Phenology of five tick species in the central Great Plains

The states of Kansas and Oklahoma, in the central Great Plains, lie at the western periphery of the geographic distributions of several tick species. As the focus of most research on ticks and tick-borne diseases has been on Lyme disease which commonly occurs in areas to the north and east, the ticks of this region have seen little research attention. Here, we report on the phenology and activity patterns shown by tick species observed at 10 sites across the two states and explore factors associated with abundance of all and life specific individuals of the dominant species. Ticks were collected in 2020-2022 using dragging, flagging and carbon-dioxide trapping techniques, designed to detect questing ticks. The dominant species was A. americanum (24098, 97%) followed by Dermacentor variabilis (370, 2%), D. albipictus (271, 1%), Ixodes scapularis (91, <1%) and A. maculatum (38, <1%). Amblyomma americanum, A. maculatum and D. variabilis were active in Spring and Summer, while D. albipictus and I. scapularis were active in Fall and Winter. Factors associated with numbers of individuals of A. americanum included day of year, habitat, and latitude. Similar associations were observed when abundance was examined by life-stage. Overall, the picture is one of broadly distributed tick species that shows seasonal limitations in the timing of their questing activity.

Rethinking ecological niches and geographic distributions in face of pervasive human influence in the Anthropocene

Species are distributed in predictable ways in geographic spaces. The three principal factors that determine geographic distributions of species are biotic interactions (B), abiotic conditions (A), and dispersal ability or mobility (M). A species is expected to be present in areas that are accessible to it and that contain suitable sets of abiotic and biotic conditions for it to persist. A species' probability of presence can be quantified as a combination of responses to B, A, and M via ecological niche modeling (ENM; also frequently referred to as species distribution modeling or SDM). This analytical approach has been used broadly in ecology and biogeography, as well as in conservation planning and decision-making, but commonly in the context of 'natural' settings. However, it is increasingly recognized that human impacts, including changes in climate, land cover, and ecosystem function, greatly influence species' geographic ranges. In this light, historical distinctions between natural and anthropogenic factors have become blurred, and a coupled human-natural landscape is recognized as the new norm. Therefore, B, A, and M (BAM) factors need to be reconsidered to understand and quantify species' distributions in a world with a pervasive signature of human impacts. Here, we present a framework, termed human-influenced BAM (Hi-BAM, for distributional ecology that (i) conceptualizes human impacts in the form of six drivers, and (ii) synthesizes previous studies to show how each driver modifies the natural BAM and species' distributions. Given the importance and prevalence of human impacts on species distributions globally, we also discuss implications of this framework for ENM/SDM methods, and explore strategies by which to incorporate increasing human impacts in the methodology. Human impacts are redefining biogeographic patterns; as such, future studies should incorporate signals of human impacts integrally in modeling and forecasting species' distributions.

Ecological niche conservatism spurs diversification in response to climate change

Lengthy debate has surrounded the theoretical and empirical science of whether climatic niche evolution is related to increased or decreased rates of biological diversification. Because species can persist for thousands to millions of years, these questions cross broad scales of time and space. Thus, short-term experiments may not provide comprehensive understanding of the system, leading to the emergence of contrasting opinions: niche evolution may increase diversity by allowing species to explore and colonize new geographic areas across which they could speciate; or, niche conservatism might augment biodiversity by supporting isolation of populations that may then undergo allopatric speciation. Here, we use a simulation approach to test how biological diversification responds to different rates and modes of niche evolution. We find that niche conservatism promotes biological diversification, whereas labile niches-whether adapting to the conditions available or changing randomly-generally led to slower diversification rates. These novel results provide a framework for understanding how Earth-life interactions produced such a diverse biota.

An evaluation of the ecological niche of Orf virus (Poxviridae): Challenges of distinguishing broad niches from no niches

Contagious ecthyma is a skin disease, caused by Orf virus, creating great economic threats to livestock farming worldwide. Zoonotic potential of this disease has gained recent attention owing to the re-emergence of disease in several parts of the world. Increased public health concern emphasizes the need for a predictive understanding of the geographic distributional potential of Orf virus. Here, we mapped the current distribution using occurrence records, and estimated the ecological niche in both geographical and environmental spaces. Twenty modeling experiments, resulting from two- and three-partition models, were performed to choose the candidate models that best represent the geographic distributional potential of Orf virus. For all of our models, it was possible to reject the null hypothesis of predictive performance no better than random expectations. However, statistical significance must be accompanied by sufficiently good predictive performance if a model is to be useful. In our case, omission of known distribution of the virus was noticed in all Maxent models, indicating inferior quality of our models. This conclusion was further confirmed by the independent final evaluation, using occurrence records sourced from the Centre for Agriculture and Bioscience International. Minimum volume ellipsoid (MVE) models indicated the broad range of environmental conditions under which Orf virus infections are found. The excluded climatic conditions from MVEs could not be considered as unsuitable owing to the broad distribution of Orf virus. These results suggest two possibilities: that the niche models fail to identify niche limits that constrain the virus, or that the virus has no detectable niche, as it can be found throughout the geographic distributions of its hosts. This potential limitation of component-based pathogen-only ENMs is discussed in detail.

Relationships among cost, citation, and access in journal publishing by an ecology and evolutionary biology department at a U.S. university

Background

Optimizing access to high-quality scientific journals has become an important priority for academic departments, including the ability to read the scientific literature and the ability to afford to publish papers in those journals. In this contribution, we assess the question of whether institutional investment in scientific journals aligns with the journals where researchers send their papers for publication, and where they serve as unpaid reviewers and editors.

Methods

We assembled a unique suite of information about the publishing habits of our Department of Ecology and Evolutionary Biology, including summaries of 3,540 journal publications by 35 faculty members. These data include economic costs of journals to institutions and to authors, benefits to authors in terms of journal prestige and citation rates, and considerations of ease of reading access for individuals both inside and outside the university. This dataset included data on institutional costs, including subscription pricing (rarely visible to scholars), and "investment" by scholars in supporting journals, such as time spent as editors and reviewers.

Results

Our results highlighted the complex set of relationships between these factors, and showed that institutional costs often do not match well with payoffs in terms of benefits to researchers (e.g., citation rate, prestige of journal, ease of access). Overall, we advocate for greater cost-benefit transparency to help compare different journals and different journal business models; such transparency would help both researchers and their institutions in investing wisely the limited resources available to academics.

Specimen collection is essential for modern science

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Mycobacterium leprae in Armadillo Tissues from Museum Collections, United States

We examined armadillos from museum collections in the United States using molecular assays to detect leprosy-causing bacilli. We found Mycobacterium leprae bacilli in samples from the United States, Bolivia, and Paraguay; prevalence was 14.8% in nine-banded armadillos. US isolates belonged to subtype 3I-2, suggesting long-term circulation of this genotype.

Impact of public sentiments on the transmission of COVID-19 across a geographical gradient

COVID-19 is a respiratory disease caused by a recently discovered, novel coronavirus, SARS-COV-2. The disease has led to over 81 million confirmed cases of COVID-19, with close to two million deaths. In the current social climate, the risk of COVID-19 infection is driven by individual and public perception of risk and sentiments. A number of factors influences public perception, including an individual's belief system, prior knowledge about a disease and information about a disease. In this article, we develop a model for COVID-19 using a system of ordinary differential equations following the natural history of the infection. The model uniquely incorporates social behavioral aspects such as quarantine and quarantine violation. The model is further driven by people's sentiments (positive and negative) which accounts for the influence of disinformation. People's sentiments were obtained by parsing through and analyzing COVID-19 related tweets from Twitter, a social media platform across six countries. Our results show that our model incorporating public sentiments is able to capture the trend in the trajectory of the epidemic curve of the reported cases. Furthermore, our results show that positive public sentiments reduce disease burden in the community. Our results also show that quarantine violation and early discharge of the infected population amplifies the disease burden on the community. Hence, it is important to account for public sentiment and individual social behavior in epidemic models developed to study diseases like COVID-19.

Mapping the global distribution of invasive pest Drosophila suzukii and parasitoid Leptopilina japonica: implications for biological control

Insect pest invasions cause significant damage to crop yields, and the resultant economic losses are truly alarming. Climate change and trade liberalization have opened new ways of pest invasions. Given the consumer preference towards organic agricultural products and environment-friendly nature of natural pest control strategies, biological control is considered to be one of the potential options for managing invasive insect pests. Drosophila suzukii (Drosophilidae) is an extremely damaging fruit pest, demanding development of effective and sustainable biological control strategies. In this study, we assessed the potential of the parasitoid Leptopilina japonica (Figitidae) as a biocontrol agent for D. suzukii using ecological niche modeling approaches. We developed global-scale models for both pest and parasitoid to identify four components necessary to derive a niche based, target oriented prioritization approach to plan biological control programs for D. suzukii: (i) potential distribution of pest D. suzukii, (ii) potential distribution of parasitoid L. japonica, (iii) the degree of overlap in potential distributions of pest and parasitoid, and (iv) biocontrol potential of this system for each country. Overlapping suitable areas of pest and parasitoid were identified at two different thresholds and at the most desirable threshold (E = 5%), potential for L. japonica mediated biocontrol management existed in 125 countries covering 1.87 × 10⁷ km², and at the maximum permitted threshold (E = 10%), land coverage was reduced to 1.44 × 10⁷ km² in 121 countries. Fly pest distributional information as a predictor variable was not found to be improving parasitoid model performance, and globally, only in half of the countries, >50% biocontrol coverage was estimated. We therefore suggest that niche specificities of both pest and parasitoid must be included in site-specific release planning of L. japonica for effective biocontrol management aimed at D. suzukii. This study can be extended to design cost-effective pre-assessment strategies for implementing any biological control management program.

Broad-scale factors shaping the ecological niche and geographic distribution of Spirodela polyrhiza

The choice of appropriate independent variables to create models characterizing ecological niches of species is of critical importance in distributional ecology. This set of dimensions in which a niche is defined can inform about what factors limit the distributional potential of a species. We used a multistep approach to select relevant variables for modeling the ecological niche of the aquatic Spirodela polyrhiza, taking into account variability arising from using distinct algorithms, calibration areas, and spatial resolutions of variables. We found that, even after an initial selection of meaningful variables, the final set of variables selected based on statistical inference varied considerably depending on the combination of algorithm, calibration area, and spatial resolution used. However, variables representing extreme temperatures and dry periods were more consistently selected than others, despite the treatment used, highlighting their importance in shaping the distribution of this species. Other variables related to seasonality of solar radiation, summer solar radiation, and some soil proxies of nutrients in water, were selected commonly but not as frequently as the ones mentioned above. We suggest that these later variables are also important to understanding the distributional potential of the species, but that their effects may be less pronounced at the scale at which they are represented for the needs of this type of modeling. Our results suggest that an informed definition of an initial set of variables, a series of statistical steps for filtering and exploring these predictors, and model selection exercises that consider multiple sets of predictors, can improve determination of variables that shape the niche and distribution of the species, despite differences derived from factors related to data or modeling algorithms.

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, that is, at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.

Low risk of acquiring melioidosis from the environment in the continental United States

Melioidosis is an underreported human disease of tropical and sub-tropical regions caused by the saprophyte Burkholderia pseudomallei. Although most global melioidosis cases are reported from tropical regions in Southeast Asia and northern Australia, there are multiple occurrences from sub-tropical regions, including the United States (U.S.). Most melioidosis cases reported from the continental U.S. are the result of acquiring the disease during travel to endemic regions or from contaminated imported materials. Only two human melioidosis cases from the continental U.S. have likely acquired B. pseudomallei directly from local environments and these cases lived only ~7 km from each other in rural Texas. In this study, we assessed the risk of acquiring melioidosis from the environment within the continental U.S. by surveying for B. pseudomallei in the environment in Texas where these two human melioidosis cases likely acquired their infections. We sampled the environment near the homes of the two cases and at additional sampling locations in surrounding counties in Texas that were selected based on ecological niche modeling. B. pseudomallei was not detected at the residences of these two cases or in the surrounding region. These negative data are important to demonstrate that B. pseudomallei is rare in the environment in the U.S. even at locations where locally acquired human cases likely have occurred, documenting the low risk of acquiring B. pseudomallei infection from the environment in the continental U.S.

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse's Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.

Climate change influences on the geographic distributional potential of the spotted fever vectors Amblyomma maculatum and Dermacentor andersoni

Amblyomma maculatum (Gulf Coast tick), and Dermacentor andersoni (Rocky Mountain wood tick) are two North American ticks that transmit spotted fevers associated Rickettsia. Amblyomma maculatum transmits Rickettsia parkeri and Francisella tularensis, while D. andersoni transmits R. rickettsii, Anaplasma marginale, Coltivirus (Colorado tick fever virus), and F. tularensis. Increases in temperature causes mild winters and more extreme dry periods during summers, which will affect tick populations in unknown ways. Here, we used ecological niche modeling (ENM) to assess the potential geographic distributions of these two medically important vector species in North America under current condition and then transfer those models to the future under different future climate scenarios with special interest in highlighting new potential expansion areas. Current model predictions for A. maculatum showed suitable areas across the southern and Midwest United States, and east coast, western and southern Mexico. For D. andersoni, our models showed broad suitable areas across northwestern United States. New potential for range expansions was anticipated for both tick species northward in response to climate change, extending across the Midwest and New England for A. maculatum, and still farther north into Canada for D. andersoni.

Spatio-temporal dynamics of rabies and habitat suitability of the common marmoset Callithrix jacchus in Brazil

Rabies transmitted by wildlife is now the main source of human rabies in the Americas. The common marmoset, Callithrix jacchus, is considered a reservoir of rabies causing sporadic and unpredictable human deaths in Brazil, but the extent of the spillover risk to humans remains unknown. In this study, we described the spatiotemporal dynamics of rabies affecting C. jacchus reported to Brazil’s Ministry of Health passive surveillance system between 2008 and 2020, and combined ecological niche modelling with C. jacchus occurrence data to predict its suitable habitat. Our results show that 67 outbreaks (91 cases) of rabies affecting C. jacchus were reported by 41 municipalities between January 2008 and October 2020, with a mean of 5 outbreaks/year [range: 1–14]. The maximum number of outbreaks and municipalities reporting cases occurred in 2018, coinciding with higher surveillance of primate deaths due to Yellow Fever. A mean of 3 [1–9] new municipalities reported outbreaks yearly, suggesting potential spatial expansions of the C. jacchus variant in northeastern Brazil and emerging rabies spillover from vampire bat Desmodus rotundus to C. jacchus in the north and south. Outbreaks were concentrated in the states of Ceará (72%) and Pernambuco (16%) up to 2012, but are now reported in Piauí since 2013, in Bahia since 2017 (D. rotundus’ antigenic variant, AgV3) and in Rio de Janeiro since 2019 (AgV3). Besides confirming suitable habitat for this primate in the northeast and the east coast of Brazil, our Maximum Entropy model also predicted suitable habitat on the north and the west states of the country but predicted low habitat suitability among inland municipalities of the Caatinga biome reporting rabies. Our findings revealed new areas reporting rabies infecting C. jacchus, highlighting the need to implement strategies limiting spillover to humans and to better understand the drivers of C. jacchus rabies dynamics.

Rabies virus is the deadliest virus affecting mammals. In Brazil, rabies transmitted by the common marmoset primate is emerging and causing unpredictable human deaths. This primate once endemic to the northeast of the country has now invaded regions in the south throughout human-mediated introductions. However, the dynamics of rabies in this primate and the extend of spillover risk to humans remain unknown. We found that outbreaks of rabies in this marmoset reported to the Ministry of Health are continuously reported in new areas, including three new states since 2012 and three states reporting rabies originated from the common vampire bat. We also showed that this primate has suitable habitat to invade other states in the north and west of Brazil. Preventive strategies should be implemented to limit further rabies spillover to humans in new areas.

ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions

The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades—including a maturation of relevant theory and key concepts—but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an “Overview” talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology.

To isolate or not to isolate: the impact of changing behavior on COVID-19 transmission

Background

The COVID-19 pandemic has caused more than 25 million cases and 800 thousand deaths worldwide to date. In early days of the pandemic, neither vaccines nor therapeutic drugs were available for this novel coronavirus. All measures to prevent the spread of COVID-19 are thus based on reducing contact between infected and susceptible individuals. Most of these measures such as quarantine and self-isolation require voluntary compliance by the population. However, humans may act in their (perceived) self-interest only.

Methods

We construct a mathematical model of COVID-19 transmission with quarantine and hospitalization coupled with a dynamic game model of adaptive human behavior. Susceptible and infected individuals adopt various behavioral strategies based on perceived prevalence and burden of the disease and sensitivity to isolation measures, and they evolve their strategies using a social learning algorithm (imitation dynamics).

Results

This results in complex interplay between the epidemiological model, which affects success of different strategies, and the game-theoretic behavioral model, which in turn affects the spread of the disease. We found that the second wave of the pandemic, which has been observed in the US, can be attributed to rational behavior of susceptible individuals, and that multiple waves of the pandemic are possible if the rate of social learning of infected individuals is sufficiently high.

Conclusions

To reduce the burden of the disease on the society, it is necessary to incentivize such altruistic behavior by infected individuals as voluntary self-isolation.

On the relationship between environmental suitability and habitat use for three neotropical mammals

Recent studies have used occupancy models (OM) and ecological niche models (ENM) to provide a better understanding of species’ distributions at different scales. One of the main ideas underlying the theoretical foundations of both OM and ENM is that they are positively related to abundance: higher occupancy implies higher density and more suitable areas are likely to have more abundant populations. Here, we analyze the relationship between habitat use measured in terms of occupancy probabilities from OM and environmental suitability derived from ENM in three different Neotropical mammal species: Leopardus wiedii, Cuniculus paca, and Dasypus novemcinctus. For ENM, we used climatic and vegetation cover variables and implemented a model calibration and selection protocol to select the most competitive models. For OM, we used a single-species, single-season model with site covariates for camera-trap data from six different sites throughout the Neotropical realm. Covariates included vegetation percentage, normalized difference vegetation index, normalized difference water index, and elevation. For each site, we fit OM using all possible combinations of variables and selected the most competitive (ΔAICc &lt; 2) to build an average OM. We explored relationships between estimated suitability and occupancy values using Spearman correlation analysis. Relationships between ENM and OM tended to be positive for the three Neotropical mammals, but the strength varied among sites, which could be explained by local factors such as site characteristics and conservation status of areas. We conjecture that ENM are suitable to understand spatial patterns at coarser geographic scales because the concept of the niche is about the species as a whole, whereas OM are more relevant to explain the distribution locally, likely reflecting transient dynamics of populations resulting from many local factors such as community composition and biotic processes.

Application of Deep Learning to Community-Science-Based Mosquito Monitoring and Detection of Novel Species

Mosquito-borne diseases account for human morbidity and mortality worldwide, caused by the parasites (e.g., malaria) or viruses (e.g., dengue, Zika) transmitted through bites of infected female mosquitoes. Globally, billions of people are at risk of infection, imposing significant economic and public health burdens. As such, efficient methods to monitor mosquito populations and prevent the spread of these diseases are at a premium. One proposed technique is to apply acoustic monitoring to the challenge of identifying wingbeats of individual mosquitoes. Although researchers have successfully used wingbeats to survey mosquito populations, implementation of these techniques in areas most affected by mosquito-borne diseases remains challenging. Here, methods utilizing easily accessible equipment and encouraging community-scientist participation are more likely to provide sufficient monitoring. We present a practical, community-science-based method of monitoring mosquito populations using smartphones. We applied deep-learning algorithms (TensorFlow Inception v3) to spectrogram images generated from smartphone recordings associated with six mosquito species to develop a multiclass mosquito identification system, and flag potential invasive vectors not present in our sound reference library. Though TensorFlow did not flag potential invasive species with high accuracy, it was able to identify species present in the reference library at an 85% correct identification rate, an identification rate markedly higher than similar studies employing expensive recording devices. Given that we used smartphone recordings with limited sample sizes, these results are promising. With further optimization, we propose this novel technique as a way to accurately and efficiently monitor mosquito populations in areas where doing so is most critical.

speciesLink: rich data and novel tools for digital assessments of biodiversity

Abstract speciesLink is a large-scale biodiversity information portal that exists thanks to a broad collaborative network of people and institutions. CRIA’s involvement with the scientific community of Brazil and other countries is responsible for the significant results achieved, currently reaching more than 15 million primary biodiversity data records, 95% of which are associated with preserved specimens and about 25% with high-quality digital images. The network provides data on over 200,000 species, of which over 110,000 occur in Brazil. This article describes thematic networks within speciesLink, as well as some of the most useful tools developed. The importance and contributions of speciesLink are outlined, as are concerns about securing stable budgetary support for such biodiversity data e-infrastructures. Here we review the value of speciesLink as a major source of biodiversity information for research, education, informed decision-making, policy development, and bioeconomy.

Potential geographic distribution of Ixodes cookei, the vector of Powassan virus

Ixodes cookei Packard, the groundhog tick or woodchuck tick, is the main known vector of Powassan virus (POWV) disease in North America and an ectoparasite that infests diverse small- and mid-size mammals for blood meals to complete its life stages. Since I. cookei spends much of its life cycle off the host and needs hosts for a blood meal in order to pass to the next life stage, it is susceptible to changes in environmental conditions. We used a maximum-entropy approach to ecological niche modeling that incorporates detailed model-selection routes to link occurrence data to climatic variables to assess the potential geographic distribution of I. cookei under current and likely future climate conditions. Our models identified suitable areas in the eastern United States, from Tennessee and North Carolina north to southern Canada, including Nova Scotia, New Brunswick, eastern Newfoundland and Labrador, southern Quebec, and Ontario; suitable areas were also in western states, including Washington and Oregon and restricted areas of northern Idaho, northwestern Montana, and adjacent British Columbia, in Canada. This study produces the first maps of the potential geographic distribution of I. cookei. Documented POWV cases overlapped with suitable areas in the northeastern states; however, the presence of this disease in areas classified by our models as not suitable by our models but with POWV cases (Minnesota and North Dakota) requires more study.

Climate change impacts on Anopheles (K.) cruzii in urban areas of Atlantic Forest of Brazil: Challenges for malaria diseases

Around 27% of South Americans live in central and southern Brazil. Of 19,400 human malaria cases in Brazil in 2018, some were from the southern and southeastern states. High abundance of malaria vectors is generally positively associated with malaria incidence. Expanding geographic distributions of Anopheles vector mosquito species (e.g. A. cruzii) in the face of climate change processes would increase risk of such malaria transmission; such risk is of particular concern in regions that hold human population concentrations near present limits of vector species' geographic distributions. We modeled effects of likely climate changes on the distribution of A. cruzii, evaluating two scenarios of future greenhouse gas emissions for 2050, as simulated in 21 general circulation models and two greenhouse gas scenarios (RCP 4.5 and RCP 8.5) for 2050. We tested 1305 candidate models, and chose among them based on statistical significance, predictive performance, and complexity. The models closely approximated the known geographic distribution of the species under current conditions. Under scenarios of future climate change, we noted increases in suitable area for the mosquito vector species in São Paulo and Rio de Janeiro states, including areas close to 30 densely populated cities. Under RCP 8.5, our models anticipate areal increases of >75% for this important malaria vector in the vicinity of 20 large Brazilian cities. We developed models that anticipate increased suitability for the mosquito species; around 50% of Brazilians reside in these areas, and ∼89% of foreign tourists visit coastal areas in this region. Under climate change thereefore, the risk and vulnerability of human populations to malaria transmission appears bound to increase.

Climatic suitability of the eastern paralysis tick, Ixodes holocyclus, and its likely geographic distribution in the year 2050

The eastern paralysis tick, Ixodes holocyclus is one of two ticks that cause potentially fatal tick paralysis in Australia, and yet information on the full extent of its present or potential future spatial distribution is not known. Occurrence data for this tick species collected over the past two decades, and gridded environmental variables at 1 km² resolution representing climate conditions, were used to derive correlative ecological niche models to predict the current and future potential distribution. Several hundreds of candidate models were constructed with varying combinations of model parameters, and the best-fitting model was chosen based on statistical significance, omission rate, and Akaike Information Criterion (AICc). The best-fitting model matches the currently known distribution but also extends through most of the coastal areas in the south, and up to the Kimbolton peninsula in Western Australia in the north. Highly suitable areas are present around south of Perth, extending towards Albany, Western Australia. Most areas in Tasmania, where the species is not currently present, are also highly suitable. Future spatial distribution of this tick in the year 2050 indicates moderate increase in climatic suitability from the present-day prediction but noticeably also moderate to low loss of climatically suitable areas elsewhere.

Genome-environment association methods comparison supports omnigenic adaptation to ecological niche in malaria vector mosquitoes

The concept of a fundamental ecological niche is central to questions of geographic distribution, population demography, species conservation, and evolutionary potential. However, robust inference of genomic regions associated with evolutionary adaptation to particular environmental conditions remains difficult due to the myriad of potential confounding processes that can generate heterogeneous patterns of variation across the genome. Here, we interrogate the potential role of genome environment association (GEA) testing as an initial step in building an understanding of the genetic basis of ecological niche. We leverage publicly available genomic data from the Anopheles gambiae 1000 Genomes (Ag1000g) Consortium to test the ability of multiple analytically unique GEA methods to handle confounding patterns of genetic variation, control false positive rates, and discern associations with broadly relevant climate variables from random allele frequency patterns throughout the genome. We found evidence supporting the ability of commonly implemented GEA methods to account for confounding patterns of spatial and genetic variation, and control false positive rates. However, we fail to find evidence supporting the ability of GEA tests to reject signals of adaptation to randomly simulated environmental variables, indicating that discerning between true signals of genome environment adaptation and genome environment correlations resulting from alternative evolutionary processes, remains challenging. Because signals of environmental adaptation are so diffuse and confounded throughout the genome, we argue that genomic adaptation to ecological niche is likely best understood under an omnigenic model wherein highly interconnected, genome-wide gene regulatory networks shape genomic adaptation to key environmental conditions.

Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

Geographic potential of the world's largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America

The Asian giant hornet (AGH, Vespa mandarinia) is the world's largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion.

Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

BACKGROUND

Biological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.

METHODS

Here, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).

RESULTS

Use of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions.

Climate change influences on the potential distribution of Dianthus polylepis Bien. ex Boiss. (Caryophyllaceae), an endemic species in the Irano-Turanian region

Endemic and restricted-range species are considered to be particularly vulnerable to the effects of environmental change, which makes assessing likely climate change effects on geographic distributions of such species important to the development of integrated conservation strategies. Here, we determined distributional patterns for an endemic species of Dianthus (Dianthus polylepis) in the Irano-Turanian region using a maximum-entropy algorithm. In total, 70 occurrence points and 19 climatic variables were used to estimate the potential distributional area under current conditions and two future representative concentration pathway (RCP2.6 and RCP8.5) scenarios under seven general circulation models for 2050. Mean diurnal range, iso-thermality, minimum temperature of coldest quarter, and annual precipitation were major factors that appeared to structure the distribution of the species. Most current potential suitable areas were located in montane regions. Model transfers to future-climate scenarios displayed upward shifts in elevation and northward shifts geographically for the species. Our results can be used to define high-priority areas in the Irano-Turanian region for conservation management plans for this species and can offer a template for analyses of other endangered and threatened species in the region.

Assessing the current and future potential geographic distribution of the American dog tick, Dermacentor variabilis (Say) (Acari: Ixodidae) in North America

The American dog tick, Dermacentor variabilis, is a veterinary- and medically- significant tick species that is known to transmit several diseases to animal and human hosts. The spatial distribution of this species in North America is not well understood, however; and knowledge of likely changes to its future geographic distribution owing to ongoing climate change is needed for proper public health planning and messaging. Two recent studies have evaluated these topics for D. variabilis; however, less-rigorous modeling approaches in those studies may have led to erroneous predictions. We evaluated the present and future distribution of this species using a correlative maximum entropy approach, using publicly available occurrence information. Future potential distributions were predicted under two representative concentration pathway (RCP) scenarios; RCP 4.5 for low-emissions and RCP 8.5 for high-emissions. Our results indicated a broader current distribution of this species in all directions relative to its currently known extent, and dramatic potential for westward and northward expansion of suitable areas under both climate change scenarios. Implications for disease ecology and public health are discussed.

Presence-only and Presence-absence Data for Comparing Species Distribution Modeling Methods

Species distribution models (SDMs) are widely used to predict and study distributions of species. Many different modeling methods and associated algorithms are used and continue to emerge. It is important to understand how different approaches perform, particularly when applied to species occurrence records that were not gathered in struc­tured surveys (e.g. opportunistic records). This need motivated a large-scale, collaborative effort, published in 2006, that aimed to create objective comparisons of algorithm performance. As a benchmark, and to facilitate future comparisons of approaches, here we publish that dataset: point location records for 226 anonymized species from six regions of the world, with accompanying predictor variables in raster (grid) and point formats. A particularly interesting characteristic of this dataset is that independent presence-absence survey data are available for evaluation alongside the presence-only species occurrence data intended for modeling. The dataset is available on Open Science Framework and as an R package and can be used as a benchmark for modeling approaches and for testing new ways to evaluate the accuracy of SDMs.

Potential Roles of Environmental and Socio-Economic Factors in the Distribution of Insecticide Resistance in Anopheles gambiae sensu lato (Culicidae: Diptera) Across Togo, West Africa

Vector control strategies recommended by the World Health Organization are threatened by resistance of Anopheles mosquitoes to insecticides. Information on the distribution of resistant genotypes of malaria vectors is increasingly needed to address the problem. Ten years of published and unpublished data on malaria vector susceptibility/resistance and resistance genes have been collected across Togo. Relationships between the spatial distribution of resistance status and environmental, socio-economic, and landscape features were tested using randomization tests, and calculating Spearman rank and Pearson correlation coefficients between mosquito mortality and different gridded values. Anopheles gambiae sensu lato was resistant to DDT, pyrethroids, and the majority of carbamates and organophosphates. Three sibling species were found (i.e., An. gambiae, Anopheles coluzzii, and Anopheles arabiensis) with four resistance genes, including kdr (L1014F, L1014S, and N1575Y) and ace1 (G119S). The most frequent resistance gene was L1014F. Overall, no association was found between the susceptibility/resistance status and environmental features, suggesting that evolution of resistance may be most closely related to extreme selection from local insecticide use. Nevertheless, further research is necessary for firm conclusions about this lack of association, and the potential role of landscape characteristics such as presence of crops and percentage of tree cover.

Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol.

Climate change implications for the distribution of the babesiosis and anaplasmosis tick vector, Rhipicephalus (Boophilus) microplus

Climate change ranks among the most important issues globally, affecting geographic distributions of vectors and pathogens, and inducing losses in livestock production among many other damaging effects. We characterized the potential geographic distribution of the ticks Rhipicephalus (Boophilus) microplus, an important vector of babesiosis and anaplasmosis globally. We evaluated potential geographic shifts in suitability patterns for this species in two periods (2050 and 2070) and under two emissions scenarios (RCPs 4.5 and 8.5). Our results anticipate increases in suitability worldwide, particularly in the highest production areas for cattle. The Indo-Malayan region resulted in the highest cattle exposure under both climate change projections (2050), with increases in suitability of > 30%. This study illustrates how ecological niche modeling can be used to explore probable effects of climate change on disease vectors, and the possible consequences on economic dimensions.

The ecology of chronic wasting disease in wildlife

Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.

Potential distributions of Bacillus anthracis and Bacillus cereus biovar anthracis causing anthrax in Africa

BACKGROUND

Bacillus cereus biovar anthracis (Bcbva) is an emergent bacterium closely related to Bacillus anthracis, the etiological agent of anthrax. The latter has a worldwide distribution and usually causes infectious disease in mammals associated with savanna ecosystems. Bcbva was identified in humid tropical forests of Côte d'Ivoire in 2001. Here, we characterize the potential geographic distributions of Bcbva in West Africa and B. anthracis in sub-Saharan Africa using an ecological niche modeling approach.

METHODOLOGY/PRINCIPAL FINDINGS

Georeferenced occurrence data for B. anthracis and Bcbva were obtained from public data repositories and the scientific literature. Combinations of temperature, humidity, vegetation greenness, and soils values served as environmental variables in model calibrations. To predict the potential distribution of suitable environments for each pathogen across the study region, parameter values derived from the median of 10 replicates of the best-performing model for each pathogen were used. We found suitable environments predicted for B. anthracis across areas of confirmed and suspected anthrax activity in sub-Saharan Africa, including an east-west corridor from Ethiopia to Sierra Leone in the Sahel region and multiple areas in eastern, central, and southern Africa. The study area for Bcbva was restricted to West and Central Africa to reflect areas that have likely been accessible to Bcbva by dispersal. Model predicted values indicated potential suitable environments within humid forested environments. Background similarity tests in geographic space indicated statistical support to reject the null hypothesis of similarity when comparing environments associated with B. anthracis to those of Bcbva and when comparing humidity values and soils values individually. We failed to reject the null hypothesis of similarity when comparing environments associated with Bcbva to those of B. anthracis, suggesting that additional investigation is needed to provide a more robust characterization of the Bcbva niche.

CONCLUSIONS/SIGNIFICANCE

This study represents the first time that the environmental and geographic distribution of Bcbva has been mapped. We document likely differences in ecological niche-and consequently in geographic distribution-between Bcbva and typical B. anthracis, and areas of possible co-occurrence between the two. We provide information crucial to guiding and improving monitoring efforts focused on these pathogens.

Predicting the potential distribution of Amblyomma americanum (Acari: Ixodidae) infestation in New Zealand, using maximum entropy-based ecological niche modelling

Although currently exotic to New Zealand, the potential geographic distribution of Amblyomma americanum (L.), the lone star tick, was modelled using maximum entropy (MaxEnt). The MaxEnt model was calibrated across the native range of A. americanum in North America using present-day climatic conditions and occurrence data from museum collections. The resulting model was then projected onto New Zealand using both present-day and future climates modelled under two greenhouse gas emission scenarios, representative concentration pathways (RCP) 4.5 (low) and RCP 8.5 (high). Three sets of WorldClim bioclimatic variables were chosen using the jackknife method and tested in MaxEnt using different combinations of model feature class functions and regularization multiplier values. The preferred model was selected based on partial receiver operating characteristic tests, the omission rate and the lowest Akaike information criterion. The final model had four bioclimatic variables, Annual Mean Temperature (BIO₁), Annual Precipitation (BIO₁₂), Precipitation Seasonality (BIO₁₅) and Precipitation of Driest Quarter (BIO₁₇), and the projected New Zealand distribution was broadly similar to that of Haemaphysalis longicornis Neumann, New Zealand's only livestock tick, but with a more extensive predicted suitability. The climate change predictions for the year 2050 under both low and high RCP scenarios projected only moderate increases in habitat suitability along the mountain valleys in the South Island. In conclusion, this analysis shows that given the opportunity and license A. americanum could and would successfully establish in New Zealand and could provide another vector for theileriosis organisms.

Diversity, above-ground biomass, and vegetation patterns in a tropical dry forest in Kimbi-Fungom National Park, Cameroon

Research highlights

This study is one of few detailed analyses of plant diversity and vegetation patterns in African dry forests. We established permanent plots to characterize plant diversity, above-ground biomass, and vegetation patterns in a tropical dry forest in Kimbi-Fungom National Park, Cameroon. Our results contribute to long-term monitoring, predictions, and management of dry forest ecosystems, which are often vulnerable to anthropogenic pressures.

Background and objectives

Considerable consensus exists regarding the importance of dry forests in species diversity and carbon storage; however, the relationship between dry forest tree species composition, species richness, and carbon stock is not well established. Also, simple baseline data on plant diversity are scarce for many dry forest ecosystems. This study seeks to characterize floristic diversity, vegetation patterns, and tree diversity in permanent plots in a tropical dry forest in Northwestern Cameroon (Kimbi-Fungom National Park) for the first time.

Materials and methods

We studied associations between above-ground biomass and species composition, and how different vegetation types vary in terms of species composition, diversity, and carbon storage, in a dry forest in Kimbi-Fungom National Park, Cameroon. Vegetation was inventoried in 17 permanent 1-ha plots. Allometric equations were used to calculate above-ground biomass and carbon.

Results

We found an average of 269.8 tree stems ha⁻¹ and 43.1 species ha⁻¹. Five vegetation types: semi-deciduous, gallery, mixed vegetation, secondary and the grassland/woody savanna forest were classified using TWINSPAN analysis. The five vegetation types had an average above-ground biomass of 149.2 t ha⁻¹ and 74.6 tC ha⁻¹ of carbon in the 17 ha analyzed. Canonical correspondence analysis (CCA) showed the importance of semi-deciduous forest over grassland/woody savanna forest.

Conclusions

This study demonstrated that the forest of the Kimbi-Fungom National Park is poor in plant diversity, biomass, and carbon, highlighting the need to implement efficient management practices. Fine-scale inventory data of species obtained in this study could be useful in developing predictive models for efficient management of tropical dry forests.