Potential Environmental Drivers Research Articles

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus).

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Two decades of dune slack restoration in North Wales: diversity, community and habitat specialists

Humid dunes slacks are a highly threatened habitat, listed as vulnerable in the EU habitat red list. Accelerated successional processes in dune systems have resulted in the loss and degradation of ideal conditions for specialist dune slack species, hence the need for conservation management. We investigated the restoration of a dune slack in North Wales, UK, where vegetation and soil removal to 10 cm depth was undertaken to reinstate nutrient‐poor, open and damp conditions. We assessed the outcomes of the management for dune slack communities over the 18 years since restoration. We also assessed the differences between restored and unrestored areas of dune slacks. The dunes were restored in the winter of 2004/2005, after which we conducted vegetation surveys in fixed quadrats for most years in the restored and adjacent, un‐restored dune slacks. Species diversity and plant community composition changes over time were assessed using Shannon's index, multivariate analysis and indicator species analysis. Comparisons between the restored and unrestored areas of the dune slacks were also made. Ellenberg indicator values (EIVs) were examined to identify potential environmental drivers of post management successional changes. After 18 years the restored dune slacks developed a species‐rich and diverse community. compared to the unrestored slacks. The establishment of species occurred rapidly in the first three years, followed by continued but slower increases in species richness and diversity. This is due to the addition of new species without losses of established species. EIVs show no significant difference over time suggesting the restored areas are still at an early stage of succession. Distinct stages of community change since restoration are characterised by different indicator species. Plants are likely to be largely recruited from an existing seed bank. Restoration by turf removal may be suitable for other low nutrient, species rich habitats dependent upon fluctuating groundwater levels.

Anchovy (Engraulis ringens) and Pacific sardine (Sardinops sagax) variability changes in northern Chile associated with the environment and inter species synchronicity: GARCH model with exogenous variable and hybrid Bayesian deep learning estimation approach

Small pelagic fish species, such as anchovy (Engraulis ringens) and Pacific sardine (Sardinops sagax), play a crucial role in marine ecosystems worldwide as they serve as an important food source for higher-order predators, such as seabirds, marine mammals, and larger fish species; also from their high productivity in terms of fishery landings, they help with maintaining food security. However, small pelagic populations are known for their variability, with fluctuations in their distribution and abundance influenced by interactions with environmental and human-related factors in different spatio-temporal scales. This study aims to investigate the variability in anchovy and sardine populations in northern Chile and their potential environmental drivers by using a class of models that address the changes in variability (i.e. variance) over time, namely Generalized autoregressive conditional heteroskedasticity (GARCH) models. In particular, this work considers a GARCH model that includes an additional term in the variance, that could help to better model the variability fluctuations of both anchovy and sardine, explained by environmental factors. Since there is no estimation procedures for those type of models, we propose a hybrid Approximate Bayesian Computation (ABC) procedure that involves the use of Deep Learning structures for estimating the parameters of the model and obtain posterior distributions. The results are two-fold: First, the proposal of a new time series model that better explain conditional variance with exogenous variables and a novel estimation procedure, and second, a novel approach for establishing explicit models that address the variability of small pelagic fisheries and their interaction with the environment.

Contribution of environmental factors to genetic variation in the Pacific white-sided dolphin

Environmental changes driven by pollution and climate change have affected many species globally. The Pacific white-sided dolphin, or Lagenorhynchus obliquidens (L. obliquidens), is threatened by water pollution, which is the product of human actions and can impact the genetic structure of species in affected areas. While researchers have studied genetic differences between populations of L. obliquidens in Japan, they failed to explore the potential environmental drivers of these differences. Our research aimed to identify the major environmental factors impacting the genetic variation of L. obliquidens, which will increase our understanding of how this species responds to changes in the environment. We studied several different variables, including salinity, ocean currents, temperature, and microplastic levels. Due to the significant presence and variation of microplastics in the ocean surrounding Japan, we hypothesized that this would have the most notable impact on the genetic variation of L. obliquidens. We began our research by gathering genetic sequencing data from a preexisting study focusing on populations along the Japanese coast. We collected environmental data and analyzed it alongside a genetic distance matrix, leveraging data analysis and machine learning tools in R. We found that the most impactful variable was current stability, which did not match our original prediction of microplastic levels having the most significant impact. We then investigated why ocean currents may have had such a strong impact on L. obliquidens and proposed that it has a connection to nutrient and prey distribution, which can be majorly impacted by changes in ocean currents.

Diskontinuum Gornje Neretve: gradienti taksonomske in funkcionalne raznolikosti bentoških nevretenčarjev v divji balkanski reki

Free-flowing rivers are highly valuable to understand the taxonomic and functional community structure of organisms that inhabit fluvial ecosystems. We investigated patterns of macroinvertebrate community composition and food web structure using stable isotopes (δ13C and δ15N), including potential environmental drivers, over a free-flowing river continuum in the upper course of the Neretva River in Bosnia and Herzegovina. Results showed a high taxonomic diversity, a high percentage of EPT taxa (Ephemeroptera, Plecoptera, Trichoptera), and a slightly heterotrophic ecosystem (average allochthonous assimilation = 54%). The taxonomic composition differed prominently between a tributary located upstream and the mainstem. However, we also found notable species turnover between the upper (headwater and midsection) reaches and the downstream reaches of the mainstem. Macroinvertebrate abundance and the percentage of EPT peaked downstream while midsection reaches showed the highest taxonomic richness and diversity and allochthonous assimilation. Most of the functional metrics (maximum and average trophic position and isotopic richness and evenness) showed pronounced discontinuities in their spatial patterns, which did not follow the predictions of the River Continuum Concept. These results highlight the uniqueness of this section of the Neretva, where natural discontinuities structure macroinvertebrate communities in ways and by mechanisms not captured by smooth ecological concepts.

Camera traps reveal a high prevalence of sarcoptic mange in red foxes from northern Spain

The mite Sarcoptes scabiei affects numerous mammal species causing the sarcoptic mange, a widespread disease with relevance for wildlife conservation, welfare, and management. The red fox (Vulpes vulpes) could become infested by direct and indirect routes leading to external skin lesions potentially recognizable by devices such as camera traps (CTs). In the present study, 86 randomly placed CTs were used to investigate the apparent prevalence and severity of S. scabiei in a red fox population from northern Spain. Their potential environmental and population-related drivers were also assessed. A total of 341 independent encounters were examined to visually identify mange-compatible lesions. The apparent prevalence was 19.16% (confidence interval (CI) 95%: 15.08–23.80) of which 82.81% (CI95%: 71.33–91.10) were severe. Our results revealed that habitat attributes such as lower altitudes, higher coverage of water-linked habitats and woodland predominance, were significant predictors of the apparent risk of mange. The models also suggested that the apparent prevalence of mange was associated with poor body condition and elevated frequencies of spatial coincidence among fox encounters, which facilitates indirect transmission. Interestingly, we did not observe mange-compatible lesions in other sympatric wild species (>15,000 encounters examined). This could be explained by the mite's host specificity and the low probability that these other potential hosts use sites where transmission among foxes usually occurs, such as dens. This study illustrates how camera trapping can be used as an interesting tool for the surveillance of wildlife diseases, thus overcoming the logistic constraints derived from direct sampling and allowing the early detection and better management of pathogens in the riskiest areas.

Major shift in the copepod functional community of the southern North Sea and potential environmental drivers

Abstract Copepods form the bulk of secondary production in marine ecosystems and are a major resource for higher trophic levels. Copepods are highly sensitive to environmental changes as they are ectotherms with a short life span whose metabolism and development depend on abiotic conditions. In turn, changes in their functional structure (i.e. functional trait composition) can have impacts on ecosystems. We examined changes in the copepod functional community in the North Sea over the past five decades, using a trait-based approach. We observed a shift around 1986–1988: the copepod community was initially dominated by larger herbivores, with a long development time, diapause ability, and highest abundances in summer. This community changed abruptly after 1986–1988, to a dominance of smaller carnivore taxa, with shorter development times, less ability to enter diapause, and that display higher abundances in autumn. This rapid reorganization could be driven by higher water temperatures, lower dinoflagellate abundances, and lower nutrient concentrations. These changes could impact adjacent trophic levels, such as phytoplankton on which several species graze or fish larvae, leading to a mismatch situation with consequences for fish recruitment. Our results emphasize the impact that global and regional changes could have on coastal ecosystems through the role played by copepods.

Ecosystem multifunctionality, maximum height, and biodiversity of shrub communities affected by precipitation fluctuations in Northwest China.

Dryland ecosystems face serious threats from climate change. Establishing the spatial pattern of ecosystem multifunctionality, maximum height and the correlation of biodiversity patterns with climate change is important for understanding changes in complex ecosystem processes. However, the understanding of their relationships across large spatial areas remains limited in drylands. Accordingly, this study examined the spatial patterns of ecosystem multifunctionality, maximum height and considered a set of potential environmental drivers by investigating natural shrub communities in Northwest China. We found that the ecosystem multifunctionality (EMF) and maximum height of shrub communities were both affected by longitude, which was positively correlated with the precipitation gradient. Specifically, the EMF was driven by high precipitation seasonality, and the maximum height was driven by high precipitation stability during the growing season. Among the multiple biodiversity predictors, species beta diversity (SD-beta) is the most common in determining EMF, although this relationship is weak. Unlike tree life form, we did not observe biodiversity-maximum height relationships in shrub communities. Based on these results, we suggest that more attention should be paid to the climatical fluctuations mediated biodiversity mechanisms, which are tightly correlated with ecosystem's service capacity and resistance capacity under a rapid climate change scenario in the future.

A step towards the integration of spatial dynamics in population dynamics models: Eastern Bering Sea snow crab as a case study

Considering spatial processes in population dynamics models can be difficult because of data limitations and computational costs. We adapted a high-resolution spatiotemporal assessment framework to better address fine-scale spatial heterogeneities based on theories of fish population dynamics and spatiotemporal statistics. Specifically, we developed a size-based state-space model for the snow crab (Chionoecetes opilio) population in the Eastern Bering Sea (EBS) to refine the representation of spatial processes in integrated population models, facilitate understanding of the drivers of spatiotemporal population dynamics, and provide new insights for management advice. The model fits to spatial survey and fishery-dependent catch data. It implicitly accounts for seasonal movement between the time of the survey and that of fishery to estimate fine-scale spatial population dynamic and fishing impacts, including potential environmental drivers. We quantify, for the first time, spatiotemporal variation in exploitable abundance, fishing mortality, recruitment, and mature and immature abundance. The model estimated declines in exploitable abundance and in fishing mortality with variable spatial distributions, and sporadic recruitment, spatially concentrated in the northeast EBS. Few spatial assessments have been used as the basis for management advice and we consider this study as a step towards the integration of spatial dynamics in stock assessment.

Spatially varying plankton synchrony patterns at seasonal and interannual scales in a well‐connected shelf sea

AbstractSpatial population synchrony, defined as spatial covariation in population density fluctuations, exists across different temporal and spatial scales. Determining the degree of spatial synchrony is useful for inferring environmental drivers of population variability in the wake of climate change. In this study, we applied novel statistical methods to detect spatial synchrony patterns of Calanus finmarchicus on the Northeast U.S. Shelf at multiple spatiotemporal scales using unevenly distributed data. Our results reveal that C. finmarchicus subpopulations connected by advection are not necessarily in synchrony, indicating that the degree of synchrony is likely influenced by heterogeneity of local habitats. In addition, regionally synchronous environmental conditions (e.g., sea surface temperature) may not play as significant a role in influencing subregional population dynamics as was previously hypothesized. Overlooking the spatial heterogeneity of synchronous patterns at different time scales could lead to erroneous inferences of potential environmental drivers responsible for C. finmarchicus variability.

Urban stream restorations increase floodplain soil carbon and nutrient retention along a chronosequence

Stream restoration is a common management practice to meet regulatory or voluntary efforts to improve water quality via nutrient and carbon (C) retention, including in the Chesapeake Bay watershed. However, most restoration projects have few quantifiable measures of project success, no standard metrics, and rarely collect pre-restoration data. Storage of nutrients, such as phosphorus (P) and nitrogen (N), in floodplain soils of restored streams can act as an easily quantifiable indicator of restoration success, particularly when the project goals include improved water quality. To determine how floodplains of restored streams change in their P and C storage as time since restoration increases, floodplain surficial soil samples (10 cm depth) were collected from 18 streams in the urbanized Piedmont region of northern Virginia, representing a chronosequence of time (1–10+ yrs.) since restoration as well as unrestored streams with high impervious surface cover (ISC) and unrestored streams with low ISC. The samples were analyzed for total carbon (TC), total nitrogen (TN) and total phosphorus (TP) storage, whereas C turnover rate and equilibrium phosphorus concentration (EPC0) were measured as metrics of C and P loss. These metrics were compared to time since restoration and potential environmental drivers, including soil moisture, pH, median particle size (D50), organic matter content (OM), and bioavailable P, iron (Fe), and aluminum (Al). These stream restorations demonstrated increasing nutrient storage for TC, TN, and TP along the chronosequence to values greater than both unrestored or reference streams, as well as decreasing C turnover and no significant changes in EPC0. Soil wetness and OM, key drivers in nutrient retention, also increased as restoration projects aged increasing C, N, and P storage. Overall, stream restoration did improve soil C, N, and P retention in floodplains as compared to unrestored sites and exceeded those of low ISC ‘reference’ sites.

Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis.

Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remain unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., Q ST -F ST comparisons). Subsequently, a redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a Q ST -F ST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of Solidago canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Did natural selection drive phenotypic trait variation among S. canadensis populations? (2) Did climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., Q ST > F ST) and stabilizing selection for physiological traits (i.e., Q ST < F ST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with the mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. A longitudinal shift in precipitation seasonality likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped the phenotypic traits of S. canadensis.

Responses of compositions, functions, and assembly processes of bacterial and microeukaryotic communities to long-range voyages in simulated ballast water

Ballast water is one of the main vectors for the spread of harmful organisms among geologically isolated waters. However, the successional processes of microbial functions and assembly processes in ballast water during the long-term shipping voyage remain unclear. In this study, the compositions, ecological functions, community assembly, and potential environmental drivers of bacteria and microeukaryotes were investigated in simulated ballast water microcosms for 120 days. The results showed that the diversity and compositions of the bacterial and microeukaryotic communities varied significantly in the initial 40 days (T0∼T40 samples) and then gradually converged. The relative abundance of Proteobacteria showed a distinct tendency to decrease (87.90%–41.44%), while that of Ascomycota exhibited an increasing trend (6.35%–62.12%). The functional groups also varied significantly over time and could be related to the variations of the microbial community. The chemoheterotrophy and aerobic chemoheterotrophy functional groups for bacteria decreased from 44.80% to 28.02% and from 43.77% to 25.39%, respectively. Additionally, co-occurrence network analysis showed that the structures of the bacterial community in T60∼T120 samples were more stable than those in T0∼T40 samples. Stochastic processes also significantly affected the community assembly of bacteria and microeukaryotes. pH played the most significant role in driving the structures and assembly processes of the bacterial and microeukaryotic communities. The results of this study could aid in the understanding of variations in the functions and ecological processes of bacterial and microeukaryotic communities in ballast water over time and provide a theoretical basis for its management.

Potential Environmental Drivers of Fossil Bones Degradation—A Metabarcoding Approach in Two Carpathian Caves

Studies on fossil bone microbial communities are scarce; even fewer studies were performed in cave deposits. For our research, sediments and fossil bones were sampled, and the whole community 16S rRNA gene-based metabarcoding analyses were performed on samples from Muierilor and Ursilor caves, some of Romania’s most important archaeological and paleontological sites. Most of the identified taxa belong to Bacteria, with Proteobacteria, Acidobacteriota, Bacteroidota, and Actinobacteriota amongst the most abundant phyla in bone samples from both caves. The sediment samples presented similar composition, with Proteobacteria and Acidobacteriota being the most abundant phyla. The inferred bacteriomes indicated the presence of environment-specific bacteria, typical bone colonizers, and bacteria found in soils and decomposing human remains or archaeological profiles as well as phosphate-solubilizing and organotrophic bacteria. Diversity indices indicated a higher diversity in bone samples from Muierilor Cave than in Ursilor Cave samples and sediment samples from both caves. Environmental conditions, especially air relative humidity, were also considered in explaining the bacteriome diversity in different cave settings. These findings help to understand fossil bones’ deposition and degradation in various environmental conditions. Furthermore, this is the first attempt to relate microenvironments and bacteria to preserving fossil bones from caves.

The diversity of molluscan faunas in marine lakes of Raja Ampat, West Papua, Indonesia

Abstract Marine lakes are bodies of seawater that are land-locked and maintain a subterranean connection to the surrounding sea. Here, we document the species diversity of benthic molluscs in 11 marine lakes in Raja Ampat, West Papua, Indonesia, using the roving diving survey method. We specifically tested for relationships between species richness and lake size and the degree of connection to the surrounding sea, and tested potential environmental drivers of community structure. We recorded 73 species, belonging to the classes Gastropoda (48 species, comprising 36 genera and 25 families), Bivalvia (24 species, consisting of 17 genera and 12 families), and Polyplacophora (one species). Molluscs from marine lakes are a subset of species also occurring in coral, seagrass, mangrove, and rocky shore habitats in the open sea. We found lake communities to mostly consist of grazers and filter feeders. The number of mollusc species significantly increased with increasing connection to the surrounding sea, but not with increasing surface area, indicating that dispersal potential may be the main driving force. Furthermore, we observed no significant influence of the environment on the variation in mollusc species composition among marine lakes. Still, we observed certain species to be exclusively present in either high or low-connected lakes, indicating a potential effect of environmental filtering. Marine lakes provide a unique ecosystem for diverse mollusc assemblages and as such should be protected.

Shared and distinct patterns of genetic structure in two sympatric large decapods

AbstractAimComparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management.LocationEuropean seas of the northeast Atlantic and Mediterranean.TaxaEuropean clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily fished decapods with extensive dispersal potential.MethodsBy RAD‐sequencing 214 H. gammarus from 32 locations and 349 P. elephas from 15 locations, we isolated 6340 and 7681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity.ResultsWe found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region.Main ConclusionsWe attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographical heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.

Latitudinal patterns of forest ecosystem stability across spatial scales as affected by biodiversity and environmental heterogeneity.

Our planet is facing a variety of serious threats from climate change that are unfolding unevenly across the globe. Uncovering the spatial patterns of ecosystem stability is important for predicting the responses of ecological processes and biodiversity patterns to climate change. However, the understanding of the latitudinal pattern of ecosystem stability across scales and of the underlying ecological drivers is still very limited. Accordingly, this study examines the latitudinal patterns of ecosystem stability at the local and regional spatial scale using a natural assembly of forest metacommunities that are distributed over a large temperate forest region, considering a range of potential environmental drivers. We found that the stability of regional communities (regional stability) and asynchronous dynamics among local communities (spatial asynchrony) both decreased with increasing latitude, whereas the stability of local communities (local stability) did not. We tested a series of hypotheses that potentially drive the spatial patterns of ecosystem stability, and found that although the ecological drivers of biodiversity, climatic history, resource conditions, climatic stability, and environmental heterogeneity varied with latitude, latitudinal patterns of ecosystem stability at multiple scales were affected by biodiversity and environmental heterogeneity. In particular, α diversity is positively associated with local stability, while β diversity is positively associated with spatial asynchrony, although both relationships are weak. Our study provides the first evidence that latitudinal patterns of the temporal stability of naturally assembled forest metacommunities across scales are driven by biodiversity and environmental heterogeneity. Our findings suggest that the preservation of plant biodiversity within and between forest communities and the maintenance of heterogeneous landscapes can be crucial to buffer forest ecosystems at higher latitudes from the faster and more intense negative impacts of climate change in the future.

Environmental Drivers of Vibrio cholerae Abundances in Mobile Bay, Alabama.

Vibrio cholerae is the etiological agent of the illness cholera. However, there are non-O1/non-O139 V. cholerae (NOVC) strains that generally lack the toxin gene (ctx) and colonization factors that cause cholera. These NOVC strains are autochthonous members of estuarine environments and a significant cause of seafood-borne gastroenteritis in the United States. The objective of this study was to identify environmental parameters that correlate with NOVC prevalence in oysters, water, and sediment at three ecologically diverse locations in Mobile Bay, AL, including Dog River (DR), Fowl River (FR), and Cedar Point (CP). Oyster, water, and sediment samples were collected twice a month when conditions were favorable for NOVC growth and once a month when they were not. A most probable number (MPN)/real-time PCR assay was used to determine NOVC abundances. Environmental parameters were measured during sampling to determine their relationship, if any, with NOVC at each site. NOVC abundances in oysters at DR, FR, and CP were 0.87, 0.87, and -0.13 log MPN/g, respectively. In water, the median NOVC levels at DR, FR, and CP were 1.18, -0.13, and -0.82 log MPN/mL, and in sediment, the levels were 1.48, 1.87, and -0.03 log MPN/g, respectively. Correlations of NOVC abundances in oyster, water, and sediment samples with environmental parameters were largely site specific. For example, the levels of NOVC in oysters at DR had a positive correlation with temperature but a negative correlation with dissolved oxygen (DO) and nutrient concentrations, NO2-, NO3-, dissolved inorganic nitrogen (DIN), total dissolved nitrogen (TDN), and dissolved inorganic phosphorus (DIP). At FR, however, the levels of NOVC in oysters displayed only a negative correlation with NO2-. When grouping NOVC abundances by temperature, the main driving factor for prevalence, additional correlations with salinity, total cell counts, dissolved organic nitrogen (DON), and dissolved organic carbon (DOC) became evident regardless of the site. IMPORTANCE NOVC can cause gastrointestinal illness in humans, which typically occurs after the consumption of raw or undercooked seafood. Incidence rates of NOVC gastroenteritis have increased during the past decade. In this study, NOVC was enumerated from oysters, sediment, and water collected at three sites in Mobile Bay, with environmental parameters measured concurrently over the course of a year, to identify potential environmental drivers of NOVC abundances. The data from this study, from an area lacking in V. cholerae research, provide a useful baseline for risk analysis of V. cholerae infections. Defining correlations between NOVC and environmental attributes at different sites and temperatures within a dynamic system such as Mobile Bay provides valuable data to better understand the occurrence and proliferation of V. cholerae in the environment.

Genetic and ecological drivers of molt in a migratory bird

The ability of animals to sync the timing and location of molting (the replacement of hair, skin, exoskeletons or feathers) with peaks in resource availability has important implications for their ecology and evolution. In migratory birds, the timing and location of pre-migratory feather molting, a period when feathers are shed and replaced with newer, more aerodynamic feathers, can vary within and between species. While hypotheses to explain the evolution of intraspecific variation in the timing and location of molt have been proposed, little is known about the genetic basis of this trait or the specific environmental drivers that may result in natural selection for distinct molting phenotypes. Here we take advantage of intraspecific variation in the timing and location of molt in the iconic songbird, the Painted Bunting (Passerina ciris) to investigate the genetic and ecological drivers of distinct molting phenotypes. Specifically, we use genome-wide genetic sequencing in combination with stable isotope analysis to determine population genetic structure and molting phenotype across thirteen breeding sites. We then use genome-wide association analysis (GWAS) to identify a suite of genes associated with molting and pair this with gene-environment association analysis (GEA) to investigate potential environmental drivers of genetic variation in this trait. Associations between genetic variation in molt-linked genes and the environment are further tested via targeted SNP genotyping in 25 additional breeding populations across the range. Together, our integrative analysis suggests that molting is in part regulated by genes linked to feather development and structure (GLI2 and CSPG4) and that genetic variation in these genes is associated with seasonal variation in precipitation and aridity. Overall, this work provides important insights into the genetic basis and potential selective forces behind phenotypic variation in what is arguably one of the most important fitness-linked traits in a migratory bird.

Temporal synchrony among juvenile marine fishes and potential climate and environmental drivers in the Bay of Biscay

The existence of synchronous fluctuations among sympatric species is an important property of a community, potentially reducing temporal stability of ecosystem services. Yet, community synchrony and its potential drivers have rarely been studied in marine ecosystems. Here, we analyzed a 14-year time-series (2007–2020) of fish abundance data collected by a scientific beam trawl survey in the Bay of Biscay, a temperate marine ecosystem located in the North-east Atlantic. We used dynamic factor analysis to reveal common trends in abundance among juvenile demersal marine fishes, and to identify potential environmental drivers. Our results revealed synchronous changes in juvenile fish abundance among the 12 marine species examined in the study. This strong temporal coherence was likely related to the influence of climate and environmental factors, notably sea bottom temperature and the East Atlantic Pattern. We also found some support for alternative drivers of early-life fish dynamics, namely the North Atlantic Oscillation and sea surface chlorophyll-a concentration, the later suggesting bottom-up trophic control. In the context of ongoing environmental changes, our findings raise questions about the future stability of the demersal marine fish community in the Bay of Biscay.