Science Enabled by Specimen Data

Amin, H., and A. Borzée. 2024. Understanding the Distribution, Behavioural Ecology, and Conservation Status of Asian Pelophylax. Diversity 16: 259. https://doi.org/10.3390/d16050259

Understanding species from an ecological and phylogenetic perspective facilitates an understanding of their conservation status in relation to the changing world. The frog genus Pelophylax is among the largest in terms of amphibian biomass in the Palearctic, but species have not been thoroughly studied at the Asian continental scale. The phylogeographic relationship, behavioural ecology, and ecological requirements within the genus need clarification, despite generally good local coverage. Here, for the first time, we conducted a literature review focused on phylogeography and behavioural ecology, supported by ecological niche modelling of twelve Asian Pelophylax lineages. Finally, we compiled the known threats for each of the lineages. We first determined the presence of twelve species and species-candidate lineages. In terms of behavioural ecology, the main difference among lineages is the time to metamorphosis and the time to reach sexual maturity. The ecological models highlighted a match between the known presence of each clade and their suitable habitat and highlighted the Syr Darya drainage on the eastern shore of the Caspian Sea for the non-described Pelophylax “Syr Darya lineage”. Finally, we highlighted the greatest variation among lineages in terms of threats, as some lineages are threatened by numerous factors, whereas others are expanding.

Luna-Aranguré, C., and E. Vázquez-Domínguez. 2024. Bears into the Niche-Space: Phylogeography and Phyloclimatic Model of the Family Ursidae. Diversity 16: 223. https://doi.org/10.3390/d16040223

Assessing niche evolution remains an open question and an actively developing area of study. The family Ursidae consists of eight extant species for which, despite being the most studied family of carnivores, little is known about the influence of climate on their evolutionary history and diversification. We evaluated their evolutionary patterns based on a combined phylogeography and niche modeling approach. We used complete mitogenomes, estimated divergence times, generated ecological niche models and applied a phyloclimatic model to determine the species evolutionary and diversification patterns associated with their respective environmental niches. We inferred the family evolutionary path along the environmental conditions of maximum temperature and minimum precipitation, from around 20 million years ago to the present. Our findings show that the phyloclimatic niches of the bear species occupy most of the environmental space available on the planet, except for the most extreme warm conditions, in accordance with the wide geographic distribution of Ursidae. Moreover, some species exhibit broader environmental niches than others, and in some cases, they explore precipitation axes more extensively than temperature axes or vice versa, suggesting that not all species are equally adaptable to these variables. We were able to elucidate potential patterns of niche conservatism and evolution, as well as niche overlapping, suggesting interspecific competitive exclusion between some of the bear species. We present valuable insights into the ecological and evolutionary processes driving the diversification and distribution of the Ursidae. Our approach also provides essential information for guiding effective conservation strategies, particularly in terms of distribution limits in the face of climate change.

Groh, S. S., P. Upchurch, J. J. Day, and P. M. Barrett. 2023. The biogeographic history of neosuchian crocodiles and the impact of saltwater tolerance variability. Royal Society Open Science 10. https://doi.org/10.1098/rsos.230725

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

Viljoen, N., J. Weyer, J. Coertse, and W. Markotter. 2023. Evaluation of Taxonomic Characteristics of Matlo and Phala Bat Rabies-Related Lyssaviruses Identified in South Africa. Viruses 15: 2047. https://doi.org/10.3390/v15102047

We report the genetic characterization of two potentially novel rabies-related lyssaviruses identified from bats in Limpopo province, South Africa. Matlo bat lyssavirus (MBLV) was identified in two Miniopterus natalensis (Natal long-fingered) bats in 2015 and 2016, and Phala bat lyssavirus (PBLV) was identified in a Nycticeinops schlieffeni (Schlieffen’s) bat in 2021. The distribution of both of these bat species is largely confined to parts of Africa, with limited reports from the Arabian Peninsula. MBLV and PBLV were demonstrated to group with the unassigned and phylogroup I lyssaviruses, respectively. MBLV was most closely related to Lyssavirus caucasicus (WCBV), whereas PBLV was most closely related to Lyssavirus formosa (TWBLV-1) and Taiwan bat lyssavirus 2 (TWBLV-2), based on analysis of the N and G genes, the concatenated N + P + M + G + L coding sequence, and the complete genome sequence. Based on our analysis, MBLV and WCBV appeared to constitute a phylogroup separate from Lyssavirus lleida (LLEBV) and Lyssavirus ikoma (IKOV). Analysis of the antigenic sites suggests that PBLV will likely be serologically distinguishable from established lyssaviruses in virus-neutralization tests, whereas MBLV appeared to be antigenically highly similar to WCBV. Taken together, the findings suggested that, while PBLV is likely a new lyssavirus species, MBLV is likely related to WCBV.

Mizerovská, D., A. A. Martynov, O. Mikula, A. Bryjová, Y. Meheretu, L. A. Lavrenchenko, and J. Bryja. 2023. Genomic diversity, evolutionary history, and species limits of the endemic Ethiopian laminate-toothed rats (genus Otomys, Rodentia: Muridae). Zoological Journal of the Linnean Society. https://doi.org/10.1093/zoolinnean/zlad063

The Ethiopian Highlands represent one of the most important centres of endemism on Earth. Six endemic species of laminate-toothed rats have been reported from Ethiopia in a previous study based mostly on morphological analyses. Largely missing genetic data for some of the species, insufficient sampling across Ethiopia, and presence of a pseudogene on cytochrome b created knowledge gaps in basic taxonomy, distribution, and phylogenetic position of the Ethiopian taxa. Here we perform an integrative taxonomic revision of the group by using the largest available sets of genomic and morphological data. We first reconstructed the mitochondrial phylogeny of the whole genus, delimited major clades, and evidenced two independent colonization events of Otomys to Ethiopia. By using genome-scale SNPs, we delimited putative Ethiopian species and analysed their phylogenetic relationships. In genetically characterized specimens we assessed morphological variation of skulls. We confirmed the presence of six previously reported species and significantly extended the known distributional range for some of them. Furthermore, we discovered a genetically and morphologically distinct lineage in northern Ethiopia, probably representing a new species. The speciation processes are similar to other Afromontane Ethiopian endemic rodent clades, with prevailing allopatric diversification combined with reticulate processes.

Graham, C. D. K., E. J. Forrestel, A. L. Schilmiller, A. T. Zemenick, and M. G. Weber. 2023. Evolutionary signatures of a trade-off in direct and indirect defenses across the wild grape genus Vitis. Evolution. https://doi.org/10.1093/evolut/qpad140

Evolutionary correlations between chemical defense and protection by mutualist bodyguards have been long predicted, but tests of these pattern remain rare. We use a phylogenetic framework to test for evolutionary correlations indicative of trade-offs or synergisms between direct defense in the form of plant secondary metabolism, and indirect defense in the form of leaf domatia, across 33 species in the wild grape genus, Vitis. We also performed a bioassay with a generalist herbivore to associate our chemical phenotypes with herbivore palatability. Finally, we tested whether defensive traits correlate with the average abiotic characteristics of each species’ contemporary range and whether these correlations were consistent with plant defense theory. We found a negative evolutionary correlation between domatia size and the diversity of secondary metabolites in Vitis leaf tissue across the genus, and also that leaves with a higher diversity and richness of secondary metabolites were less palatable to a generalist herbivore, consistent with a trade-off in chemical and mutualistic defense investment. Predictions from plant defense theory were not supported by associations between investment in defense phenotypes and abiotic variables. Our work demonstrates an evolutionary pattern indicative of a trade-off between indirect and direct defense strategies across the Vitis genus.

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. https://doi.org/10.1098/rsos.230021

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.

Dobson, R., A. J. Challinor, R. A. Cheke, S. Jennings, S. G. Willis, and M. Dallimer. 2023. dynamicSDM  : An R package for species geographical distribution and abundance modelling at high spatiotemporal resolution. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.14101

Species distribution models (SDM) are widely applied to understand changing species geographical distribution and abundance patterns. However, existing SDM tools are inherently static and inadequate for modelling species distributions that are driven by dynamic environmental conditions.dynamicSDM provides novel tools that explicitly consider the temporal dimension at key SDM stages, including functions for: (a) Cleaning and filtering species occurrence records by spatial and temporal qualities; (b) Generating pseudo‐absence records through space and time; (c) Extracting spatiotemporally buffered explanatory variables; (d) Fitting SDMs whilst accounting for temporal biases and autocorrelation and (e) Projecting intra‐ and inter‐ annual geographical distributions and abundances at high spatiotemporal resolution.Package functions have been designed to be: flexible for targeting specific study species; compatible with other SDM tools; and, by utilising Google Earth Engine and Google Drive, to have low computing power and storage needs. We illustrate dynamicSDM functions with an example of a nomadic bird in southern Africa, the red‐billed quelea Quelea quelea.As dynamicSDM functions are flexible and easily applied, we suggest that these tools could be readily applied to other taxa and systems globally.

Higino, G. T., F. Banville, G. Dansereau, N. R. Forero Muñoz, F. Windsor, and T. Poisot. 2023. Mismatch between IUCN range maps and species interactions data illustrated using the Serengeti food web. PeerJ 11: e14620. https://doi.org/10.7717/peerj.14620

Background Range maps are a useful tool to describe the spatial distribution of species. However, they need to be used with caution, as they essentially represent a rough approximation of a species’ suitable habitats. When stacked together, the resulting communities in each grid cell may not always be realistic, especially when species interactions are taken into account. Here we show the extent of the mismatch between range maps, provided by the International Union for Conservation of Nature (IUCN), and species interactions data. More precisely, we show that local networks built from those stacked range maps often yield unrealistic communities, where species of higher trophic levels are completely disconnected from primary producers. Methodology We used the well-described Serengeti food web of mammals and plants as our case study, and identify areas of data mismatch within predators’ range maps by taking into account food web structure. We then used occurrence data from the Global Biodiversity Information Facility (GBIF) to investigate where data is most lacking. Results We found that most predator ranges comprised large areas without any overlapping distribution of their prey. However, many of these areas contained GBIF occurrences of the predator. Conclusions Our results suggest that the mismatch between both data sources could be due either to the lack of information about ecological interactions or the geographical occurrence of prey. We finally discuss general guidelines to help identify defective data among distributions and interactions data, and we recommend this method as a valuable way to assess whether the occurrence data that are being used, even if incomplete, are ecologically accurate.

Xu, A., J. Zhang, Q. Li, Z. Li, and Q. Zhu. 2023. The benefits of being smaller: Consistent pattern for climate-induced range shift and morphological difference of three falconiforme species. Avian Research 14: 100079. https://doi.org/10.1016/j.avrs.2023.100079

Climate exerts a dominant control over the distribution of species. Generally, species migrate to higher elevations to track thermal niches, but variations in morphological traits can result in trait-specific responses to climate change. Here we attempted to explore how three sympatrically distributed raptor species (the Upland Buzzard Buteo hemilasius, UB; the Common Kestrel, also called Eurasian ​Kestrel Falco tinnunculus, EK; and the Saker Falcon Falco cherrug, SF) would respond to climate change over time, and whether their responses would bias by different morphology. We tested the alternative hypotheses for Allen's rule for UB, EK, and SF in Qinghai Province, China, by modeling their current and future habitat suitability and confirming whether a consistent pattern exists between climate-induced range shifts and morphological differences among species. The extent of the projected distribution range within protected areas was also calculated for each species. We identified the future downward elevation shift for all the species, but with the notable northeastward shifting of the suitable climate space for UB and SF. Climate change would induce range contraction in the future, and the most acute influence is always the result of the pessimistic SSP585 scenario. No obvious pattern in climate-induced range shift was found for EK, for whom the morphological traits were significantly smaller all the time. More seriously, the ratios of highly suitable habitats being protected for our three raptor species were almost at a deficient level (below 1%). This study firstly tested the alternative hypothesis of Allen's rule among raptors in Qinghai Province unprecedently, confirmed the morphological basis for different responses to changing climate across species, and demonstrated the protection deficiency under the current protected area design. We advocate more related studies in the future to verify our findings across more taxa.