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Results for “Royal Society Open Science”

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At least 19 recordsLinked to original sources
USGS2015

A pheromone outweighs temperature in influencing migration of sea lamprey

Organisms continuously acquire and process information from surrounding cues. While some cues complement one another in delivering more reliable information, others may provide conflicting information. How organisms extract and use reliable information from a multitude of cues is largely unknown. We examined movement decisions of sea lampreys ( Petromyzon marinus L.) exposed to a conspecific and an environmental cue during pre-spawning migration. Specifically, we predicted that the mature male-released sex pheromone 3-keto petromyzonol sulfate (3kPZS) will outweigh the locomotor inhibiting effects of cold stream temperature (less than 15°C). Using large-scale stream bioassays, we found that 3kPZS elicits an increase (more than 40%) in upstream movement of pre-spawning lampreys when the water temperatures were below 15°C. Both warming temperatures and conspecific cues increase upstream movement when the water temperature rose above 15°C. These patterns define an interaction between abiotic and conspecific cues in modulating animal decision-making, providing an example of the hierarchy of contradictory information.

Royal Society Open Science↗
USGS2016

Spatial variation in risk and consequence of Batrachochytrium salamandrivorans introduction in the USA

A newly identified fungal pathogen, Batrachochytrium salamandrivorans ( Bsal ), is responsible for mass mortality events and severe population declines in European salamanders. The eastern USA has the highest diversity of salamanders in the world and the introduction of this pathogen is likely to be devastating. Although data are inevitably limited for new pathogens, disease-risk assessments use best available data to inform management decisions. Using characteristics of Bsal ecology, spatial data on imports and pet trade establishments, and salamander species diversity, we identify high-risk areas with both a high likelihood of introduction and severe consequences for local salamanders. We predict that the Pacific coast, southern Appalachian Mountains and mid-Atlantic regions will have the highest relative risk from Bsal . Management of invasive pathogens becomes difficult once they are established in wildlife populations; therefore, import restrictions to limit pathogen introduction and early detection through surveillance of high-risk areas are priorities for preventing the next crisis for North American salamanders.

Royal Society Open Science↗
USGS2016

When environmentally persistent pathogens transform good habitat into ecological traps

Habitat quality plays an important role in the dynamics and stability of wildlife metapopulations. However, the benefits of high-quality habitat may be modulated by the presence of an environmentally persistent pathogen. In some cases, the presence of environmental pathogen reservoirs on high-quality habitat may lead to the creation of ecological traps, wherein host individuals preferentially colonize high-quality habitat, but are then exposed to increased infection risk and disease-induced mortality. We explored this possibility through the development of a stochastic patch occupancy model, where we varied the pathogen’s virulence, transmission rate and environmental persistence as well as the distribution of habitat quality in the host metapopulation. This model suggests that for pathogens with intermediate levels of spread, high-quality habitat can serve as an ecological trap, and can be detrimental to host persistence relative to low-quality habitat. This inversion of the relative roles of high- and low-quality habitat highlights the importance of considering the interaction between spatial structure and pathogen transmission when managing wildlife populations exposed to an environmentally persistent pathogen.

Royal Society Open Science↗
USGS2016

Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering

Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark–recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark–recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus ( Odobenus rosmarus divergens ) and fishers ( Pekania pennanti ). A novel two-stage clustering approach is demonstrated for genetic mark–recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark–recapture studies. Moderately sized SNP (64+) and MSAT (10–15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding.

Royal Society Open Science↗
USGS2017

Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata)

West Nile virus (WNV) is a widespread arbovirus that imposes a significant cost to both human and wildlife health. WNV exists in a bird-mosquito transmission cycle in which passerine birds act as the primary reservoir host. As a public health concern, the mammalian immune response to WNV has been studied in detail. Little, however, is known about the avian immune response to WNV. Avian taxa show variable susceptibility to WNV and what drives this variation is unknown. Thus, to study the immune response to WNV in birds, we experimentally infected captive zebra finches ( Taeniopygia guttata ). Zebra finches provide a useful model, as like many natural avian hosts they are moderately susceptible to WNV and thus provide sufficient viremia to infect mosquitoes. We performed RNAseq in spleen tissue during peak viremia to provide an overview of the transcriptional response. In general, we find strong parallels with the mammalian immune response to WNV, including upregulation of five genes in the Rig-I-like receptor signalling pathway, and offer insights into avian-specific responses. Together with complementary immunological assays, we provide a model of the avian immune response to WNV and set the stage for future comparative studies among variably susceptible populations and species.

Royal Society Open Science↗
USGS2017

Cambrian origin of the CYP27C1-mediated vitamin A1-to-A2 switch, a key mechanism of vertebrate sensory plasticity

The spectral composition of ambient light varies across both space and time. Many species of jawed vertebrates adapt to this variation by tuning the sensitivity of their photoreceptors via the expression of CYP27C1, an enzyme that converts vitamin A 1 into vitamin A 2 , thereby shifting the ratio of vitamin A 1 -based rhodopsin to red-shifted vitamin A 2 -based porphyropsin in the eye. Here, we show that the sea lamprey ( Petromyzon marinus ), a jawless vertebrate that diverged from jawed vertebrates during the Cambrian period (approx. 500 Ma), dynamically shifts its photoreceptor spectral sensitivity via vitamin A 1 -to-A 2 chromophore exchange as it transitions between photically divergent aquatic habitats. We further show that this shift correlates with high-level expression of the lamprey orthologue of CYP27C1, specifically in the retinal pigment epithelium as in jawed vertebrates. Our results suggest that the CYP27C1-mediated vitamin A 1 -to-A 2 switch is an evolutionarily ancient mechanism of sensory plasticity that appeared not long after the origin of vertebrates.

Royal Society Open Science↗
USGS2017

Monarch butterfly population decline in North America: identifying the threatening processes

The monarch butterfly ( Danaus plexippus ) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids). While climatic factors, principally breeding season temperature, were important determinants of annual variation in abundance, our results indicated strong negative relationships between population size and habitat loss variables, principally glyphosate use, but also weaker negative effects from the loss of overwinter forest and breeding season use of neonicotinoids. Further declines in population size because of glyphosate application are not expected. Thus, if remaining threats to habitat are mitigated we expect climate-induced stochastic variation of the eastern migratory population of monarch butterfly around a relatively stationary population size.

Royal Society Open Science↗
USGS2018

Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim

Pathogens entering the marine environment as pollutants exhibit a spatial signature driven by their transport mechanisms. The sea otter ( Enhydra lutris ), a marine animal which lives much of its life within sight of land, presents a unique opportunity to understand land–sea pathogen transmission. Using a dataset on Toxoplasma gondii prevalence across sea otter range from Alaska to California, we found that the dominant drivers of infection risk vary depending upon the spatial scale of analysis. At the population level, regions with high T. gondii prevalence had higher human population density and a greater proportion of human-dominated land uses, suggesting a strong role for population density of the felid definitive host of this parasite. This relationship persisted when a subset of data were analysed at the individual level: large-scale patterns in sea otter T. gondii infection prevalence were largely explained by individual exposure to areas of high human housing unit density, and other landscape features associated with anthropogenic land use, such as impervious surfaces and cropping land. These results contrast with the small-scale, within-region analysis, in which age, sex and prey choice accounted for most of the variation in infection risk, and terrestrial environmental features provided little variation to help in explaining observed patterns. These results underscore the importance of spatial scale in study design when quantifying both individual-level risk factors and landscape-scale variation in infection risk.

California↗
USGS2021

The roles of environmental variation and parasite survival in virulence–transmission relationships

Disease outbreaks are a consequence of interactions among the three components of a host–parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host–parasite coevolution. Here, we review research on how environmental context alters virulence–transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related ‘approaches’ that have dominated the study of the evolution of virulence and transmission for different host–parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence–transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence–transmission relationships across a diversity of host–parasite systems that have eluded experimental study of parasite life history.

Royal Society Open Science↗
USGS2022

Vulnerability of avian populations to renewable energy production

Renewable energy production can kill individual birds, but little is known about how it affects avian populations. We assessed the vulnerability of populations for 23 priority bird species killed at wind and solar facilities in California, USA. Bayesian hierarchical models suggested that 48% of these species were vulnerable to population-level effects from added fatalities caused by renewables and other sources. Effects of renewables extended far beyond the location of energy production to impact bird populations in distant regions across continental migration networks. Populations of species associated with grasslands where turbines were located were most vulnerable to wind. Populations of nocturnal migrant species were most vulnerable to solar, despite not typically being associated with deserts where the solar facilities we evaluated were located. Our findings indicate that addressing declines of North American bird populations requires consideration of the effects of renewables and other anthropogenic threats on both nearby and distant populations of vulnerable species.

California↗
USGS2023

The ties that bind the sagebrush biome: Integrating genetic connectivity into range-wide conservation of greater sage-grouse

Conserving genetic connectivity is fundamental to species persistence, yet rarely is made actionable into spatial planning for imperilled species. Climate change and habitat degradation have added urgency to embrace connectivity into networks of protected areas. Our two-step process integrates a network model with a functional connectivity model, to identify population centres important to maintaining genetic connectivity then to delineate those pathways most likely to facilitate connectivity thereamong for the greater sage-grouse ( Centrocercus urophasianus ), a species of conservation concern ranging across eleven western US states and into two Canadian provinces. This replicable process yielded spatial action maps, able to be prioritized by importance to maintaining range-wide genetic connectivity. We used these maps to investigate the efficacy of 3.2 million ha designated as priority areas for conservation (PACs) to encompass functional connectivity. We discovered that PACs encompassed 41.1% of cumulative functional connectivity—twice the amount of connectivity as random—and disproportionately encompassed the highest-connectivity landscapes. Comparing spatial action maps to impedances to connectivity such as cultivation and woodland expansion allows both planning for future management and tracking outcomes from past efforts.

western United States↗
USGS2023

Conserved grasslands support similar pollinator diversity as pollinator-specific practice regardless of proximal cropland and pesticide exposure

Pollinator diversity and abundance are declining globally. Cropland agriculture and the corresponding use of agricultural pesticides may contribute to these declines, while increased pollinator habitat (flowering plants) can help mitigate them. Here we tested whether the relative effect of wildflower plantings on pollinator diversity and counts were modified by proportion of nearby agricultural land cover and pesticide exposure in 24 conserved grasslands in Iowa, USA. Compared with general grassland conservation practices, wildflower plantings led to only a 5% increase in pollinator diversity and no change in counts regardless of the proportion of cropland agriculture within a 1 km radius. Pollinator diversity increased earlier in the growing season and with per cent flower cover. Unexpectedly, neither insecticide nor total pesticide concentrations on above-ground passive samplers were related to pollinator diversity. However, pollinator community composition was most strongly related to date of sampling, total pesticide concentration, and forb or flower cover. Our results indicate very little difference in pollinator diversity between grassland conservation practices with and without wildflower plantings. Given the relatively high economic costs of wildflower plantings, our research provides initial evidence that investment in general grassland conservation may efficiently conserve pollinator diversity in temperate regions of intensive cropland agriculture.

Iowa↗
USGS2024

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog ( Rana boylii ) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897–2005) and field samples (2005–2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

California↗
USGS2025

Ecosystem-engineered infections: Beaver-modified wetlands are associated with conflicting drivers of amphibian pathogen prevalence

Beavers are ecosystem engineers and keystone species that protect freshwater resources and increase biodiversity. Beaver reintroductions are promoted for amphibian conservation, yet their impact on Batrachochytrium dendrobatidis (Bd), a pathogen linked with amphibian population declines worldwide, remains unclear. We investigated the abiotic and biotic drivers of Bd prevalence in Columbia spotted frogs ( Rana luteiventris ) and western toads ( Anaxyrus boreas ) in 20 beaver-modified and 23 non-beaver wetlands in Glacier National Park, USA. We found that beavers increased wetland hydroperiod, which was associated with higher Bd prevalence. However, beavers also reduced wetland canopy cover, which was associated with lower Bd prevalence. Our models also predicted higher Bd prevalence associated with higher adult density of both species of amphibians, although species’ densities were similar in beaver-modified and non-beaver wetlands. These results suggest that beavers have a cumulatively negligible net effect on Bd prevalence owing to their effects on both hydroperiod and canopy cover, which is encouraging for amphibian conservation. Our findings also suggest that decreasing canopy cover may be a potential management option to reduce Bd prevalence. In addition, these findings indicate that beaver-mimicking restoration projects may harm amphibian populations if they increase wetland hydroperiods without reducing canopy cover.

Montana↗
USGS2026

Improved abundance trajectories with Bayesian population dynamics model: Case study with a Hawaiian honeycreeper

Many wildlife monitoring programmes collect annual data on population abundance. The resulting abundance estimates fluctuate over time partly because of true population change and partly because of observation error. These two components of variation can be separated by fitting the estimates to a population dynamics model within a Bayesian state-space modelling framework. By constraining the population trajectory to be biologically realistic, more precise estimates can be obtained. Independent biological knowledge can be incorporated through choice of model structure and by specifying informative prior distributions on demographic parameters. We illustrate the approach using a 31-year point transect study of the Hawai’i ’ākepa ( Loxops coccineus ). We fitted five models, each making different assumptions about how population change, recruitment and/or adult survival varied over time. Overall, the ’ākepa geometric mean growth rate was 1.02, indicating an increasing population over the 31-year time series, although there were periods of slow decline potentially associated with low recruitment and more rapid recovery associated with pulses of high recruitment. Abundance estimates derived from the population models were substantially more precise than the ‘raw’ point transect estimates: 95% credible interval (CrI) was on average 51.7% (s.d. = 14.1%) narrower.

Hawaii↗
USGS2026

Small cumulative survival costs of enzootic disease could suppress long-term population size

Fungal pathogens can cause epizootics that result in widespread mortality and rapid population declines in some species. However, even in the absence of high disease-induced mortality, enzootic mycoses could have large-scale impacts on host population dynamics. Here, we examined the effects of ophidiomycosis, an enzootic fungal disease, on a Louisiana snake community over a 3-year period using a multi-state Jolly–Seber model with disease-state misclassification. We did not detect a difference between the average weekly apparent survival probability of uninfected and infected hosts for either Nerodia species or Thamnophis proximus . We also found a strong positive association between snout-to-vent length and weekly apparent survival probability across all species. We found that recruitment of infected hosts was slightly higher than recruitment of uninfected hosts for two of the three species. Population projections suggested divergent trajectories between disease-present and disease-absent scenarios, where disease-absent populations had higher abundance than disease-present populations. Our results highlight that small differences in survival can accumulate over time, as well as the challenges of quantifying population-level impacts of enzootic diseases when survival differences are not readily detected, underscoring the importance of continued long-term monitoring to assess whether ophidiomycosis affects snake population dynamics.

Louisiana↗
USGS2025

How will we prepare for an uncertain future? The value of open data and code for unborn generations facing climate change

As the impacts of climate change continue to intensify, humans face new challenges to long-term survival. Humans will likely be battling these problems long after 2100, when many climate projections currently end. A more forward-thinking view on our science and its direction may help better prepare for the future of our species. Researchers may consider datasets the basic units of knowledge, whose preservation is arguably more important than the articles that are written about them. Storing data and code in long-term repositories offers insurance against our uncertain future. To ensure open data are useful, data must be FAIR (Findable, Accessible, Interoperable, and Reusable) and be complete with all appropriate metadata. By embracing open science practices, contemporary scientists give the future of humanity the information to make better decisions, save time and other valuable resources, and increase global equity as access to information is made free. This, in turn, will enable and inspire a diversity of solutions, to the benefit of many. Imagine the collective science conducted, the models built, and the questions answered if all of the data researchers have collectively gathered were organized and immediately accessible and usable by everyone. Investing in open science today may ensure a brighter future for unborn generations.

Proceedings of the Royal Society, B↗
USGS2002

Spatio-temporal dynamics of species richness in coastal fish communities

Determining patterns of change in species richness and the processes underlying the dynamics of biodiversity are of key interest within the field of ecology, but few studies have investigated the dynamics of vertebrate communities at a decadal temporal scale. Here, we report findings on the spado-temporal variability in the richness and composition of fish communities along the Norwegian Skagerrak coast having been surveyed for more than half a century. Using statistical models incorporating non-detection and associated sampling variance, we estimate local species richness and changes in species composition allowing us to compute temporal variability in species richness. We tested whether temporal variation could be related to distance to the open sea and to local levels of pollution. Clear differences in mean species richness and temporal variability are observed between fjords that were and were not exposed to the effects of pollution. Altogether this indicates that the fjord is an appropriate scale for studying changes in coastal fish communities in space and time. The year-to-year rates of local extinction and turnover were found to be smaller than spatial differences in community composition. At the regional level, exposure to the open sea plays a homogenizing role, possibly due to coastal currents and advection.

Proceedings of the Royal Society B: Biological Sci↗