloacal papillae, and one or two unpaired papillae in the median ventral line; spicules corresponding to the "sigmodontis" species group; and microfilaria with a sheath stuck to the body and visible in the anterior extremity. We also describe a fourth-stage female larva. Oligoryzomys nigripes is a new host record of L. esslingeri; this enlarges the host record to eight species highlighting the low specificity of this species.

High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

Bayou virus detected in non-oryzomyine rodent hosts: an assessment of habitat composition, reservoir community structure, and marsh rice rat social dynamics.

In the United States, Bayou virus (BAYV) ranks second only to Sin Nombre virus (SNV) in terms of hantavirus pulmonary syndrome (HPS) incidents, having been confirmed in cases from Texas and Louisiana since its discovery in 1994. This study on BAYV infection among sympatric, non-oryzomyine rodents ("spillover") in Freeport, TX, is the first to link patterns of hantavirus interspecific spillover with the spatiotemporal ecology of the primary host (marsh rice rat, Oryzomys palustris). Mark-recapture and/or harvest methods were employed from March 2002 through May 2004 in two macrohabitat types. Rodent blood samples were screened for the presence of IgG antibody to BAYV antigen by IFA after which Ab-positive blood, saliva, and urine were analyzed for the presence of viral RNA by nested RT-PCR. From 727 non-oryzomyine captures, five seropositive (but not viral RNA positive) individuals were detected: one each of Baiomys taylori, Peromyscus leucopus, and Reithrodontomys fulvescens; and two Sigmodon hispidus. Spillover hosts were not associated with macrohabitat where O. palustris abundance, density, or seroprevalence was highest. Rather, spillover occurred in the macrohabitat indicative of greater overall disturbance (as indicated by grazing and exotic plant diversity) and overall biodiversity. Spillover occurred during periods of high seroprevalence detected elsewhere within the study region. Spillover locations differed significantly from all other capture locations in terms of percent water, shrub, and grass cover. Although greater habitat and mammal diversity of old-fields may serve to reduce seroprevalence levels by tempering intraspecific contacts between rice rats, greater diversity also may create an ecologically opportunistic setting for BAYV spillover. Impacts of varying levels of disturbance and biodiversity on transmission dynamics represent a vastly uncharacterized component of the evolutionary ecology of hantaviruses.

A longitudinal study of Bayou virus, hosts, and habitat.

What is currently known about the ecology of North American hantaviruses has come largely from studies on Sin Nombre virus (SNV). We conducted a longitudinal study of Bayou virus (BAYV), the second-leading agent of hantavirus pulmonary syndrome in the United States. Antibodies to hantavirus were detected from Oryzomys palustris (most commonly infected species), Sigmodon hispidus, Peromyscus leucopus, Reithrodontomys fulvescens, and Baiomys taylori. However, only O. palustris had viral RNA in tissues and excreta, suggesting that antibodies detected in other species may have resulted from spill-over infection. Seroprevalence rates averaged around 16% for O. palustris and varied seasonally. The heaviest males exhibited the highest levels of seroprevalence. Seroprevalence was higher in coastal prairie (20.0%) than old-fields (10.5%) and was associated with host abundance. These patterns are similar to those of SNV and can be used in identification of potentially at-risk areas.