Remote Habitats Research Articles

Tree Longevity: Multifaceted Genetic Strategies and Beyond.

Old trees are remarkable for their ability to endure for centuries or even millennia, acting as recordkeepers of historical climate and custodians of genetic diversity. The secret to their longevity has long been a subject of fascination. Despite the challenges associated with studying old trees, such as massive size, slow growth rate, long lifespan and often remote habitat, accumulating studies have investigated the mechanisms underlying tree aging and longevity over the past decade. The recent publication of high-quality genomes of long-lived tree species, coupled with research on stem cell function and secondary metabolites in longevity, has brought us closer to unlocking the secrets of arboreal longevity. This review provides an overview of the global distribution of old trees and examines the environmental and anthropogenic factors that shape their presence. We summarize the contributions of physiological characteristics, stem cell activity, and immune system responses to their extraordinary longevity. We also explore the genetic and epigenetic 'longevity code', which consists of resistance and defense genes, DNA repair genes and patterns of DNA methylation modification. Further, we highlight key areas for future research that could enhance our understanding of the mechanisms underlying tree longevity.

Wildlife Tracker using Deep Learning

Wildlife tracker using deep learning is a project aimed at developing a system that can automatically detect wild animals using deep learning techniques. Conservationists and researchers face challenges in accurately and efficiently detecting and monitoring wildlife populations in vast and often remote habitats. Traditional methods of wildlife monitoring, such as manual surveys or camera traps, are labour-intensive, time-consuming, and may not provide real-time insights into population dynamics or threats facing wildlife species. The proposed system aims to address these challenges by developing an automated animal detection system using the YOLOv8 object detection model. The system will be trained on a diverse dataset of wildlife images, encompassing various species and environmental conditions. Upon deployment, the system will analyse input images and accurately identify and localize animals within the scene in real-time. Through this approach, the system will provide conservationists and researchers with timely and actionable information for monitoring wildlife populations, assessing habitat health, and implementing targeted conservation interventions. Evaluation of the system's performance will involve metrics such as detection accuracy, precision, recall, and processing speed, ensuring reliable and efficient wildlife detection capabilities. Overall, the proposed system seeks to enhance wildlife conservation efforts by leveraging advanced technology to improve wildlife monitoring and management practices and provide real-time alert.

Gastrointestinal parasites of Wolffsohn's viscacha (Chinchillidae: Lagidium wolffsohni), an endemic rodent species from the wild Patagonia.

Parasites are ubiquitous in wildlife populations and have a profound impact on population dynamics. Interest in parasites of wildlife has increased significantly in recent years, particularly in those with relevant conservation status. Patagonia is one of the wildest and remote areas of the world. The Wolffsohn's viscacha lives in a small mountainous area of Patagonia. Until now, little is known about the biology and ecology of this species. The aim of this research was to study the gastrointestinal parasite diversity in this rodent from a coprological survey. A total of 125 fecal samples from 25 colonies were examined. Each sample was rehydrated, homogenized, and analyzed using three parasitological techniques: spontaneous sedimentation, Mini-FLOTAC, and centrifugation-flotation in sucrose-saturated solution, followed by examination under optical microscopy. The samples, eggs, and oocysts of parasites were described, measured, and photographed. All colonies were positive for at least one parasite species. A total of 10 parasitic species were identified: Viscachataenia sp., possibly V. quadrata, Monoecocestus sp., an unidentified anoplocephalid, Heteroxynema sp., possibly H. (Cavioxyura) viscaciae, Helminthoxys sp., possibly H. effilatus, an unidentified strongylid-type egg, Trichuris sp., two morphologies of unidentified coccidians and Eimeria sp. This is the first exhaustive study of gastrointestinal parasites in L. wolffsohni and a large number of eggs and oocysts of parasites were found. Our results highlight the use of noninvasive techniques for the study of parasites of wildlife hosts; as in the case of this rodent with a remote habitat, which makes sampling difficult. The results of our study provide baseline information on gastrointestinal parasite infections in this species.

Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount

The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim of promoting the conservation and stewardship of these remote habitats. To efficiently evaluate fish biodiversity around a seamount, we compared environmental DNA (eDNA) methods using seawater and sponge samples against methods using imagery obtained with a remotely operated vehicle (ROV) and a free-fall deep-sea camera lander called the Edokko Mark I on the Takuyo-Daigo Seamount (153.0°E, 23.5°N) in the northwestern Pacific Ocean. We detected a total of 18 fish families by these methods. The fish fauna detected on the seamount included many families commonly found in deep-sea areas and were similar to the fish fauna of other seamounts located at similar latitudes in the northwestern Pacific. Significant differences in the patterns of detection of fish families between the eDNA and imaging methods is attributed to the differing powers of detection of some fish groups between methods (related to primer compatibility and fish size). For deep-sea fish, the difference in fish composition at the family level between seawater and sponge eDNA methods was not significant, but the difference between Edokko Mark I and ROV methods was significant; the latter difference is likely due to whether or not bait is used to attract fish. Although the eDNA workflow implemented here requires improvements, the use of eDNA and imaging methods in combination provided better insight into the biodiversity of deep-sea fishes in the deep-sea around a seamount, where our knowledge of the fish fauna has been extremely limited. Our recovery of eDNA from seawater and sponge samples around the seamount demonstrates the potential of these methods for facilitating environmental baseline surveys and impact assessments of mining activities to obtain results not previously possible with the use of visual methods only.

The Bee Gut Microbiota: Bridging Infective Agents Potential in the One Health Context.

The bee gut microbiota plays an important role in the services the bees pay to the environment, humans and animals. Alongside, gut-associated microorganisms are vehiculated between apparently remote habitats, promoting microbial heterogeneity of the visited microcosms and the transfer of the microbial genetic elements. To date, no metaproteomics studies dealing with the functional bee microbiota are available. Here, we employ a metaproteomics approach to explore a fraction of the bacterial, fungal, and unicellular parasites inhabiting the bee gut. The bacterial community portrays a dynamic composition, accounting for specimens of human and animal concern. Their functional features highlight the vehiculation of virulence and antimicrobial resistance traits. The fungal and unicellular parasite fractions include environment- and animal-related specimens, whose metabolic activities support the spatial spreading of functional features. Host proteome depicts the major bee physiological activities, supporting the metaproteomics strategy for the simultaneous study of multiple microbial specimens and their host-crosstalks. Altogether, the present study provides a better definition of the structure and function of the bee gut microbiota, highlighting its impact in a variety of strategies aimed at improving/overcoming several current hot topic issues such as antimicrobial resistance, environmental pollution and the promotion of environmental health.

Population trends in the vulnerable Grey-headed flying-fox, Pteropus poliocephalus; results from a long-term, range-wide study.

Monitoring is necessary for the management of any threatened species if its predicament and status are to improve. Monitoring establishes baseline data for tracking trends in distribution and abundance and is a key tool for informing threatened species management. Across much of the Old World, bats in the genus Pteropus (Pteropodidae, Chiroptera) face significant threats from habitat loss, conflict with humans, and hunting. Despite conflict with humans and their threatened status, few Pteropus are being monitored. Often, this is because of difficulties associated with their high mobility, large and easily disturbed aggregations, and their use of unknown or remote habitat. Here we describe 10 years of results from the National Flying-fox Monitoring Program (NFFMP) for the grey-headed flying-fox, (Pteropus poliocephalus) in Australia. Range-wide quarterly surveys were conducted over a three-day period since November 2012 using standardized methods appropriate to conditions encountered at each roost. For our analysis of the population and its trend, we used a state-space model to account for the ecology of the grey-headed flying-fox and the errors associated with the surveying process. Despite the general perception that the species is in decline, our raw data and the modelled population trend suggest the grey-headed flying-fox population has remained stable during the NFFMP period, with the range also stable. These results indicate that the species' extreme mobility and broad diet bestow it with a high level of resilience to various disturbance events. Long-term, range-wide studies such as this one, are crucial for understanding relatively long-lived and highly nomadic species such as the grey-headed flying-fox. The outcomes of this study highlight the need for such systematic population monitoring of all threatened Pteropus species.

Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large scale.

Despite optimistic predictions on the eventual end of COVID-19 (Coronavirus Disease 2019), caution is necessary regarding the emergence of new variants to sustain a positive outlook and effectively address any potential future outbreaks. However, ongoing efforts to track COVID-19 variants are concentrated in developed countries and unique social practices and remote habitats of indigenous peoples present additional challenges. By combining small-sized equipment that is easily accessible and inexpensive, we performed SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) whole genome sequencing and measured the sample-to-answer time and accuracy of this portable variant tracking tool. Our portable design determined the variant of SARS-CoV-2 in an infected individual within 9 hours and 15 minutes without external power or internet connection, surpassing the speed of previous portable tools. It took only 16 minutes to complete sequencing run, whole genome assembly, and lineage determination using a single standalone laptop. We then demonstrated the capability to produce 289 SARS-CoV-2 whole genome sequences in a single portable sequencing run, representing a significant improvement over an existing throughput of 96 sequences per run. We verified the accuracy of portable sequencing by comparison with two other independent sequencing methods. We showed that our high-throughput data consistently represented the circulating variants in Los Angeles, United States, when compared with publicly available sequences. Our scheme is designed to be flexible, rapid, and accurate, making it a valuable tool for large-scale surveillance operations in low- and middle-income countries as well as targeted surveys for vulnerable populations in remote locations.IMPORTANCEThere have been significant efforts to track COVID-19 (Coronavirus Disease 2019) variants, accumulating over 15 million SARS-CoV-2 sequences as of 2023. However, the distribution of global survey data is highly skewed, with nearly half of all countries having inadequate or low levels of genomic surveillance. In addition, indigenous peoples face more severe threats from COVID-19, due to their generally remote residence and unique social practices. Cost-effective portable sequencing tools have been used to investigate Ebola and Zika outbreaks. However, these tools have a sample-to-answer time of around 24 hours and require an internet connection for data transfer to an off-site cloud server. In our study, we rapidly determined COVID-19 variants using only small and inexpensive equipment, with a completion time of 9 hours and 15 minutes. Furthermore, we produced 289 near-full-length SARS-CoV-2 genome sequences from a single portable Nanopore sequencing run, representing a threefold increase in throughput compared with existing Nanopore sequencing methods.

Vocal signatures affected by population identity and environmental sound levels.

Passive acoustic monitoring has improved our understanding of vocalizing organisms in remote habitats and during all weather conditions. Many vocally active species are highly mobile, and their populations overlap. However, distinct vocalizations allow the tracking and discrimination of individuals or populations. Using signature whistles, the individually distinct calls of bottlenose dolphins, we calculated a minimum abundance of individuals, characterized and compared signature whistles from five locations, and determined reoccurrences of individuals throughout the Mid-Atlantic Bight and Chesapeake Bay, USA. We identified 1,888 signature whistles in which the duration, number of extrema, start, end, and minimum frequencies of signature whistles varied significantly by site. All characteristics of signature whistles were deemed important for determining from which site the whistle originated and due to the distinct signature whistle characteristics and lack of spatial mixing of the dolphins detected at the Offshore site, we suspect that these dolphins are of a different population than those at the Coastal and Bay sites. Signature whistles were also found to be shorter when sound levels were higher. Using only the passively recorded vocalizations of this marine top predator, we obtained information about its population and how it is affected by ambient sound levels, which will increase as offshore wind energy is developed. In this rapidly developing area, these calls offer critical management insights for this protected species.

Trans-equatorial migration links oceanic frontal habitats across the Pacific Ocean: year-round movements and foraging activity of a small gadfly petrel

Gadfly petrels are among the widest-ranging birds and inhabit oceanic regions beyond the legislative protection of national jurisdictions (the High Seas). Detailed information on breeding phenology, at-sea distributions, and habitat requirements is crucial for understanding threats and designing conservation measures for this highly threatened group. We tracked 10 Stejneger’s petrels Pterodroma longirostris, endemic to Isla Alejandro Selkirk, Juan Fernández Islands in the southeast Pacific Ocean, with geolocator-immersion loggers over two years to examine year-round movements, phenology, habitat use, and activity patterns. Birds conducted round-trip trans-equatorial migrations of 54,725 km to the northwest Pacific Ocean between Hawaii and Japan. Across the boreal summer, birds followed the c. 1000 km northward movement of the North Pacific Transition Zone Chlorophyll Front, before their return migration which took a long detour south toward New Zealand before heading east at 40–50°S, presumably benefitting from Antarctic circumpolar winds. To our knowledge, a comparable triangular migration is unique among seabirds. During the pre-laying exodus, birds traveled southwest to the Sub-Antarctic Front, and unlike congeners, there was no evidence of sexual segregation. Foraging areas during incubation were similar to pre-laying, with trips lasting 13 d and taking birds up to 4810 km southwest of the colony. Petrels spent > 75% of their time flying during breeding and migration, yet flight activity was substantially lower during non-breeding, presumably due to flight feather molt. Birds spent 87% of their time at sea within the High Seas and their apparent preference for oceanic frontal regions demonstrates the importance of protecting these remote habitats.

Taxonomic and functional diversity of subtidal benthic communities associated with hard substrates at Crozet archipelago (sub-Antarctic, Southern Ocean)

Sub-Antarctic coastal marine ecosystems harbor rich and diverse benthic communities. Despite their ecological uniqueness and vulnerability to global changes, studies on benthic communities remain limited. Using underwater video-imagery, we investigated the taxonomic and functional diversity of benthic communities associated with hard substrates at Baie du Marin (Ile de la Possession, Crozet archipelago). The Baie du Marin species richness and diversity were additively partitioned to evaluate spatial patterns of species through the following spatial scales: within images, among images within transects, and among transects. We analyzed imagery data from seven transects located at different sites inside Baie du Marin and covering contrasting natural rocky habitats and underwater artificial cable substrates. A total of 50 faunal (mainly represented by Echinodermata and Porifera phyla) and 14 algae (mainly represented by Rhodophyta phylum) taxa were identified. Rocky substrates were dominated by high densities of the polychaetes Parasabella sp. and Lanice marionensis, whereas submarine cables were dominated by high densities of the bivalve Kidderia sp. attached to macroalgae. Our results show contrasted distribution patterns in the faunal and algal assemblages within the Baie du Marin, with significant ecological differences between submarine cables and natural rocky substrates. Larger spatial scale (i.e., among transects) accounted for most of the bay richness and diversity, highlighting a high-level of habitat heterogeneity within the bay. Through a trait-based approach, our findings revealed that Crozet benthic communities are characterized by low functional richness, evenness, and redundancy, highlighting a potential vulnerability to current and future natural and anthropogenic changes. This study provides a novel bentho-ecological baseline for future assessments of natural and anthropogenic impacts on the marine environment of the Crozet archipelago; and for the conservation management of these remote habitats that make part of the French Southern Territories Marine Protected Area, recently inscribed on the UNESCO World Heritage list.

Dispersal and Distribution of Thermophilic Endospores in Deep-Sea Ecosystems

The distance-decay relationship is a central concept in biogeography and spatial biodiversity, describing how two distinct entities decrease in similarity as the distance between them increases. The decay of community similarity with geographical distance is driven by multiple factors, such as gene drift, environmental selection, and the accumulation of mutations over time. While the distance-decay relationship has been recognized for several decades, there are certain circumstances where the biogeographical patterns of certain species and communities cannot be predicted by this relationship. The example addressed in this project is the case of thermophilic endospore-forming bacteria found in permanently cold deep ocean sediments. Thermophilic endospores (thermospores) are routinely found on the deep ocean floor, a permanently cold environment that does not support their metabolic activity (Hubert et al. 2009). Thermospores are metabolically dormant states developed by some thermophilic bacteria having optimal growth temperatures between 40°C and 70°C. There is evidence that these heat-loving bacteria originate from the deep subsurface and are transported upward to the deep ocean via geological features of the oceanic crust including geofluid fluxes in high-temperature axial systems and natural hydrocarbon seeps (Gittins et al. 2022). Due to the ability of endospores to stay viable for thousands of years and resist a wide range of physicochemical stressors, they can disperse over long distances while remaining unaffected by changing factors such as selection, drift, or mutation (Gittins et al. 2022; Fig. 1). Consequently, these thermospores have the potential to challenge the distance-decay relationship and exhibit unique biogeographical patterns. This work quantifies endospores in sediment cores at and around hydrocarbon seeps using cores from deep-sea Scotian Slope sediments. Given the challenge of quantifying specific groups of endospores (e.g., thermophiles but not mesophiles), high-temperature germination assays that allow tracking of an exponential increase in signal as spores in marine sediment samples germinate and grow can be used. Distinct exponential increases can be attributed to different populations of germinated thermospores in the post-germination growth phase and are being monitored through measurements of sulfate reduction rates (using radiolabelled 35SO4), strain-specific quantitative PCR (qPCR), and fluorescence in-situ hybridization (FISH) (Rezende et al. 2017). These measurements revealed growth dynamics enabling an estimation of the initial cell numbers using exponential functions. These approaches are being applied to samples obtained via push coring using a remotely operated vehicle at different distances from deep sea hydrocarbon seeps, to test for the presence of abundance gradients of different thermospores. Current results already show a difference in thermospore abundance between sites at different distances from the seep. Quantitative tracking of the dispersal of thermospores by oceanic currents in the deep sea provides an excellent opportunity to investigate their distribution and potential to colonize more remote habitats, improving the understanding of microbial biodiversity and biogeography on our planet. By investigating thermospores and their interactions with the geophysical features of the deep sea and deep subsurface, this study aims to challenge the canonical idea that speciation occurs with distance and presents new perspectives on the theme of microbial biogeography. The evidence supporting the subsurface origin of thermophilic endospores, along with the proposed model for their dispersal and distribution, will contribute toward improving an integrated understanding of ecology and geology and their intersection in the microbial realm.

Morphological and Genetical Identification of <i>Harpacticella inopinata</i> Sars (Harpacticoida, Copepoda) from Lake Baikal and the Enisey River

The work presents the results of comparative studies of the morphology and genetics of the Baikal subendemic – the harpacticoid copepod Harpacticella inopinata Sars, 1908. The material was obtained from the southern part of Baikal Lake and the Yenisei River within the of Krasnoyarsk city in 1969, 2017–2022. It is shown that morphological variability within the species appeared most in the structure of the antenna exopodite, the number of pores and sensillas on the integument of thoracic somites. The genetic variation of the studied sample of H. inopinata was described by four clades with a distance between them of 0.26, the genetic distances between individuals within the detected genetic groups did not exceed 0.005. It was determined that H. inopinata from geographically remote habitats (Baikal Lake and Yenisei River) forms a single morphological and genetic group. Analysis of the genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei, probably associated with an anthropogenic moving into the river.

Acoustic recording complements camera traps for monitoring sensitive penguin populations

In the face of global biodiversity loss that threatens social–ecological sustainability, we must improve our knowledge of species' behaviours, life histories and populations. Enhanced understanding is especially critical for taxa like seabirds that live in remote habitats where monitoring is logistically challenging, and technology‐based approaches could lead to major advances. Considering conservation threats and breeding behaviours, penguins represent a promising taxon for further exploration of monitoring methods. Only five of 18 penguin species are currently considered species of Least Concern by the IUCN, and the sensitivity of penguins to ecological disturbances makes them important indicators of ecosystem dynamics. Penguins regularly congregate in dense breeding colonies and are visually and aurally conspicuous animals, making them relatively easy to monitor in some respects. In situ observations and visual remote sensing monitoring methods (i.e. camera traps, uncrewed aerial vehicles and satellite imagery) currently provide highly valuable information on penguin behaviour and population dynamics, but these methods have a number of shortcomings. Several rely on human presence in remote areas, some require clean lines of sight with no visual obstructions, and some offer limited spatial and temporal resolution. In this study we explore the use of passive acoustic monitoring (PAM) as a complementary remote sensing method to monitor penguin behaviour and populations at high spatial and temporal resolution without visual constraints or the need for continuous human presence. We conducted observations of vocalization rates and placed automated acoustic recorders in colonies of Magellanic Penguins Spheniscus magellanicus and Southern Rockhopper Penguins Eudyptes chrysocome in conjunction with camera traps. We found positive relationships between acoustic activity and counts of Magellanic Penguins in camera trap photos. We also identified clear diel patterns of acoustic activity that differed between breeding stages, and we found positive correlations between acoustic activity and estimates of colony density for various times of day and radii around recorders. While much work remains to improve this method and refine interpretation, PAM holds great promise as a complementary tool for monitoring the relative abundance and behavioural dynamics of penguins and other colonial animals, particularly those that burrow or nest in dense vegetation that impairs visual monitoring techniques.

Preliminary observations on the coral reef communities in Angria Bank, an isolated carbonate bank in the Northern Indian Ocean

Submerged carbonate banks are of significant geological and biological importance and relatively little is known about the biodiversity of these deeper and less accessible habitats. This study provides pilot information on the biodiversity and spatial distribution of the coral reef communities in Angria Bank, a submerged carbonate platform along the central west coast of India. An exploratory survey was carried out in January 2014 to document the habitat characteristics and biodiversity of different reef communities across a gradient from the western to the eastern edge of the Angria Bank. The western zone of the bank comprises rocky and coralline substrates in contrast to the eastern zone which is sandy with calcareous deposits. The overall biodiversity includes 16 genera of corals from 10 families and 82 species of reef fish from 26 families, comparatively lower than the other major reef formations in the Indian Ocean. The study sites between the depths of 25–29 m along the eastern edge of the bank host abundant and diverse coral communities. The macroalgae was equally abundant in three of the five dive sites along the east zone reflecting the homogeneous distribution of reef communities in the Angria bank. Other invertebrates including members of the phylum Porifera, Mollusca, Annelida, Arthropoda, Echinodermata, and Cnidaria account for 28 species. Angria Bank signifies a biodiversity hotspot and these remote habitats hold the potential to serve as a refugium for the shallow reef communities for a range of environmental disturbances. Further research to understand the effect of climate-associated stress on the reef communities of Angria bank is vital to evolve a conservation strategy to sustain the biodiversity and resilience of these communities.

First in-situ monitoring of sponge response and recovery to an industrial sedimentation event

Assessment of risks to seabed habitats from industrial activities is based on the resilience and potential for recovery. Increased sedimentation, a key impact of many offshore industries, results in burial and smothering of benthic organisms. Sponges are particularly vulnerable to increases in suspended and deposited sediment, but response and recovery have not been observed in-situ. We quantified the impact of sedimentation from offshore hydrocarbon drilling over ∼5 days on a lamellate demosponge, and its recovery in-situ over ∼40 days using hourly time-lapse photographs with measurements of backscatter (a proxy of suspended sediment) and current speed. Sediment accumulated on the sponge then cleared largely gradually but occasionally sharply, though it did not return to the initial state. This partial recovery likely involved a combination of active and passive removal. We discuss the use of in-situ observing, which is critical to monitoring impacts in remote habitats, and need for calibration to laboratory conditions.

Multi-taxa marine isoscapes provide insight into large-scale trophic dynamics in the North Pacific

Quantifying large scale trophic dynamics and interactions in marine systems remains a key challenge in ecological research and conservation, particularly in remote habitats which are difficult and costly to access. Stable isotope (SI) analysis has emerged as an effective tool for studying ecosystem interactions, especially when used to construct isotopic landscapes, or “isoscapes”. We used a combination of empirical SI data, global modeled phytoplankton isoscapes, and oceanographic data to investigate how large SI datasets might be harnessed to describe and predict patterns of regional food web dynamics and trophic structuring. We collated data from 99 published and author-contributed datasets of carbon and nitrogen SI data for open-ocean and neritic nektonic fish and invertebrates in the North Pacific Ocean to estimate mean SI values for successive trophic level groups within Longhurst biogeographic provinces. We found that these estimates reflected geographic patterns predicted by modeled phytoplankton isoscapes, suggesting that baseline SI ratios are consistently propagated up through regional food webs. This was further corroborated by significant correlations between our estimated SI values with the same oceanographic and geographic variables known to influence phytoplankton SI ratios. However, we observed variable amounts of isotopic offset between successive trophic level groups within and across provinces, indicating that the underlying drivers of trophic dynamics differ across regions. We found evidence of decreased isotopic differences between higher level trophic groups, suggesting the possibility of trophic compression and highlighting the importance of using taxa- and tissue-specific trophic discrimination factors (TDFs) when comparing or predicting consumer SI ratios. We used stable isotopic niche analyses to demonstrate that coupled use of δ13C and δ15N data increased capacity to differentiate province-specific consumer groups, particularly where adjacent provinces had similar ranges of values for a single SI. We also found that baseline isoscapes may be a viable tool for predicting broad trends of consumer SI ratios by calculating ‘predicted’ δ13C and δ15N values for successive trophic groups across provinces using modeled phytoplankton data and diet-dependent discrimination factors. These predicted values were significantly correlated with our estimates based on empirical data, with similarity of predicted δ13C values increasing for higher trophic level groups. We conclude that regional SI patterns remain consistent across diverse ecosystems. With increased spatiotemporal resolution of SI data across ocean basins and increased availability of species-specific life history traits and physiologies, multi-taxa isoscapes hold great potential for studying large scale marine trophodynamics and movement patterns of highly mobile marine species.

A cautionary tale comparing spatial count and partial identity models for estimating densities of threatened and unmarked populations

Population monitoring is critical to wildlife conservation, but density estimation is difficult for wide-ranging, unmarked species inhabiting remote habitats. Furthermore, recent investigations into density estimation with camera trap data has revealed unmarked models to be potentially unreliable, prompting cautious application and continued model development. Two related approaches with increasing appeal include spatial count (SC), which infer latent identities from the spatial pattern of detections, and spatial partial identity models (SPIM), which additionally leverage partial identity covariates (e.g., sex, antler point count, and presence of GPS/radio collar). To assess the performance of unmarked density models, we applied SC and SPIM to camera trap data of threatened boreal caribou in Canada, which are declining but have few rigorous density estimates across their broad distribution to inform conservation efforts. In particular, we focused on two spatially proximate caribou ranges in northern Alberta, Canada that differ in estimated caribou demographic trends, disturbance histories, and abundances of caribou predators and apparent competitors. Estimates of caribou density varied over a 4 year period (2016 – 2019), and were higher in the region with more stable reported growth rates and less anthropogenic disturbance (mode SPIM estimates: 155 – 225/1000 km 2 vs. 19 – 96/1000 km 2 ). However, density estimates differed by modeling approach and had low and variable precision, hindering inferences about population status and trajectories. Simulations suggest that SPIM estimates may have been less biased and more precise. SC models likely underestimated density by mistaking detections of neighboring individuals as recaptures of a single individual, although SPIM may also have overestimated density by inflating assignment probabilities of detections to non-existent individuals. Findings highlight the need to explore how grouping dynamics and non-independent movement violate assumptions and reduce the ability to distinguish individuals. We advocate continued investigation into the accuracy of unmarked density estimation approaches, the ecological and sampling conditions appropriate for different unmarked density models, and coordination across sampling efforts and analyses to improve population inferences.

An automated work-flow for pinniped surveys: A new tool for monitoring population dynamics

Detecting changes in population trends depends on the accuracy of estimated mean population growth rates and thus the quality of input data. However, monitoring wildlife populations poses economic and logistic challenges especially in complex and remote habitats. Declines in wildlife populations can remain undetected for years unless effective monitoring techniques are developed, guiding appropriate management actions. We developed an automated survey workflow using unmanned aerial vehicles (drones) to quantify the number and size of individual animals, using the well-studied Scandinavian harbour seal (Phoca vitulina) as a model species. We compared ground-based counts using telescopes with manual flights, using a zoom photo/video, and pre-programmed flights producing orthomosaic photo maps. We used machine learning to identify and count both pups and older seals and we present a new method for measuring body size automatically. We evaluate the population’s reproductive success using drone data, historical counts and predictions from a Leslie matrix population model. The most accurate and time-efficient results were achieved by performing pre-programmed flights where individual seals are identified by machine learning and their body sizes are measured automatically. The accuracy of the machine learning detector was 95–97% and the classification error was 4.6 ± 2.9 for pups and 3.1 ± 2.1 for older seals during good light conditions. There was a clear distinction between the body sizes of pups and older seals during breeding time. We estimated 320 pups in the breeding season 2021 with the drone, which is well beyond the expected number, based on historical data on pup production. The new high quality data from the drone survey confirms earlier indications of a deteriorating reproductive rate in this important harbour seal colony. We show that aerial drones and machine learning are powerful tools for monitoring wildlife in inaccessible areas which can be used to assess annual recruitment and seasonal variations in body condition.

Active management fosters species richness of wild bees in limestone quarries

Open and unreclaimed quarries often host species-rich plant and animal communities. However, the specific factors that determine biodiversity in such anthropogenic habitats are largely unknown. This applies in particular to diverse groups of insects. We therefore studied bee assemblages of 16 limestone quarries, eight active and eight abandoned ones, in a Central European landscape with a long history of quarrying. We analysed the influence of macroclimate, landscape quality and habitat quality on overall species richness as well as on the number of threatened and oligolectic species. Our study revealed strong differences in habitat quality and composition of bee assemblages between active and abandoned quarries. Active quarries were larger, had more different pollen sources and a higher cover of early but a lower cover of later successional stages than abandoned quarries. As a result, species richness of bees was higher in active compared to abandoned quarries. Additionally, active quarries were characterized by a unique bee assemblage consisting of several indicator species. Availability of pollen sources and nesting habitats predicted bee species richness in the quarries. Overall, habitat quality and composition of bee assemblages were strongly dependent on quarry management. Active mining continuously created early-successional stages rich in pollen sources and sunlit nesting habitats, favouring species richness of bees in general and of threatened and oligolectic species in particular. Successional speed is generally low in quarries. Nevertheless, in abandoned quarries, later successional stages increasingly dominated due to ongoing succession and, hence, habitat quality and species richness of bees decreased. Considering this, we propose to expand existing quarries rather than build new ones. From a conservation point of view, this approach has several advantages: (i) existing quarries are often already refuges for colonies of rare species; (ii) many species of conservation concern have a low mobility and are therefore unable to occupy remote habitats and (iii) in the impoverished modern-day landscapes, source population that may colonize new quarries are often lacking.

Evaluating environmental DNA metabarcoding as a survey tool for unionid mussel assessments

Abstract Freshwater unionid mussels are a taxa‐rich group of bivalves that play a critical role in maintaining freshwater ecosystems, but are heavily imperilled due to anthropogenic influences. Environmental DNA (eDNA) provides potential benefits for the monitoring of unionids through higher detection sensitivity, lower costs, less intrusion on the environment, and added advantages for sampling challenging and remote habitats. We compare an extensive mussel rescue survey conducted as part of the demolition of a dam with the detection of mussels using eDNA metabarcoding. The unique mussel rescue survey provided a rare opportunity for an in‐depth analysis of unionid eDNA detection across both small sampling cells and a large sampling region. Environmental DNA detected 22 of the 24 (91.67%) species sampled in the rescue survey, with the two absent species found as only single individuals. A species missed by the rescue survey was detected with eDNA (Potamilus alatus), along with hidden cryptic diversity within the genus Pyganodon. Both survey methods detected the presence of two federally listed species from multiple sampling cells (Plethobasus cyphyus and Theliderma cylindrica). Furthermore, eDNA provided similar estimates of relative mussel abundances across the sampling region. Estimates of mussel diversity were similar between the two methods, and eDNA successfully detected the two federally listed species present. These results contribute to the growing knowledge of eDNA‐based biological assessments and provide valuable insight into comparing sampling effort and detection rates from conventional and eDNA survey methods. As eDNA collection can widen the traditional sampling season and improve the ability to sample difficult or dangerous environments, these results demonstrate the practicality of eDNA metabarcoding as a supplemental sampling method to describe diverse mussel communities and improve the detection of threatened and endangered species.