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.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

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 (Aphelocoma californica) and Woodhouse's Scrub-Jay (Aphelocoma 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 (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.].

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.

The NIH public access policy did not harm biomedical journals.

The United States National Institutes of Health (NIH) imposed a public access policy on all publications for which the research was supported by their grants; the policy was drafted in 2004 and took effect in 2008. The policy is now 11 years old, yet no analysis has been presented to assess whether in fact this largest-scale US-based public access policy affected the vitality of the scholarly publishing enterprise, as manifested in changed mortality or natality rates of biomedical journals. We show here that implementation of the NIH policy was associated with slightly elevated mortality rates and mildly depressed natality rates of biomedical journals, but that birth rates so exceeded death rates that numbers of biomedical journals continued to rise, even in the face of the implementation of such a sweeping public access policy.

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.

Earth history and the passerine superradiation.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

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.

Relationships between population densities and niche-centroid distances in North American birds.

Correlational ecological niche models have seen intensive use and exploration as a means of estimating the limits of actual and potential geographic distributions of species, yet their application to explaining geographic abundance patterns has been debated. We developed a detailed test of this latter possibility based on the North American Breeding Bird Survey. Correlations between abundances and niche-centroid distances were mostly negative, as per expectations of niche theory and the abundant niche-centre relationship. The negative relationships were not distributed randomly among species: terrestrial, non-migratory, small-bodied, small-niche-breadth and restricted-range species had the strongest negative associations. Distances to niche centroids as estimated from correlational analyses of presence-only data thus offer a unique means by which to infer geographic abundance patterns, which otherwise are enormously difficult to characterise.

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.

Reconstructing Ecological Niche Evolution When Niches Are Incompletely Characterized.

Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches often produce incomplete characterizations, as they are inferred from present-day distributions that may be limited in full expression of the fundamental ecological niche by biotic interactions, dispersal limitations, and the existing set of environmental conditions. Here, we test whether incomplete niche characterizations inherent in most estimates of species' niches bias phylogenetic reconstructions of niche evolution, using simulations of virtual species with known niches. Results establish that incompletely characterized niches inflate estimates of evolutionary change and lead to error in ancestral state reconstructions. Our analyses also provide a potential mechanism to explain the frequent observation that maximum thermal tolerances are more conserved than minimum thermal tolerances: populations and species experience more spatial variation in minimum temperature than in maximum temperature across their distributions and, consequently, may experience stronger diversifying selection for cold tolerance.

Biodiversity governance: a Tower of Babel of scales and cultures.

The recently created Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), originally focused on multilateral and global issues, is shifting its focus to address local issues and to include in its assessments local stakeholders and indigenous and traditional systems of knowledge. Acknowledging that full biodiversity governance is unavoidably rooted in participation of local actors and their problems and knowledge, we suggest that to deal successfully with the complexity and diversity of local issues, including indigenous knowledge systems, IPBES must recognize a key role of local institutions.

The Importance of Biodiversity E-infrastructures for Megadiverse Countries.

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil's speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2-4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.

Assumption-versus data-based approaches to summarizing species' ranges.

For conservation decision making, species' geographic distributions are mapped using various approaches. Some such efforts have downscaled versions of coarse-resolution extent-of-occurrence maps to fine resolutions for conservation planning. We examined the quality of the extent-of-occurrence maps as range summaries and the utility of refining those maps into fine-resolution distributional hypotheses. Extent-of-occurrence maps tend to be overly simple, omit many known and well-documented populations, and likely frequently include many areas not holding populations. Refinement steps involve typological assumptions about habitat preferences and elevational ranges of species, which can introduce substantial error in estimates of species' true areas of distribution. However, no model-evaluation steps are taken to assess the predictive ability of these models, so model inaccuracies are not noticed. Whereas range summaries derived by these methods may be useful in coarse-grained, global-extent studies, their continued use in on-the-ground conservation applications at fine spatial resolutions is not advisable in light of reliance on assumptions, lack of real spatial resolution, and lack of testing. In contrast, data-driven techniques that integrate primary data on biodiversity occurrence with remotely sensed data that summarize environmental dimensions (i.e., ecological niche modeling or species distribution modeling) offer data-driven solutions based on a minimum of assumptions that can be evaluated and validated quantitatively to offer a well-founded, widely accepted method for summarizing species' distributional patterns for conservation applications.

Summary results of the 2014-2015 DARPA Chikungunya challenge.

BACKGROUND: Emerging pathogens such as Zika, chikungunya, Ebola, and dengue viruses are serious threats to national and global health security. Accurate forecasts of emerging epidemics and their severity are critical to minimizing subsequent mortality, morbidity, and economic loss. The recent introduction of chikungunya and Zika virus to the Americas underscores the need for better methods for disease surveillance and forecasting. METHODS: To explore the suitability of current approaches to forecasting emerging diseases, the Defense Advanced Research Projects Agency (DARPA) launched the 2014-2015 DARPA Chikungunya Challenge to forecast the number of cases and spread of chikungunya disease in the Americas. Challenge participants (n=38 during final evaluation) provided predictions of chikungunya epidemics across the Americas for a six-month period, from September 1, 2014 to February 16, 2015, to be evaluated by comparison with incidence data reported to the Pan American Health Organization (PAHO). This manuscript presents an overview of the challenge and a summary of the approaches used by the winners. RESULTS: Participant submissions were evaluated by a team of non-competing government subject matter experts based on numerical accuracy and methodology. Although this manuscript does not include in-depth analyses of the results, cursory analyses suggest that simpler models appear to outperform more complex approaches that included, for example, demographic information and transportation dynamics, due to the reporting biases, which can be implicitly captured in statistical models. Mosquito-dynamics, population specific information, and dengue-specific information correlated best with prediction accuracy. CONCLUSION: We conclude that with careful consideration and understanding of the relative advantages and disadvantages of particular methods, implementation of an effective prediction system is feasible. However, there is a need to improve the quality of the data in order to more accurately predict the course of epidemics.

Compatible ecological niche signals between biological and archaeological datasets for late-surviving Neandertals.

OBJECTIVES: To assess ecological niche similarity for biological and archaeological samples representing late-surviving Neandertals in Europe to evaluate the validity of combining these two types of data in ecological niche modeling analyses. MATERIALS AND METHODS: Tests of niche conservatism were used to assess niche similarity and niche identity of samples of morphologically diagnostic Neandertal remains and Middle Paleolithic (MP) archaeological sites dating to the time period leading up to Neandertal extinction. Paleoenvironmental reconstructions for the Pre-H4 (43.3-40.2 ky cal BP) were used as environmental space analyses. RESULTS: Null hypotheses of niche similarity and identity of the two types of samples could not be rejected. CONCLUSIONS: As primary and secondary evidence of Neandertal occurrence during the Pre-H4 show high levels of niche similarity and identity, combining the two types of occurrence data to create larger samples for niche analyses is justified without the concern that different environmental signals could complicate future research.

Distributional ecology of Andes hantavirus: a macroecological approach.

BACKGROUND: Hantavirus pulmonary syndrome (HPS) is an infection endemic in Chile and Argentina, caused by Andes hantavirus (ANDV). The rodent Oligoryzomys longicaudatus is suggested as the main reservoir, although several other species of Sigmodontinae are known hosts of ANDV. Here, we explore potential ANDV transmission risk to humans in southern South America, based on eco-epidemiological associations among: six rodent host species, seropositive rodents, and human HPS cases. METHODS: We used ecological niche modeling and macroecological approaches to determine potential geographic distributions and assess environmental similarity among rodents and human HPS cases. RESULTS: Highest numbers of rodent species (five) were in Chile between 35° and 41°S latitude. Background similarity tests showed niche similarity in 14 of the 56 possible comparisons: similarity between human HPS cases and the background of all species and seropositive rodents was supported (except for Abrothrix sanborni). Of interest among the results is the likely role of O. longicaudatus, Loxodontomys micropus, Abrothrix olivaceus, and Abrothrix longipilis in HPS transmission to humans. CONCLUSIONS: Our results support a role of rodent species' distributions as a risk factor for human HPS at coarse scales, and suggest that the role of the main reservoir (O. longicaudatus) may be supported by the broader rodent host community in some areas.

Predictable invasion dynamics in North American populations of the Eurasian collared dove Streptopelia decaocto.

Species invasions represent a significant dimension of global change yet the dynamics of invasions remain poorly understood and are considered rather unpredictable. We explored interannual dynamics of the invasion process in the Eurasian collared dove (Streptopelia decaocto) and tested whether the advance of the invasion front of the species in North America relates to centrality (versus peripherality) within its estimated fundamental ecological niche. We used ecological niche modelling approaches to estimate the dimensions of the fundamental ecological niche on the Old World distribution of the species, and then transferred that model to the New World as measures of centrality versus peripherality within the niche for the species. Although our hypothesis was that the invasion front would advance faster over more favourable (i.e. more central) conditions, the reverse was the case: the invasion expanded faster in areas presenting less favourable (i.e. more peripheral) conditions for the species as it advanced across North America. This result offers a first view of a predictive approach to the dynamics of species' invasions, and thereby has relevant implications for the management of invasive species, as such a predictive understanding would allow better anticipation of coming steps and advances in the progress of invasions, important to designing and guiding effective remediation and mitigation efforts.

Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers.

Weaverbirds are a diverse passerine group with species diversity concentrated in sub-Saharan Africa. No comprehensive phylogenetic hypothesis regarding relationships of weaverbirds has been produced, however, so we developed a first extensive phylogeny for the family Ploceidae, based on a multilocus dataset of three mitochondrial loci and four nuclear markers. Analysis of these data offered strong support for monophyly of the family and revealed seven distinct clades within Ploceidae. A major feature of our results is broad polyphyly of Ploceus: Asian Ploceus species should retain the generic name, whereas African Ploceus, together with Anaplectes, should be placed in Malimbus. In light of deep divergence, we assign the Malagasy Ploceus species to their own genus, Nelicurvius. Divergence time analysis based on DNA substitution rates suggests a mid-Miocene origin of the family. This study lays a foundation for an array of future studies of character evolution, biogeography, and evolutionary history of the family.