Biology subjects

Becker, D. J.

Publications and source records attributed to Becker, D. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular and ecological determinants of effective reassortment in orthohantaviruses

A central unsolved problem in RNA virus evolution is understanding why some viral reassortants establish and persist while others do not. To answer this question, we reconstructed reassortant histories across 553 viral genomes from seven orthohantavirus species between 1983 and 2024 using phylogenetic reconciliation and molecular dating. We found that the frequency of retained reassortants varied among orthohantaviruses. For example, reassortment ranged from absent in Andes virus to frequent in Dobrava-Belgrade, Sin Nombre, Seoul, Puumala, and Tula viruses, showing that effective reassortment is not a genus-wide constant. Our Bayesian hierarchical models identified local host overlap as the strongest ecological factor associated with viral reassortment, while cross-segment linkage and terminal RNA structure serve as a molecular filter. We found that the probability of reassortment establishment is highest when ecological opportunity is paired with molecular permissiveness, with their interaction term inferred as the strongest signal in our establishment models (posterior probability = 0.97). These results suggest that reassortment in orthohantaviruses is a sequentially filtered evolutionary process in which divergent lineages must first meet in a host through ecological overlap, exchange segments that are molecularly compatible, and do so within a lineage background permissive to establishment in the host population.

evolutionary biology↗

bioRxiv2026

Bartonella and hemotropic Mycoplasma species in synanthropic bats in Kenya

Identifying and characterizing zoonotic pathogens in wildlife is essential for understanding disease risk to humans. In Sub-Saharan Africa, many people live with bats in their houses and are exposed to their pathogens, yet little is known about the bacterial pathogens in Afrotropical bat species. Globally, Bartonella spp. (bartonellae) and hemotropic Mycoplasma spp. (hemoplasmas) are common bacterial pathogens in bats, and some lineages are known to spill over and cause infections in humans. To evaluate this disease risk, we screened three common synanthropic bat species in Kenya, and their ectoparasites, for hemoplasmas and bartonellae and assessed their relatedness to known human pathogens. Of 767 bats across 21 sites, 17.9% of bats were Bartonella spp. positive and 19.3% were hemoplasma positive. Bat ectoparasites had similar Bartonella prevalence (13.5-25.0%) and, for most bat species, ectoparasite loads were not associated with increased likelihood of Bartonella infection. We found that Bartonella lineages displayed phylogenetic overlap between different bat species and ectoparasites, suggesting pathogen sharing between species, while hemoplasma lineages corresponded strictly to host taxonomy. Finally, we found that 16S rRNA sequences from one heart-nosed bat (Cardioderma cor) were 97.85% similar to a human-associated hemoplasma found previously in Schreibers bats (Miniopterus schreibersii) in Spain. We show that synanthropic bats host bacteria of potential public health concern, highlighting the need to investigate the emerging impacts of these pathogens on human health in Kenya and elsewhere in Sub-Saharan Africa.

ecology↗

bioRxiv2026

Cross-Continental Analysis of Vampire Bat Betaherpesvirus Reveals Limited Interference Among Strains and Local Geographic Spread

Desmodus rotundus Betaherpesvirus (DrBHV) is a candidate vector for a transmissible vaccine targeting the circulation of rabies virus within its vampire bat reservoir. Studies assessing the potential for DrBHV as a vector have not considered its geographic range, potential for transboundary spread or how the diversity of wildtype DrBHV in natural bat populations might impede the spread of a modified vaccine strain. Here, by sequencing DrBHVs from vampire bats spanning 15 regions across 7 rabies-affected countries in Latin America and the Caribbean, we characterise the continent-scale distribution of DrBHV diversity and demonstrate widespread and apparently unconstrained co-infection. DrBHV occurred in all regions, forming a monophyletic clade consistent with a single introduction to vampire bats or host-virus co-speciation rather than frequent host switching. Phylogeographic analyses revealed cross-boundary spread that was predicted by geographic proximity. We identified 50 putative DrBHV strains and 79% of DrBHV-infected bats harboured multiple strains. No strains were over- or under-represented in co-infection and co-infections occurred proportionately to local strain prevalence. Whether strains circulated in given populations was predominantly driven by the geographic proximity of other populations containing that strain. The evolutionary relatedness of strains constrained neither rates of co-infection within individuals nor whether strains co-circulated within regions, suggesting vaccine vectors might be locally sourced rather than requiring imported, divergent strains to ameliorate interference. These results support the viability of DrBHV-vectored vaccines for mitigating rabies virus across Latin America and the Caribbean, despite widespread circulation of wildtype viruses.

genomics↗

bioRxiv2025

Vampire bats in Belize harbor multiple Trypanosoma cruzi genotypes: implications for parasite transmission at the wildlife-domestic-human interface

BackgroundChagas disease, caused by Trypanosoma cruzi, is a neglected tropical disease with complex sylvatic and domestic transmission cycles involving vectors, mammalian hosts, and humans. The common vampire bat (Desmodus rotundus) is an obligate blood-feeding species that frequently interacts with livestock and humans, yet their role in parasite maintenance in Central America remains poorly characterized. Methodology/Principal FindingsWe analyzed 205 blood samples from vampire bats collected at two sites in northern Belize over three years (2019, 2021, 2022). PCR screening revealed an overall T. cruzi prevalence of 41.5% and increasing infection risks over time. The amplicon-based next-generation sequencing of the parasite mini-exon locus identified 36 unique haplotypes belonging to five DTUs: TcI, TcIV, TcV, TcVI, and TcBat. TcBat was present in half of the samples sequenced. TcBat and TcVI, were detected in Belize for the first time. Belizean TcBat haplotypes clustered closely with Colombian reference sequences, and a subset formed a Belize-specific clade, indicating previously unrecognized TcBat diversity in the region; in contrast, Brazilian TcBat sequences were more distantly related. Conclusions/SignificanceVampire bats in Belize harbor diverse T. cruzi genotypes, including DTUs with established roles in human disease. Given their obligate blood diet, frequent feeding on livestock, and occasional biting of humans, vampire bats may serve as bridge hosts linking sylvatic, domestic, and human transmission cycles. Together with a recent report of an acute human Chagas disease case in northern Belize, these results underscore the need for integrated One Health surveillance of bats, vectors, livestock, and humans to better evaluate and mitigate the risk of Chagas disease in Central America. Author SummaryChagas disease, caused by the parasite Trypanosoma cruzi, is a major public health concern in the Americas but remains neglected in many regions, including Central America. The parasite is typically transmitted by kissing bugs, but wild mammals also serve as important hosts. Vampire bats (Desmodus rotundus) are unique because they feed exclusively blood and frequently bite livestock, and occasionally humans, creating opportunities for parasite transmission across different environments. In this study, we screened 205 vampire bats from northern Belize and found that over 40% were infected with T. cruzi. By sequencing parasite DNA, we discovered a surprising diversity of DTUs, including TcI, TcIV, TcV, TcVI, and TcBat. The detection of TcVI is particularly important, because this DTU, associated with human infections in South America, had not been previously reported in Belize. TcBat haplotypes were highly prevalent and genetically diverse. Our results show that vampire bats are important hosts of diverse T. cruzi genotypes in Belize and may act as bridge hosts between wildlife, livestock, human transmission cycles. Enhanced One Health surveillance across vectors, bats, domestic animals, and humans will be critical for understanding and preventing Chagas disease emergence in Central America.

molecular biology↗

bioRxiv2025

Neotropical bats as bioindicators for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing

Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as bioindicators that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we surveyed the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis. qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as bioindicators. Author SummaryTracking the spread of new and emerging zoonotic diseases is a major component of global health research. Pathogen surveillance is a vital part of predicting and reducing the consequences of disease outbreaks. Bats are a diverse group of mammals that can host and potentially transmit many pathogens that pose potential risks to human and environmental health. Our study surveyed blood samples (n=263) from 20 bat species collected from the Orange Walk District of Belize in 2019, 2022, and 2023. Metagenomic next-generation sequencing identified 1,430 different microorganisms that are considered potentially relevant to human or animal health. Among the microorganisms detected was Trypanosoma cruzi (T. cruzi), the protozoan causative agent of Chagas disease. T. cruzi was of particular interest due to its presence throughout the Americas and relevance to public health. We surveyed the types of microorganisms circulating throughout bat populations in northern Belize to demonstrate the ability of bats to act as bioindicators.

microbiology↗

bioRxiv2025

Biodiversity databases as underutilized resources for pathogen discovery: a quantitative synthesis of bat and rodent tissue collections in natural history museums

Zoonotic spillovers are becoming increasingly frequent, and the devastating effects of the SARS-CoV-2 pandemic demonstrate our continued inability to combat their consequences effectively. Natural history museums can enhance the study of zoonoses by serving as valuable resources for understanding the ecology and evolutionary history of pathogens and their wildlife hosts. Despite the growing interest in the role museums can play in pathobiology research and zoonotic risk assessment, there remains a lack of centralized resources for locating tissue samples that may be leveraged for pathogen discovery. Using the worlds most significant global aggregator of museum specimens, The Global Biodiversity Information Facility (GBIF), we examined how such tools could be adopted to identify specimens that might be sources of viral genetic material. Focusing on tissue samples from the mammalian orders Rodentia and Chiroptera, speciose taxa that host a high diversity of known zoonotic viruses, we examined temporal, spatial, and taxonomic gaps and patterns in the available tissue samples. Our analyses reveal a heavy bias toward tissue samples collected from the Americas (and consequently, taxonomic groups found in the Americas), with most collected samples housed in North American institutions. This limits the scope of future pathogen discovery efforts and presents a barrier to pandemic preparedness in the Global South. We also examine gaps in metadata quality (e.g., descriptions of preservation method and storage medium) and outline recommendations for GBIF to facilitate future biosurveillance projects and effectively incorporate natural history museums into One Health disease research. Author SummaryThe SARS-CoV-2 pandemic has driven a greater research focus on understanding wildlife reservoirs of zoonotic pathogens. As a complement to field-based sampling of wildlife, natural history museum collections house millions of specimens that could be used by researchers to study pathogens quickly, safely, and cost-effectively. Digital databases of museum specimens and their associated tissue samples were originally created for biodiversity research, but these could be adapted to guide pathogen discovery research. Using the largest of these databases, The Global Biodiversity Information Facility, we explored tissue samples from rodents and bats, which have been shown to carry a disproportionate number of zoonotic pathogens. We searched for keywords that would indicate the presence of relevant tissue samples and then mapped the results visually. This revealed disproportionate distributions of tissue samples across time, space, and taxonomy. Our study is the first attempt to assess how a biodiversity database can be used for this novel purpose. We suggest changes that would improve these databases for zoonotic disease research.

ecology↗

bioRxiv2025

Longitudinal impacts of habitat fragmentation on Bartonella and hemotropic Mycoplasma dynamics in vampire bats

Habitat fragmentation can have negative impacts on wildlife including increased risk of infectious disease. To assess spatiotemporal changes in pathogen dynamics in vampire bats (Desmodus rotundus) in response to habitat fragmentation, we used general linear mixed models to investigate the influence of site, year, and tree cover on the prevalence of Bartonella and hemotropic Mycoplasma (hemoplasma) in bats in one large and one small forest fragment in northern Belize across seven years. Bartonella was marginally more prevalent in later years, while year and site differences in hemoplasma infections were driven by a peak in prevalence in the third year of the study in the small fragment. Bartonella prevalence increased with forest loss, but only in the large fragment, whereas hemoplasma prevalence showed a marginal negative response to forest loss. The effects of site, year, and forest loss on infection likelihood varied by pathogen genotype. Neither site nor year affected Bartonella genotypes, but one genotype was positively associated with tree cover. Two hemoplasma genotypes were influenced by year, but with differing trends. One genotype increased with tree cover regardless of site while another increased with forest loss at the small fragment only. Our work demonstrates that the effects of habitat fragmentation on infection prevalence depended on both the pathogen and specific genotype. Our findings complicate expectations of how habitat fragmentation affects infectious disease dynamics in bats. As such, management practices aimed at mitigating the impacts of infectious diseases in fragmented systems should be tailored to specific pathogens of concern.

ecology↗

bioRxiv2025

229E- and NL63-like coronaviruses in phyllostomid bats, Belize

We report novel and previously identified alphacoronavirus (-CoV) diversity in three phyllostomid bat species (Desmodus rotundus, Carollia sowelli, and Sturnira parvidens) in Belize. Phylogenetic analysis suggests strong similarity between two Neotropical bat -CoV lineages and human CoVs (229E and NL63) compared to prior bat -CoVs.

ecology↗

bioRxiv2025

Paramyxoviruses in Old World fruit bats (Pteropodidae): an open database and synthesis of sampling effort, viral positivity, and coevolution

Over the past 25 years, research interest in the links between Old World fruit bats (family Pteropodidae) and paramyxoviruses has driven a rapid proliferation of surveillance studies in this system. We performed a systematic review and data synthesis of all published paramyxovirus studies of wild pteropodids. Here, we present an open, static, PRISMA-compliant database called pteroparamyxo, which includes 1,482 records of prevalence or seroprevalence from 119 studies published between 1971 and 2023. Using this dataset, we examined biases in sampling effort, predictors of viral positivity, tissue tropism, and pteropodid-paramyxovirus coevolution. We found significant spatial and taxonomic bias in sampling effort, largely driven by overrepresentation of Pteropus-henipavirus systems; in particular, African bats were undersampled for paramyxoviruses relative to Asian and Oceanian taxa. On the viral side, henipaviruses (specifically Hendra, Nipah, and Cedar viruses) were overrepresented relative to pararubulaviruses. We also identified substantial non-random variability in paramyxovirus prevalence and seroprevalence. Spleens and pooled fecal samples from pteropodids yielded the highest PCR positivity, while samples from Oceania tended to have slightly higher seroprevalence than those from Asia and Africa. Collection year was not a significant predictor of positivity, suggesting limited overall change in paramyxovirus PCR prevalence or seroprevalence over the last several decades. Finally, we found weak evidence of pteropodid-paramyxovirus coevolution, supporting relatively frequent host-switching within this system. Our study highlights critical sampling gaps to address in future surveillance studies and provides preliminary evidence for sample and tissue types to prioritize in field- and museum-based sampling. Author SummaryParamyxoviruses are a family of viruses that include the human measles and mumps viruses as well as emerging zoonoses like Hendra and Nipah henipaviruses. These henipaviruses spill over from wild fruit bats to domestic animals and humans in Australia and Asia, causing high fatality rates with no known human treatments or vaccines. The occurrence and prevalence of paramyxoviruses across the entire fruit bat family (Pteropodidae) has never been formally investigated, as published detection attempts have not yet been consolidated into a database. We conducted a systematic review of the existing literature on pteropodid-paramyxovirus sampling efforts and compiled an open database for researchers to reference and use. We then leveraged this novel database for a suite of analyses and demonstrated that Australian and Asian fruit bats are disproportionately sampled for paramyxoviruses while African species are understudied, despite the fact that African samples have slightly higher rates of paramyxovirus detection. We identified sample types that may be particularly likely to yield viral detections, a finding which can help guide future survey efforts using field studies as well as museum collections. We also demonstrate that paramyxoviruses appear liable to switch host species within Pteropodidae, challenging earlier hypotheses that these viruses are host specific.

ecology↗

bioRxiv2024

Risk assessment of zoonotic viruses in urban-adapted wildlife

The repeated emergence of pandemic viruses underscores the linkages between land-use change and wildlife disease, and urban-adapted wildlife are of special interest due to their close proximity to humans. However, viral diversity within urban-adapted species and their zoonotic potential remains largely unexplored. We compiled a large dataset on seven priority urban-adapted mammal species and their viruses covering over 115 countries from 1574 to 2023. These urban-adapted species host 286 virus species spanning 24 orders and 38 families, 14 of which are potentially high risk for human infection. Raccoons carried the most high-risk viruses, while raccoon dogs had increased viral positivity in urban habitats compared to raccoons, wild boars, and red foxes. Many viruses in urban-adapted species were phylogenetically related to those found in humans, and we also observed evidence of possible viral spillback. These results highlight zoonotic risks associated with urban-adapted species and suggest enhanced surveillance to mitigate future outbreaks.

ecology↗

bioRxiv2024

Density-dependent network structuring within and across wild animal systems

High population density should drive individuals to more frequently share space and interact, producing better-connected spatial and social networks [1-4]. Although this theory is fundamental to our understanding of disease dynamics [2,5-8], it remains unconfirmed how local density generally drives individuals positions within their networks, which reduces our ability to understand and predict density-dependent processes [4,9,10]. Here we provide the first general evidence that density drives greater network connectedness at fine spatiotemporal scales, at the scale of individuals within wild animal populations. We analysed 36 datasets of simultaneous spatial and social behaviour in >58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals, and insects. 80% of systems exhibited strong positive relationships between local density and network centrality. However, >80% of relationships were nonlinear and 75% became shallower at higher values, signifying that demographic and behavioural processes counteract densitys effects, thereby producing saturating trends [11-15]. Densitys effect was much stronger and less saturating for spatial than social networks, such that individuals become disproportionately spatially connected rather than socially at higher densities. Consequently, ecological processes that depend on spatial connections (e.g. indirect pathogen transmission, resource competition, and territory formation) are likely more density-dependent than those involving social interactions (e.g. direct pathogen transmission, aggression, and social learning). These findings reveal fundamental ecological rules governing societal structuring, with widespread implications. Identifying scaling rules based on processes that generalise across systems, such as these patterns of density dependence, might provide the ability to predict network structures in novel systems.

ecology↗

bioRxiv2023

Environmental and ecological signals predict periods of nutritional stress for Eastern Australian flying fox populations.

Food availability determines where animals use space across a landscape and therefore affects the risk of encounters that lead to zoonotic spillover. This relationship is evident in Australian flying foxes (Pteropus spp; fruit bats), where acute food shortages precede clusters of Hendra virus spillovers. Using explainable artificial intelligence, we predicted months of food shortages from climatological and ecological covariates (1996-2022) in eastern Australia. Overall accuracy in predicting months of low food availability on a test set from 2018 up to 2022 reached 93.33% and 92.59% based on climatological and bat-level features, respectively. Seasonality and Oceanic El Nino Index were the most important environmental features, while the number of bats in rescue centers and their body weights were the most important bat-level features. These models support predictive signals up to nine months in advance, facilitating action to mitigate spillover risk.

ecology↗

bioRxiv2023

Viral genomic features predict orthopoxvirus reservoir hosts

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs. We demonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.

microbiology↗

bioRxiv2023

Ecological and Evolutionary Characteristics of Anthropogenic Roosting Ability in Bats of the World

Although the global conversion of wildlife habitat to built environments often has negative impacts on biodiversity, some wildlife have the ability to cope by living in human-made structures. However, the determinants of this adaptation on a global scale are not well understood and may signify species with unique conservation needs at the human-wildlife interface. Here, we identify the trait profile associated with anthropogenic roosting in bats globally and characterize the evolution of this phenotype using an original dataset of roosting behavior developed across 1,279 extant species. Trait-based analyses showed that anthropogenic roosting is predictable across bats and is associated with habitat generalism, small geographic ranges, small body size, temperate zone distributions, and insectivory. We identified moderate phylogenetic signal in this complex phenotype, which has undergone both gains and losses across bat evolution and for which speciation rates are lower compared to natural roosting bats.

ecology↗

bioRxiv2023

Bat cellular immunity varies by year and dietary habit in an increasingly fragmented landscape

Monitoring the health of wildlife populations is essential in the face of increased agricultural expansion and forest fragmentation. Loss of habitat and habitat degradation can negatively affect an animals physiological state, possibly resulting in immunosuppression and increased morbidity or mortality. We sought to determine how fragmentation may differentially impact cellular immunity and infection risk in Neotropical bats species regularly infected with bloodborne pathogens, and to evaluate how effects may vary over time and by dietary habit. We studied common vampire bats (Desmodus rotundus), northern yellow-shouldered bats (Sturnira parvidens), and Mesoamerican mustached bats (Pteronotus mesoamericanus), representing the dietary habits of sanguinivory, frugivory, and insectivory respectively, in northern Belize. We compared estimated total white blood cell counts, leukocyte differentials, and infection status with two blood-borne bacterial pathogens (Bartonella spp. and hemoplasmas) of 118 bats captured in a broadleaf, secondary forest over a three-year period (2017-2019) of increasing habitat fragmentation. We found evidence for bat species-specific responses of cellular immunity between years, with neutrophil counts increasing in D. rotundus, but decreasing in S. parvidens and P. mesoamericanus from 2018 to 2019. However, the odds of infection with Bartonella spp. and hemoplasma spp. between 2017 and 2019 did not differ between bat species, contrary to our prediction that pathogen prevalence may increase with increased fragmentation. We conclude that each bat species invested differently in cellular immunity in ways that changed over years of increasing fragmentation. We recommend further research on the interactions between habitat fragmentation, cellular immunity, and infection across dietary habits of Neotropical bats for informed management and conservation.

ecology↗

bioRxiv2022

Novel Rickettsia spp. in two common overwintering North American passerines

American robins and dark-eyed juncos migrate across North America, but their contributions to arthropod-borne disease remain poorly characterized. We identified novel Rickettsia spp. in one wintering migrant per bird species related to bellii, transitional, and spotted fever group rickettsiae and suggest spring migration could disperse these pathogens hundreds-to-thousands of kilometers.

ecology↗

bioRxiv2022

Sampling strategies and pre-pandemic surveillance gaps for bat coronaviruses

The emergence of SARS-CoV-2, and the challenge of pinpointing its ecological and evolutionary context, has highlighted the importance of evidence-based strategies for monitoring viral dynamics in bat reservoir hosts. Here, we compiled the results of 93,877 samples collected from bats across 111 studies between 1996 and 2018, and used these to develop an unprecedented open database, with over 2,400 estimates of coronavirus infection prevalence or seroprevalence at the finest methodological, spatiotemporal, and phylogenetic level of detail possible from public records. These data revealed a high degree of heterogeneity in viral prevalence, reflecting both real spatiotemporal variation in viral dynamics and the effect of variation in sampling design. Phylogenetically controlled meta-analysis revealed that the most significant determinant of successful viral detection was repeat sampling (i.e., returning to the same site multiple times); however, fewer than one in five studies longitudinally collected and reported data. Viral detection was also more successful in some seasons and from certain tissues, but was not improved by the use of euthanasia, indicating that viral detection may not be improved by terminal sampling. Finally, we found that prior to the pandemic, sampling effort was highly concentrated in ways that reflected concerns about zoonotic risk, leaving several broad geographic regions (e.g., South Asia, Latin America and the Caribbean, and most of Sub-Saharan Africa) and bat subfamilies (e.g., Stenodermatinae and Pteropodinae) measurably undersampled. These gaps constitute a notable vulnerability for global health security and will likely be a future barrier to contextualizing the origin of novel zoonotic coronaviruses.

ecology↗

bioRxiv2021

Plasticity in female timing may explain current shifts in breeding phenology of a North American songbird

O_LIClimate change has driven changes in breeding phenology. Identifying the magnitude of phenological shifts and whether selection in response to climate change drives these shifts is key for determining species reproductive success and persistence in a changing world. C_LIO_LIWe investigated reproductive timing in a primarily sedentary population of the dark-eyed junco (Junco hyemalis) over 32 years. We predicted that juncos would breed earlier in warmer springs in response to selection favouring earlier breeding. C_LIO_LITo test this prediction, we compared the annual median date for reproductive onset (i.e., egg one date) to monthly spring temperatures and examined evidence for selection favouring earlier breeding and for plasticity in timing. C_LIO_LIEgg one dates occurred earlier over time, with the timing of breeding advancing up to 24 days over the 32-year period. Breeding timing also strongly covaried with maximum April temperature. We found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier egg one dates) that became stronger over time, but strength of selection was not predicted by temperature. Lastly, individual females exhibited plastic responses to temperature across years. C_LIO_LIOur findings provide further evidence that phenotypic plasticity plays a crucial role in driving phenological shifts in response to climate change. For multi-brooded bird populations, a warming climate might extend the breeding season and provide more opportunities to re-nest rather than drive earlier breeding in response to potential phenological mismatches. However, as plasticity will likely be insufficient for long-term survival in the face of climate change, further research in understanding the mechanisms of female reproductive timing will be essential for forecasting the effects of climate change on population persistence. C_LI

ecology↗