Science Enabled by Specimen Data

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.

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.

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.

Ecke, F., B. A. Han, B. Hörnfeldt, H. Khalil, M. Magnusson, N. J. Singh, and R. S. Ostfeld. 2022. Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses. Nature Communications 13.

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species’ synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world. Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.

Zhang, D., H. She, F. E. Rheindt, L. Wu, H. Wang, K. Zhang, Y. Cheng, et al. 2022. Genomic and phenotypic changes associated with alterations of migratory behavior in a songbird. Molecular Ecology.

The seasonal migration of birds is a fascinating natural wonder. Avian migratory behavior changes are common and are likely a polygenic process, as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotated near‐chromosomal level de novo genome assembly, 50 re‐sequenced genomes, hundreds of morphometric data and species distribution information, we investigate population structure and genomic and phenotypic differences associated with differences in migratory behavior in a songbird species, Yellow‐throated Bunting Emberiza elegans (Aves: Emberizidae). Population genomic analyses reveal extensive gene flow between the southern resident and the northern migratory populations of this species. The hand‐wing index is significantly lower in the resident populations than in the migratory populations, indicating reduced flight efficiency of the resident populations. We discuss the possibility that non‐migratory populations may have originated from migratory populations though migration loss. We further infer that the alterations of genes related to energy metabolism, nervous system and circadian rhythm may have played major roles in regulating migration change. Our study sheds light on phenotypic and polygenic changes involving migration change.

Dong, F., Q. Zhang, Y. Chen, F. Lei, S. Li, F. Wu, and X. Yang. 2022. Potential millennial‐scale avian declines by humans in southern China. Global Change Biology 28: 5505–5513.

Mounting observational records demonstrate human‐caused faunal decline in recent decades, while accumulating archaeological evidence suggests an early biodiversity impact of human activities during the Holocene. A fundamental question arises concerning whether modern wildlife population declines began during early human disturbance. Here, we performed population genomic analysis of six common forest birds in East Asia to address this question. For five of them, demographic history inference based on 25‐33 genomes of each species revealed dramatic population declines by 4‐48‐fold over millennia (e.g., two to five thousand years ago). Nevertheless, Summary statistics detected nonsignificant correlations between these population size trajectories and Holocene temperature variations, and ecological niche models explicitly predicted extensive range persistence during the Holocene, implying limited demographic consequence of Holocene climate change. Further analyses suggest high negative correlations between the reconstructed population declines and human disturbance intensities and indicate a potential driver of human activities. These findings provide a deep‐time and large‐scale insight into the recently recognized avifaunal decline and support an early origin hypothesis of human effects on biodiversity. Overall, our study sheds light on the current biodiversity crisis in the context of long‐term human‐environment interactions and offers a multievidential framework for quantitatively assessing the ecological consequences of human disturbance.

Tanaka, K., C. Haga, K. Hori, and T. Matsui. 2022. Renewable energy Nexus: Interlinkages with biodiversity and social issues in Japan. Energy Nexus 6: 100069.

Renewable energy is one of the most important sources of energy for a decarbonized future. The use of renewable energy necessitates the thorough study of interlinkages with social issues such as the Sustainable Development Goals (SDGs). However, there are no high-resolution renewable energy datasets for analyzing interlinkages. The goal of this research is to 1) create a high-resolution geographically explicit renewable energy potential map, 2) evaluate the SDGs nexus using the potential map, 3) discuss the improvement of renewable energy dataset, and 4) discuss nexus issues for implementing renewable energy systems in Japan. Our potential map has the same resolution of 500 m and unit of annual electricity generation on each energy. The occurence of endangered birds was overlapping with the area having a lot of solar energy potential. Local renewable energy is difficult to access on a small spatial scale, especially in urban regions like Tokyo. Our potential map can be used as a database for site selection and area zoning. The findings suggest that implementing decentralized renewable energy systems in today's highly concentrated megacities, such as the Tokyo Metropolitan Area, is extremely challenging, and that this type of centralized-oriented land design is likely to exacerbate the problem of energy poverty.

Estrada-Peña, A., and N. Fernández-Ruiz. 2022. Is composition of vertebrates an indicator of the prevalence of tick-borne pathogens? Infection Ecology & Epidemiology 12.

Communities of vertebrates tend to appear together under similar ranges of environmental features. This study explores whether an explicit combination of vertebrates and their contact rates with a tick vector might constitute an indicator of the prevalence of a pathogen in the quest for ticks at the…

Solovyeva, D., I. Bysykatova-Harmey, S. L. Vartanyan, A. Kondratyev, and F. Huettmann. 2021. Modeling Eastern Russian High Arctic Geese (Anser fabalis, A. albifrons) during moult and brood rearing in the ‘New Digital Arctic’. Scientific Reports 11.

Many polar species and habitats are now affected by man-made global climate change and underlying infrastructure. These anthropogenic forces have resulted in clear implications and many significant changes in the arctic, leading to the emergence of new climate, habitats and other issues including di…

Cardador, L., P. Abellán, and T. M. Blackburn. 2021. Incorporating phylogeographic information in alien bird distribution models increases geographic extent but not accuracy of predictions. Biological Invasions 24: 683–695.

Species distribution models (SDM) have been proposed as valuable first screening tools for predicting species responses to new environmental conditions. SDMs are usually conducted at the species level, assuming that species-environment relationships are a species-specific feature that do not evolve …

Savini, T., M. Namkhan, and N. Sukumal. 2021. Conservation status of Southeast Asian natural habitat estimated using Galliformes spatio-temporal range decline. Global Ecology and Conservation 29: e01723.

Southeast Asia has arguably the highest biodiversity loss due to the high deforestation rate and hunting pressure. In the region, 55 species of the family Phasianidae can be found in all available land habitats from lowland plains up to high-elevation mountainous areas. As ground-dwelling birds, the…