Science Enabled by Specimen Data

Amador, L. I., J. S. Arias, and N. P. Giannini. 2024. Historical biogeography of the Neotropical noctilionoid bats (Chiroptera: Noctilionoidea), revisited through a geographically explicit analysis. Cladistics.

Biogeographic studies have generally relied on methods that use a few, large predefined areas, which may overlook fine‐scale patterns. Here we test previous hypotheses about the biogeographic history of a diverse bat clade regarding its association with major Neotropical geological formations, particularly the Antilles, the South American Dry Diagonal, the Andes and the Panamanian land bridge, by applying a recently available method that uses actual distributions instead of predefined areas. We compiled and curated spatially explicit, georeferenced data of 173 bat species (Mammalia: Chiroptera: Noctilionoidea) from the online database Global Biodiversity Information Facility. By taking a previous comprehensive phylogeny as an evolutionary framework, we performed computationally intensive analyses using the Geographically‐explicit Event Model. This method uses the observed species distributions to reconstruct the ancestral areas and biogeographic events at each phylogeny node. We found that sympatric speciation was the most frequently reconstructed event, and involved mainly the Panamanian Isthmus and northern South America (SA), but all sympatry reconstructions were different and specific to each node. Allopatric events were important in the Andes; vicariance caused both west/east and north/south disjunctions that went unnoticed previously. Founder events indicated bidirectional dispersal between the mainland and the Antilles since the Miocene, and across the incomplete Panamanian bridge and the SA Dry Diagonal since the early Pliocene. Overall, we found support for previous hypotheses on the influence of major Neotropical paleogeographic events in the diversification of the group, but additionally revealed multi‐scale patterns that are embedded within the mainland and were previously overlooked. Our results highlight a trans‐isthmian centre of diversification in the biogeographic history of Noctilionoidea including the Panamanian Isthmus and Northern SA.

DuBose, T. P., V. Catalan, C. E. Moore, V. R. Farallo, A. L. Benson, J. L. Dade, W. A. Hopkins, and M. C. Mims. 2024. Thermal Traits of Anurans Database for the Southeastern United States (TRAD): A Database of Thermal Trait Values for 40 Anuran Species. Ichthyology & Herpetology 112.

Thermal traits, or how an animal responds to changing temperatures, impacts species persistence and thus biodiversity. Trait databases, as repositories of consolidated, measured organismal attributes, allow researchers to link study species with specific trait values, enabling comparisons within and among species. Trait databases also help lay the groundwork to build mechanistic linkages between organisms and the environment. However, missing or hidden physiological trait data preclude building mechanistic estimates of climate change vulnerability for many species. Thus, physiologically focused trait databases present an opportunity to consolidate data and enable species-specific or multispecies, mechanistic evaluations of climate change vulnerability. Here, we present TRAD: thermal traits of anurans database for the southeastern United States, a database of thermal trait values related to physiological thermoregulation (critical thermal minima and maxima, preferred temperature), behavioral thermoregulation (activity period, retreat emergence temperature, basking temperature, minimum and maximum foraging temperatures), and body mass for 37 anuran species found within the southeastern United States. In total, TRAD contains 858 reported trait values for 37 of 40 species found in the region from 267 peer-reviewed papers, dissertations, or theses and is easily linked with trait data available in ATraiU, an ecological trait database for anurans in the United States. TRAD contains trait values for multiple life stages and a summarization of interspecific adult trait values. Availability of trait data varied widely among traits and species. Estimates of mass were the most common trait values reported, with values available for 32 species. Behavioral trait values comprised 23% of our database, with activity period available for 34 species. We found the most trait values for Cope's Gray Treefrog (Dryophytes chrysoscelis), with at least one trait value for eight traits in the database. Conversely, species in the genus Pseudacris generally had the fewest trait values available. Species with the largest geographic range sizes also had the greatest coverage of data across traits (rho 5 0.75, P , 0.001). TRAD can aid studies of anuran response to changing temperatures, physiological niche space and limitations, and potential drivers of anuran geographic range limits, influencing our understanding of other ecological and evolutionary patterns and processes and enabling multispecies comparisons of potential risk and resilience in the face of climate change.

Ortiz-Acosta, M. Á., J. Galindo-González, A. A. Castro-Luna, and C. Mota-Vargas. 2023. Potential distribution of marsupials (Didelphimorphia: Didelphidae) in Mexico under 2 climate change scenarios M. Vieira [ed.],. Journal of Mammalogy.

Climate change is one of the main threats to biodiversity in the 21st century. However, the effects that it may have on different mammal species are unknown, making it difficult to implement conservation strategies. In this paper, we used species distribution models (SDM) to assess the effect of global climate change on the potential distribution of the 8 of the 9 marsupial species in Mexico, and analyzed their distribution in the current system of natural protected areas (NPAs). We used presence records for each species and bioclimatic variables from the present and the future (2050 and 2080) with 2 contrasting possible scenarios (representative concentration pathways RCP 4.5 and 8.5). We found that Tlacuatzin canescens would have the most stable potential range under any climate change scenario, while the remaining species (Caluromys derbianus, Chironectes minimus, Didelphis marsupialis, D. virginiana, Philander opossum, Marmosa mexicana, and Metachirus nudicaudatus) would undergo notable range losses in the future, though there would not only be losses—according to our SDMs, for all species there would be some range gain under the different climate scenarios, assuming the vegetation cover remained. The current system of NPAs in Mexico currently protects and under the 2 future scenarios would protect less than 20% of the potential range of marsupials, so a reevaluation of their areas beyond the NPAs is highly recommended for the long-term conservation of this group. Our results provide relevant information on the estimated effects of global climate change on marsupials, allowing us to design more effective methodologies for the protection of this portion of the mammalian fauna in Mexico.

Cruz, J. A., J. A. Velasco, J. Arroyo-Cabrales, and E. Johnson. 2023. Paleoclimatic Reconstruction Based on the Late Pleistocene San Josecito Cave Stratum 720 Fauna Using Fossil Mammals, Reptiles, and Birds. Diversity 15: 881.

Advances in technology have equipped paleobiologists with new analytical tools to assess the fossil record. The functional traits of vertebrates have been used to infer paleoenvironmental conditions. In Quaternary deposits, birds are the second-most-studied group after mammals. They are considered a poor paleoambiental proxy because their high vagility and phenotypic plasticity allow them to respond more effectively to climate change. Investigating multiple groups is important, but it is not often attempted. Biogeographical and climatic niche information concerning small mammals, reptiles, and birds have been used to infer the paleoclimatic conditions present during the Late Pleistocene at San Josecito Cave (~28,000 14C years BP), Mexico. Warmer and dryer conditions are inferred with respect to the present. The use of all of the groups of small vertebrates is recommended because they represent an assemblage of species that have gone through a series of environmental filters in the past. Individually, different vertebrate groups provide different paleoclimatic information. Birds are a good proxy for inferring paleoprecipitation but not paleotemperature. Together, reptiles and small mammals are a good proxy for inferring paleoprecipitation and paleotemperature, but reptiles alone are a bad proxy, and mammals alone are a good proxy for inferring paleotemperature and precipitation. The current paleoclimatic results coupled with those of a previous vegetation structure analysis indicate the presence of non-analog paleoenvironmental conditions during the Late Pleistocene in the San Josecito Cave area. This situation would explain the presence of a disharmonious fauna and the extinction of several taxa when these conditions later disappeared and do not reappear again.

Fell, H. G., M. Jones, S. Atkinson, N. C. Stenseth, and A. C. Algar. 2023. The role of reservoir species in mediating plague’s dynamic response to climate. Royal Society Open Science 10.

The distribution and transmission of Yersinia pestis , the bacterial agent of plague, responds dynamically to climate, both within wildlife reservoirs and human populations. The exact mechanisms mediating plague's response to climate are still poorly understood, particularly across large environmentally heterogeneous regions encompassing several reservoir species. A heterogeneous response to precipitation was observed in plague intensity across northern and southern China during the Third Pandemic. This has been attributed to the response of reservoir species in each region. We use environmental niche modelling and hindcasting methods to test the response of a broad range of reservoir species to precipitation. We find little support for the hypothesis that the response of reservoir species to precipitation mediated the impact of precipitation on plague intensity. We instead observed that precipitation variables were of limited importance in defining species niches and rarely showed the expected response to precipitation across northern and southern China. These findings do not suggest that precipitation–reservoir species dynamics never influence plague intensity but that instead, the response of reservoir species to precipitation across a single biome cannot be assumed and that limited numbers of reservoir species may have a disproportional impact upon plague intensity.

Boyd, R. J., M. A. Aizen, R. M. Barahona‐Segovia, L. Flores‐Prado, F. E. Fontúrbel, T. M. Francoy, M. Lopez‐Aliste, et al. 2022. Inferring trends in pollinator distributions across the Neotropics from publicly available data remains challenging despite mobilization efforts Y. Fourcade [ed.],. Diversity and Distributions 28: 1404–1415.

Aim Aggregated species occurrence data are increasingly accessible through public databases for the analysis of temporal trends in the geographic distributions of species. However, biases in these data present challenges for statistical inference. We assessed potential biases in data available through GBIF on the occurrences of four flower-visiting taxa: bees (Anthophila), hoverflies (Syrphidae), leaf-nosed bats (Phyllostomidae) and hummingbirds (Trochilidae). We also assessed whether and to what extent data mobilization efforts improved our ability to estimate trends in species' distributions. Location The Neotropics. Methods We used five data-driven heuristics to screen the data for potential geographic, temporal and taxonomic biases. We began with a continental-scale assessment of the data for all four taxa. We then identified two recent data mobilization efforts (2021) that drastically increased the quantity of records of bees collected in Chile available through GBIF. We compared the dataset before and after the addition of these new records in terms of their biases and estimated trends in species' distributions. Results We found evidence of potential sampling biases for all taxa. The addition of newly-mobilized records of bees in Chile decreased some biases but introduced others. Despite increasing the quantity of data for bees in Chile sixfold, estimates of trends in species' distributions derived using the postmobilization dataset were broadly similar to what would have been estimated before their introduction, albeit more precise. Main conclusions Our results highlight the challenges associated with drawing robust inferences about trends in species' distributions using publicly available data. Mobilizing historic records will not always enable trend estimation because more data do not necessarily equal less bias. Analysts should carefully assess their data before conducting analyses: this might enable the estimation of more robust trends and help to identify strategies for effective data mobilization. Our study also reinforces the need for targeted monitoring of pollinators worldwide.

Fell, H. G., O. G. Osborne, M. D. Jones, S. Atkinson, S. Tarr, S. H. Keddie, and A. C. Algar. 2022. Biotic factors limit the invasion of the plague pathogen ( Yersinia pestis ) in novel geographical settings P. Kamath [ed.],. Global Ecology and Biogeography 31: 672–684.

Aim: The distribution of Yersinia pestis, the pathogen that causes plague in humans, is reliant upon transmission between host species; however, the degree to which host species distributions dictate the distribution of Y. pestis, compared with limitations imposed by the environmental niche of Y. pe…

Méndez-Camacho, K., O. Leon-Alvarado, and D. R. Miranda-Esquivel. 2021. Biogeographic evidence supports the Old Amazon hypothesis for the formation of the Amazon fluvial system. PeerJ 9: e12533.

The Amazon has high biodiversity, which has been attributed to different geological events such as the formation of rivers. The Old and Young Amazon hypotheses have been proposed regarding the date of the formation of the Amazon basin. Different studies of historical biogeography support the Young A…

Ellestad, P., F. Forest, M. Serpe, S. J. Novak, and S. Buerki. 2021. Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae). Botanical Journal of the Linnean Society 196: 407–422.

Although vanilla is one of the most popular flavours in the world, there is still uncertainty concerning the native distribution of the species that produces it, Vanilla planifolia. To circumscribe the native geographical extent of this economically important species more precisely, we propose a new…

Le Sage, E. H., S. I. Duncan, T. Seaborn, J. Cundiff, L. J. Rissler, and E. J. Crespi. 2021. Ecological adaptation drives wood frog population divergence in life history traits. Heredity 126: 790–804.

Phenotypic variation among populations is thought to be generated from spatial heterogeneity in environments that exert selection pressures that overcome the effects of gene flow and genetic drift. Here, we tested for evidence of isolation by distance or by ecology (i.e., ecological adaptation) to g…