Sampling Effort Research Articles

Diversity patterns and knowledge gaps of Atlantic Forest epiphyllous bryophytes: a highly neglected group.

Epiphyllous bryophytes are a group of plants with complex adaptations to colonize the leaves of vascular plants and are considered one of the most specialized and sensitive groups to environmental changes. Despite their specificity and ecological importance, these plants represent a largely neglected group in relation to scientific research and ecological data. This lack of information directly affects our understanding of biodiversity patterns and compromises the conservation of this group in threatened ecosystems. Based on the compilation of data from a systematic review and virtual herbarium databases, we provide the first biogeographic assessment of diversity patterns of epiphyllous bryophytes in the Atlantic Forest hotspot. We also identify their phorophytes and assess sampling bias, knowledge gaps, and the current conservation state of epiphyllous bryophytes. The state of knowledge about epiphyllous bryophytes in the Atlantic Forest is still incipient and taxonomic and geographically biased. Sampling effort and climate variation highly influenced species richness patterns. Notably, Bromeliophila natans, a threatened and endemic species, has not been recorded in the past 20 years, possibly indicating extinction due to anthropogenic activities such as habitat loss. We found that the occurrence information, distributed across the domain, was positively influenced by the presence of protected areas, forest cover and density of cities, whereas it was negatively influenced by distance to access roads and research centers. More fieldwork and taxonomic and molecular studies are urgently needed to uncover biodiversity patterns and conservation priorities of this sensitive group. Without an increased collection effort, we may lose important species and their contributions to people.

Large-scale and long-term wildlife research and monitoring using camera traps: a continental synthesis.

Camera traps are widely used in wildlife research and monitoring, so it is imperative to understand their strengths, limitations, and potential for increasing impact. We investigated a decade of use of wildlife cameras (2012-2022) with a case study on Australian terrestrial vertebrates using a multifaceted approach. We (i) synthesised information from a literature review; (ii) conducted an online questionnaire of 132 professionals; (iii) hosted an in-person workshop of 28 leading experts representing academia, non-governmental organisations (NGOs), and government; and (iv) mapped camera trap usage based on all sources. We predicted that the last decade would have shown: (i) exponentially increasing sampling effort, a continuation of camera usage trends up to 2012; (ii) analytics to have shifted from naive presence/absence and capture rates towards hierarchical modelling that accounts for imperfect detection, thereby improving the quality of outputs and inferences on occupancy, abundance, and density; and (iii) broader research scales in terms of multi-species, multi-site and multi-year studies. However, the results showed that the sampling effort has reached a plateau, with publication rates increasing only modestly. Users reported reaching a saturation point in terms of images that could be processed by humans and time for complex analyses and academic writing. There were strong taxonomic and geographic biases towards medium-large mammals (>500 g) in forests along Australia's southeastern coastlines, reflecting proximity to major cities. Regarding analytical choices, bias-prone indices still accounted for ~50% of outputs and this was consistent across user groups. Multi-species, multi-site and multiple-year studies were rare, largely driven by hesitancy around collaboration and data sharing. There is no widely used repository for wildlife camera images and the Atlas of Living Australia (ALA) is the dominant repository for sharing tabular occurrence records. However, the ALA is presence-only and thus is unsuitable for creating detection histories with absences, inhibiting hierarchical modelling. Workshop discussions identified a pressing need for collaboration to enhance the efficiency, quality and scale of research and management outcomes, leading to the proposal of a Wildlife Observatory of Australia (WildObs). To encourage data standards and sharing, WildObs should (i) promote a metadata collection app; (ii) create a tagged image repository to facilitate artificial intelligence/machine learning (AI/ML) computer vision research in this space; (iii) address the image identification bottleneck via the use of AI/ML-powered image-processing platforms; (iv) create data commons for detection histories that are suitable for hierarchical modelling; and (v) provide capacity building and tools for hierarchical modelling. Our review highlights that while Australia's investments in monitoring biodiversity with cameras position it to be a global leader in this context, realising that potential requires a paradigm shift towards best practices for collecting, curating, sharing and analysing 'Big Data'. Our findings and framework have broad applicability outside Australia to enhance camera usage to meet conservation and management objectives ranging from local to global scales. This review articulates a country/continental observatory approach that is also suitable for international collaborative wildlife research networks.

Towards estimating the proportion of dead and missing vines at the field level

This work aimed to improve practices for estimating dead and missing vines, particularly when these estimations are made via sampling. Vine mortality is a well-known phenomenon that many studies have attempted to better explain, but only a few have focused on estimating the number of dead and missing vines at the field-level, which remains a challenging task for grapegrowers. The present article aimed to determine to what extend an increased an increased sampling effort improves estimation accuracy and thus help practitioners define a sample size adapted to vineyard properties and the accuracy expected by the grower. The first part of the study investigated whether vineyard properties (year of planting and variety) and available ancillary data (soil resistivity and fraction of vegetation cover [Fcover]) can provide a priori information on the proportion of dead and missing vines and guide the sampling strategy. The analysis was based on an exhaustive dataset created by individually mapping 14,199 dead and missing vines across 29 fields in a 20 ha vineyard. In this vineyard, regression models showed an increase in dead and missing vines of around 2.2 % per year from the tenth year onwards. Plantation year, variety and vigour (assessed by Fcover) were identified as providing valuable prior information on the proportion of dead and missing vines within the fields. The second part of the study focused on characterising the estimation error values that can result from these estimations. It focuses on sampling estimation, highlighting to what extent field properties (such as the number of dead and missing vines and their spatial autocorrelation) affect the accuracy of estimates. The results showed that the same sampling protocol can result in different accuracies from one field to another. Thus, they underline the importance of leveraging prior information, such as available field data, to tailor sampling efforts accordingly. Based on these results, this article introduces new guidelines to facilitate the estimation of the proportion of dead and missing vines in vineyards.

Persistence of Ancestral KhoeSan Mitochondrial Patterns in Contemporary South African Populations.

Southern Africa has been inhabited by hunter-gatherers for at least 20,000 years and has received diverse immigration flows in the last 2000 years. The original inhabitants have interacted with the pastoralist migrants from Eastern Africa (∼2000 ybp), followed by the southern Bantu migration arriving some 1000 ybp, and more recently with the European and Asian settlers after the 17th century. Many of the original Khoekhoe and San inhabitants have either become extinct or have disappeared through admixture in South Africa (SA), in a sex-biased manner involving KhoeSan women. In this study, we generated mitochondrial DNA (mtDNA) control region (CR) sequences for 247 South African individuals. The sampling effort was concentrated in regions and populations with historical links to the KhoeSan population groups: admixed (Coloured, Griqua), Nama (Khoekhoe) and Bantu in three provinces. Here we evaluate the composition and extent of connectivity between population groups and regions, and to assess the distribution of haplotypes for the practical application of mtDNA CR data in forensic identifications. The analysis of the newly generated sequences revealed 142 distinct haplotypes, of which 122 were unique. Haplogroup L0 was predominant (overall 71.7%). A high-frequency L0d2a haplotype dominated the pool of the admixed groups with 10%-12.5% incidence overall or per region. Comparative analysis with 545 extant mtDNA CR sequences from South African KhoeSan and admixed descendants revealed extensive population structure and high within-group haplotype sharing. The observed population and regional variations, combined with the prevalence of high-frequency haplotypes, align with patterns of matrilocality. These findings highlight the limitations of using mtDNA control region analysis for forensic applications in South Africa.

English

Abstract While previous studies have explored the impact of behavior and life history on environmental DNA (eDNA), little research has been conducted on the impact of molting on eDNA detectability and particle size for aquatic arthropods like crayfish. To address this knowledge gap, we conducted a study examining how molting affects eDNA detectability over a range of particle sizes using marbled crayfish (Procambarus virginalis Lyko, 2017). We collected water samples from aquariums at pre- and post-molt time intervals and filtered our samples using sequential filtration from large to small filter pore sizes. We found that molting had a weak negative effect on eDNA detectability, and P. virginalis eDNA was most detectable throughout the study at our largest filter pore size (5.0 μm) regardless of molt status. Additionally, time spent in aquariums had a strong, positive effect on eDNA detectability for P. virginalis. Given that molting had a weak effect on eDNA detectability for our study crayfish, we suggest that researchers align their sampling efforts with other seasonal life history events, like reproduction or egg extrusion, that have been demonstrated to improve eDNA detectability.

Mite diversity of cupuaçu trees (Theobroma grandiflorum: Malvaceae) in the state of Pará, Amazon, Brazil

ABSTRACT The aim of this study was to identify the mite fauna associated with cupuaçu plantations in Bragança and Augusto Corrêa, Pará, Brazil. In order to investigate the variability and composition of these organisms in cupuaçu plantations in two different locations, systematic collections were carried out at specific times throughout two periods. In addition to mite collection, environmental data such as temperature, relative humidity, atmospheric pressure and precipitation were recorded. Statistical data were obtained through sampling effort and diversity, Hill’s diversity profile and nonmetric multidimensional scaling (NMDS). A total of 868 mites belonging to 53 species were sampled. Seventeen families/suborders of mites were identified, the five most abundant being: Eriophyidae (44.7%), Phytoseiidae (21.1%), Cunaxidae (9%), Oribatida (5.5%) and Tenuipalpidae (3.5%). The data indicated a greater number of mites sampled during the rainy season compared to the dry season, representing approximately 90% more mites in the rainy season. Greater richness was observed during the dry season, with 38 taxa identified. Bragança contributed a total of 551 individuals, while Augusto Corrêa recorded 317 mites. For the Shannon- Wiener index, the municipalities presented similar diversity. Therefore, we highlight the importance of these results for understanding the mite community associated with cupuaçu trees.

Species Composition of Crustaceans of Korapuzha Estuary, Kerala, India

The Korapuzha estuarine ecosystem, acting as a link between the freshwater expanse of Akalapuzha and the seawater at Elathur, is characterized by delicate and fragile features. Besides its ecological importance, scientific studies on faunal diversity of Korapuzha is very scarce which emphasizes the necessity of elaborate studies. The present study focusses on species composition of crustaceans, playing a vital role in biogeochemical cycles. The study aims to undertake comprehensive study on crustaceans of Korapuzha estuary, thus minimizing the critical gap in understanding the estuarine ecosystem. Sampling efforts were from 2021 to 2023 involving local participation using various gears. 30 crustaceans were identified under 21 genera, 11 families and two orders, showcasing the complexity in faunal diversity of crustaceans. Shrimps (Fenneropenaeus indicus) and crabs (Scylla serrata) were the dominant species of commercial fisheries. The study highlighted the non-commercial species like Clibanarius infraspinatus (hermit crabs), Balanus Amphitrite and Balanus balanoides (Barnales) and Oratosquilla sp (mantis shrimp). The present study focused on understanding of Korapuzha estuary in detail, thus generating baseline data for conservation and management of estuary. The study also stresses on the economic importance of commercial crustaceans and shows the need for long-term effective conservational measures.

The older, the better: a comprehensive survey of soil organic carbon under commercial oil palm plantations

Soil conditions of croplands are a frequent topic of scientific research. In contrast, less is known about large-scale commercial plantations of perennial crops such as oil palm. Oil palm is a globally important tropical commodity crop which contributes to both food and energy security due to its exceptional productivity. However, oil palm crops are associated with short lifecycles and high nutrient demands, which may disproportionately affect soil health. With the goal of exploring baseline soil properties in commercial oil palm plantations, we evaluated data from two large-scale soil surveys carried out in 2014/2015 and 2018/2019 across more than 400 fields located throughout Peninsular Malaysia. We examined variation in field-measured soil quality indicators with a focus on soil organic carbon content at three depths (0–15 cm, 15–30 cm, 30–45 cm) and investigated links with spatial covariates, including plantation age. We found SOC contents to be low (1.6–2%) across the sampled locations with limited correlation with spatial predictors employed in soil organic carbon modelling. Furthermore, we found that immature and young mature plantations, which consisted of fields that were re-planted as part of a 20-year-long oil palm rotation, were characterised by significantly lower soil organic carbon content than the mature plantations. This suggests that management practices should target younger oil palm plantations for soil organic conservation measures to increase the overall baseline SOC content, which will subsequently accumulate over the plantation’s lifespan. We further provide recommendations for future soil sampling efforts, which could increase the robustness of collected data and facilitate their use for soil monitoring through modelling approaches involving, for example, digital soil mapping.

Fish fauna of the Upper Grande River basin: checklist and distribution patterns

ABSTRACT The Neotropical region exhibits a remarkable diversity of freshwater fish, with the Upper Grande River in the La Plata basin emerging as a significant yet underexplored hotspot. However, this region is confronted with escalating threats from human activities, such as hydroelectric damming and urbanization, which jeopardize its ichthyofauna. This research conducted a comprehensive inventory of the ichthyofauna in the Upper Grande River, covering diverse environments and sub-basins. Fish sampling at 185 sites revealed over 94 species, indicating a high richness and abundance of migratory fish, as well as the presence of two endangered species. While the study provides valuable insights into fish species richness and distribution, accumulation curves suggest the need for additional sampling efforts. The presence of non-native species, especially in the Aiuruoca and Grande sub-basins, raises conservation concerns. The study underscores the Upper Grande River’s critical role as an area for fish diversity, emphasizing the necessity for ongoing monitoring, conservation efforts, and additional sampling to fully uncover the extent of its ichthyofauna.

DNA Barcoding of Tabanids (Diptera: Tabanidae) from Veracruz, Mexico, with Notes on Morphology and Taxonomy

(1) Background: Tabanids are one of the most neglected and difficult-to-identify groups within the order Diptera despite their medical–veterinary importance. Since 2010, DNA barcoding has proved to be a promising method for the identification of horseflies in the Old World, but until now it had explored little with regards to Neotropical species. In Mexico, faunal studies continue to be focused on certain regions of the country, which has limited the generation of taxonomic keys. Here, we employed the DNA barcoding approach to contribute to the knowledge of horsefly species in one of the least explored biogeographic provinces in Mexico, the state of Veracruz. (2) Methods: Tabanids were collected at two localities using Malaise traps during two seasons. With a sampling effort of 300 h per trap per site, a total of 22 specimens were collected and identified using taxonomic keys and partial amplification and sequencing of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). (3) Results: Five species of the Tabanus genus were identified through taxonomic keys, and three of these species were confirmed through molecular analyses: T. oculus, T. commixtus, and T. pungens. (4) Conclusions: This is the first contribution of the sequence data of the Tabanidae family for Mexico and demonstrates that DNA barcoding is a vital tool for the recognition of Neotropical species.

Macrophyte banks and fish early stages in a cascade of small hydropower reservoirs (south-eastern Brazil): temporal changes along the reproductive cycle and influence of the limnological and spatial organisation

Context Small hydroelectric power plants (SHPs) are worldwide-distributed infrastructures, the ecological impacts of which are still poorly known. Aim To evaluate the role of littoral macrophytes as nursery areas for fishes in a cascade of three SHP reservoirs in south-eastern Brazil. Methods Three random macrophyte banks, from the intermediate and lentic compartments of each reservoir, were sampled (with manual sieves and gillnets) monthly along the peak of the reproductive period. Basic limnological variables were simultaneously measured. Key results In all, 88 larvae and 393 juveniles were captured, corresponding to 29 taxa, constituting almost 30% of the regional pool of fishes in the river. Non-migrants and short-distance migrants (with or without parental care) predominated. The species accumulation curve tended to an asymptotic configuration (whole dataset sampling effort). Fish abundance differed, mainly temporally, and, at a lower degree, spatially. Higher diversity (rarefaction and extrapolation curves) occurred both at the beginning of the reproductive peak and in the first (upstream) reservoir, where there was also a good correspondence between observed and estimated richness, i.e. 90%. Conclusions The macrophyte banks in these SHP reservoirs are effectively used as nursery areas. Implications Results have provided important insights for actions of conservation and management of the local and regional ichthyofauna, in a condition where typical nursery areas do not exist.

Reducing Uncertainty of Groundwater Redox Condition Predictions at National Scale, for Decision Making and Policy.

Understanding hydrogeochemical heterogeneity, associated with natural nitrate attenuation, is an integral part of implementing integrated land and water management on a regional or national scale. Redox conditions are a key indicator of naturally occurring denitrification in the groundwater environment, and often used to inform spatial planning and targeted regulation. This work describes the development of a statistical redox condition model for the groundwater environment at a national scale, using spatially variable physiochemical descriptors as predictors. The proposed approach builds on previous work, by complementing the available data with expert knowledge, in the form of synthetic data. Special care is given so that the synthetic data do not overfit and create further imbalances to the training dataset. The predictor dataset is further complemented by the results of a data driven model of the water table developed for this study, which is used both as a predictive parameter and a reference level for groundwater redox condition predictions at different depths. The developed model predicted the redox class for 84% of the samples in the out-of-bag datasets. We also propose an alternative approach for the communication of prediction uncertainty. We use the concept of a discriminate function to identify model classifications that may be ambiguous. Our results show a marked reduction in prediction uncertainty at shallow depths, with uncertainty in reduced environments decreasing from 76 to 12%, and overall uncertainty reduced by approximately 20%, though improvements at greater depths are less pronounced. We conclude that this approach can highlight robust model predictions that are defendable for decision making and can identify areas where monitoring or sampling efforts can be focused for improved outcomes.

How fast are viruses spreading in the wild?

Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics that can be informative of the dispersal dynamics and the capacity to spread among hosts. Heterogeneous sampling efforts of genomic sequences can however impact the accuracy of phylogeographic dispersal metrics. While the impact of spatial sampling bias on the outcomes of continuous phylogeographic inference has previously been explored, the impact of sampling intensity (i.e., sampling size) when aiming to characterise dispersal patterns through continuous phylogeographic reconstructions has not yet been thoroughly evaluated. In our study, we use simulations to evaluate the robustness of 3 dispersal metrics - a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance (IBD) signal metric - to the sampling intensity. Our results reveal that both the diffusion coefficient and IBD signal metrics appear to be the most robust to the number of samples considered for the phylogeographic reconstruction. We then use these 2 dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of IBD patterns and diffusion coefficients mostly reflecting the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade. Overall, our study provides key recommendations for the use of lineage dispersal metrics to consider in future studies and illustrates their application to compare the spread of viruses in various settings.

Study design and the sampling of deleterious rare variants in biobank-scale datasets.

One key component of study design in population genetics is the "geographic breadth" of a sample (i.e., how broad a region across which individuals are sampled). How the geographic breadth of a sample impacts observations of rare, deleterious variants is unclear, even though such variants are of particular interest for biomedical and evolutionary applications. Here, in order to gain insight into the effects of sample design on ascertained genetic variants, we formulate a stochastic model of dispersal, genetic drift, selection, mutation, and geographically concentrated sampling. We use this model to understand the effects of the geographic breadth of sampling effort on the discovery of negatively selected variants. We find that samples which are more geographically broad will discover a greater number variants as compared geographically narrow samples (an effect we label "discovery"); though the variants will be detected at lower average frequency than in narrow samples (e.g. as singletons, an effect we label "dilution"). Importantly, these effects are amplified for larger sample sizes and moderated by the magnitude of fitness effects. We validate these results using both population genetic simulations and empirical analyses in the UK Biobank. Our results are particularly important in two contexts: the association of large-effect rare variants with particular phenotypes and the inference of negative selection from allele frequency data. Overall, our findings emphasize the importance of considering geographic breadth when designing and carrying out genetic studies, especially at biobank scale.

Leveraging local wildlife surveys for robust occupancy trend estimation

Natural resource agencies are frequently tasked with monitoring populations of at-risk species to ensure management activities do not negatively affect the viability of wildlife populations. Typically, these monitoring efforts evaluate trends in a population’s abundance, occupancy, or geographic distribution. Often, surveys provide local information, but results are generally not incorporated into broad-scale monitoring efforts that focus on range-wide population changes due to their variable nature in both spatial extent and effort. We investigated whether aggregating these local (hereafter “variable”) surveys can generate enough statistical power to estimate broad-scale population trends using simulations of declining populations of fishers (Pekaniapennati) over a 10-year time horizon. Our simulations included three population sizes which we refer to as abundant, common, and rare (N0 = 700, 350, and 100 individuals, respectively) with each declining at a rapid and moderate pace (λ = 0.933, and 0.977, respectively). For each population, we simulated variable surveys using an occupancy framework to subsample the population with parameters that mimic combining multiple independent monitoring efforts which vary annually in location, and effort. Regardless of spatial consistency of annual sampling, there was minimal variation in statistical power under both high and low detection probability simulations. However, when sampling effort varied each year, statistical power was lower for most populations and sampling scenarios when compared to consistent sampling effort unless some baseline level of sampling effort was reliably achieved in all years. In many cases, adding low-level consistent baseline sampling to variable surveys resulted in statistical power close to that of consistent sampling efforts. Our results suggest statistical power is driven by annual consistency in the proportion of landscape sampled rather than spatial consistency in sampling locations. This result indicates that current variable surveys could be leveraged and combined to detect population declines for at-risk species at broad-scales if a baseline proportion of landscape is robustly sampled. The level of baseline sampling is highly dependent on population size and magnitudes of population change. In simulations with a common or abundant population experiencing a rapid decline, a baseline survey effort of at least 5% of the landscape in combination with variable surveys resulted in statistical power consistently above the standard threshold of 0.80 for occupancy monitoring. Leveraging existing local efforts to achieve high detection probability and baseline sampling would reduce financial and logistical burdens of broad-scale wildlife monitoring efforts.

Human Impacts and Larger Geographic Area Explain the Highest Number of Non‐Native Species of Freshwater Fishes Into Brazilian Protected Area

ABSTRACTNon‐native species represent a significant threat to biodiversity, particularly in aquatic environments where they are often introduced for purposes such as fishing or the aquarium trade. This study aimed to evaluate the influence of isolation and the size of federal protected areas (PAs) on the number of non‐native and native freshwater fish species in Brazilian PAs. Data from Brazilian PAs were gathered, including year of creation, buffer of human impacts around the PA, PA categories, coverage by freshwater, tourist visits, sampling sites, geographical coordinates (predictor variables) and information on the number of non‐native and native freshwater fish species (response variables). Linear regression analysis was employed to examine the influence of predictor variables on the number of non‐native and native fish species. A total of 33 different non‐native fish species were identified, with Poecilia reticulata, Hyphessobrycon eques, Hoplias lacerda and Cichla kelberi being the most widespread, occurring in 15, 7, 5 and 4 distinct PAs, respectively. The overall fish biodiversity within PAs encompassed 2670 species, with the National Park of Anavilhanas and the Environmental Protection Area of Ilha e Várzea do Paraná exhibiting the highest species richness. Greater human impact, larger coverage by freshwater and increased sampling effort were positively correlated with the number of recorded non‐native species. Factors such as year of creation, type of PA and tourist visitation did not have a significant effect. In contrast, native species exhibited a higher number of occurrences in PAs with lower human impact, longer histories, larger freshwater coverage areas and more extensive sampling efforts. These findings underscore the necessity for comprehensive management strategies to mitigate the impact of non‐native species on biodiversity within PAs.

Using occupancy modeling to provide insights into suitable habitat characteristics for the already restricted and critically endangered Olalla's titi monkey (Plecturocebus olallae)

Knowledge about changes in wildlife populations over time is essential for making informed decisions regarding their conservation. We evaluated the influence of distinct habitat factors on the occupancy of Olalla's titi monkey (Plecturocebus olallae), a Critically Endangered primate endemic to Bolivia. We assessed the presence of titi monkey groups using the playback technique, employing point counts in 582 quadrants of approximately 6.25 hectares. Utilizing single-species and single-season occupancy models, we estimated an occupancy (ψ) of 0.21 and found that the presence of P. olallae groups was positively related to heterogenous plant composition forests which indicates they may be more likely to occur in areas of high floristic diversity. We also found that groups of this already range restricted species do not occur in all the forest coverage within their distributional range. This complements previous considerations regarding the habitat in which P. olallae occurs based on its natural history knowledge and highlights the limited suitable habitat for this species. From our sampling effort, we calculated a power of 81% to detect a population change of 30%, showing the potential of occupancy modeling for population monitoring of P. olallae. Thus, we provide an information baseline that will be useful in further population monitoring actions for the conservation of these endemic Bolivian titi monkeys.

Occurrence of cetacean strandings on the coast of São Paulo, Brazil: a spatio-temporal assessment from 2017 to 2021

This study is part of the Projeto de Monitoramento de Praia– Bacia de Santos - (PMP-BS, Santos Basin Beach Monitoring Project) and is based on data from stranded cetaceans collected during beach monitoring in the state of São Paulo, between 2017 and 2021. Our aim was to assess the temporal and spatial patterns of strandings, including the main recorded species, stranding locations, and their distribution throughout the year. The analysis covered 258 beaches along the coast of São Paulo, which was divided into three mesoregions: South Coast (LSP), Central Coast (LCP), and North Coast (LNP). We calculated the number of regularly monitored beach kilometers and the number of cetacean records for each of these mesoregions. These records were termed ‘Strandings per Unit of Sampling Effort’ (EPUE). The total regular daily monitoring covered 430,596.36 kilometers along the beaches, with a record of 2,055 stranded individuals belonging to 18 cetacean species. On average, there were 411 ± 38 stranded individuals per year, ranging from 387 in 2019 to 470 in 2021. The species most frequently encountered were Franciscana dolphin (Pontoporia blainvillei), Guiana dolphin (Sotalia guianensis), humpback whale (Megaptera novaeangliae), and Atlantic spotted dolphin (Stenella frontalis). The Franciscana and Guiana dolphins accounted for 86% of records. Forty-three percent of strandings (877) was located in LSP , 33% (670) in LCP, and 25% (508) in LNP. These results were expected and supported by previous studies, as LSP encompasses important priority conservation areas with a diversity of ecosystems and the presence of endemic and endangered species. Keywords: beach monitoring, cetaceans, conservation, mesoregions, São Paulo coast, strandings

Evidence for extirpation of native kokanee in a large impounded watershed following introduction of a conspecific

AbstractObjectiveWilliston Reservoir in north‐central British Columbia was stocked with kokanee Oncorhynchus nerka from the Columbia River during the 1990s. A native population of kokanee already existed in the reservoir, but that population has not been found in sampling efforts since 2000. Most of the recent sampling, however, has targeted tributaries, and the stocked Columbia River‐type kokanee are stream spawners, whereas Thutade Lake kokanee, from which the native Williston Reservoir kokanee originated, are shore spawners.MethodsIn August 2021, pelagic surveys were conducted in Williston Reservoir by gillnetting and trawling to capture kokanee for subsequent genotyping to assess whether the native Williston Reservoir kokanee have persisted. We used 14 microsatellite loci to genotype 165 samples from the pelagic surveys and compared them to 623 previously genotyped kokanee from four reference populations: native reservoir fish; fish from the source population (Thutade Lake) that naturally colonized the reservoir; fish from isolated lakes in the Williston Reservoir watershed; and Columbia River‐type fish that now spawn in tributaries to the reservoir.ResultKokanee collected from the pelagic survey conducted in Williston Reservoir were entirely assigned to the Columbia River type by using the Bayesian clustering program STRUCTURE and a discriminant analysis of principal components. We found no evidence of any native Williston Reservoir genotypes.ConclusionFormation of Williston Reservoir favored pelagic species, such as kokanee, which have gradually increased in proportion over time—particularly since the introduction of kokanee from the Columbia River. Unfortunately, native Williston Reservoir kokanee appear to have been extirpated from the reservoir and were likely outcompeted by the introduced Columbia River‐origin kokanee.

Plotting the major proteins of borealpox virus

In an era marked by rapid environmental transformations, the viability of numerous species hinges crucially on their ability to navigate and adjust to shifting climatic conditions through migration. Yet, amidst this natural quest for survival, a consequential and often overlooked consequence emerges: the inadvertent transportation of a diverse array of parasites and pathogens across landscapes. This phenomenon poses a substantial and tangible threat to global health, particularly in the wake of recent outbreaks and pandemics fueled by zoonotic viruses, which leap from animals to humans. These viruses, originating in animals but capable of infecting humans, serve as poignant reminders of the intricate relationship between human and wildlife health, and the potential dangers of disregarding this delicate balance. In 2015, the borealpox virus (BRPV) [formerly Alaskapox virus (AKPV)], classified as an Orthopoxvirus, was first identified in a woman living near Fairbanks, Alaska. The BRPV causes borealpox disease. The first recorded fatality attributed to BRPV infection occurred in January 2024. Current evidence suggests that BRPV primarily targets small mammals, particularly red-backed voles and shrews, as evidenced by sampling efforts in the Fairbanks North Star Borough. However, it is likely that the virus is more widespread among Alaska’s small mammal populations, potentially leading to undiagnosed human infections. Additionally, domestic pets, such as cats and dogs, may also contribute to the transmission of the virus. To date, no instances of human-to-human transmission have been documented, but the lack of diagnostics and vaccines for BRPV remains a concerning gap. This paper aims to address this issue by reporting the structure and epitopes of the major proteins of BRPV. This data could serve as a foundation for the development of novel diagnostics and vaccines to combat BRPV, thereby mitigating its impact on both human and animal populations.