Quantitative fatty acid signature analysis reveals a high level of dietary specialization in killer whales across the North Atlantic

Quantifying the diet composition of apex marine predators such as killer whales (Orcinus orca) is critical to assessing their food web impacts. Yet, with few exceptions, the feeding ecology of these apex predators remains poorly understood. Here, we use our newly validated quantitative fatty acid signature analysis (QFASA) approach on nearly 200 killer whales and over 900 potential prey to model their diets across the 5000 km span of the North Atlantic. Diet estimates show that killer whales mainly consume other whales in the western North Atlantic (Canadian Arctic, Eastern Canada), seals in the mid-North Atlantic (Greenland), and fish in the eastern North Atlantic (Iceland, Faroe Islands, Norway). Nonetheless, diet estimates also varied widely among individuals within most regions. This level of inter-individual feeding variation should be considered for future ecological studies focusing on killer whales in the North Atlantic and other oceans. These estimates reveal remarkable population- and individual-level variation in the trophic ecology of these killer whales, which can help to assess how their predation impacts community and ecosystem dynamics in changing North Atlantic marine ecosystems. This new approach provides researchers with an invaluable tool to study the feeding ecology of oceanic top predators

Quantitative Trait Locus (QTL) Mapping Reveals a Role for Unstudied Genes in Aspergillus Virulence

Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL) affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91). We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP) spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7–24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as “hypothetical”. This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="manipulative_experiment.csv">manipulative_experiment.csv</a> (MD5: 28379fc1321dc2e9d53d3cdefac130a0)</p> <p><a href="mensurative_study.csv">mensurative_study.csv</a> (MD5: 9715ac8059fddc7856d7990d66cffcd3)</p> </div><h2>Description</h2><div> <p> Our data set describes the abundance of seaweeds and invertebrates found in rocky intertidal habitats on the Atlantic coast of Nova Scotia, Canada. One subset of data resulted from a manipulative experiment that tested the effects of macroalgal ecosystem engineers (<i>Ascophyllum nodosum</i> and <i>Fucus</i> spp.) on the richness, diversity, and composition of understory communities along the environmental stress gradient that occurs across elevations because of tides. Abundance data for all understory taxa are provided for 120 quadrats that characterized two macroalgal canopy treatments (canopy vs. no canopy) and three elevation zones (high, middle, and low). Another subset of data resulted from a mensurative study done regionally based on four locations spanning 350 km of coastline. Data from that study describe the abundance of seaweeds (including the canopy-forming species mentioned above) and invertebrates found at three elevation zones (high, middle, and low) for a total of 1170 quadrats. Both the manipulative experiment and the mensurative study revealed that intertidal macroalgal canopies affect the structure of benthic communities at high and middle elevations (where the canopies ameliorate the otherwise harsh conditions during low tides) but have no effects at low elevations (where conditions remain mild during low tides due to short aerial exposures). Because of its taxonomic amplitude and coverage of a wide environmental stress gradient, our data set is potentially useful to address in novel or infrequent ways other broad ecological issues, such as abundance–occupancy relationships, species co-occurrence, species abundance distributions, dominance and rarity, spatial scales of population and community variability, and distribution of phylogenetic diversity. </p> <p> <i>Key words</i>: <i> abundance; alga; canopy; ecosystem engineer; environmental stress gradient; intertidal; invertebrate; rocky shore; seaweed; species distribution.</i> </p> </div

Species richness and diversity in different functional groups across environmental stress gradients:A model for marine rocky shores

We present a model predicting how the species richness and diversity within benthic functional groups should vary across the full environmental stress gradient across which a regional biota from marine rocky shores can occur. Built upon previous models, our model makes predictions for sessile species (macroalgae and filter feeders), herbivores, and carnivores. We tested some of its predictions by surveying vertical (intertidal elevation) and horizontal (wave exposure and ice scour) stress gradients in northern Nova Scotia, Canada. Because of harsh winter conditions, these coasts only depict approximately intermediate-to-high yearly levels of stress that the cold-temperate, rocky intertidal biota from the northwestern Atlantic can experience. The observed trends matched predictions for sessile species in 75% of the studied gradients, and showed a moderate agreement for herbivores and carnivores only when they were combined as mobile consumers. Agreement meant that both richness and diversity increased from the most stressful to the most benign habitats that can be found in northern Nova Scotia. Also as predicted, sessile species generally showed a faster rate of increase in richness than mobile consumers. Our model also predicted a higher overall richness for sessile species than for mobile consumers, which was true by a factor of 3. Therefore, our model may constitute a useful tool to understanding community composition as a function of abiotic stress, which may in turn facilitate studies on community functioning. Model predictions for lower stress ranges could be tested on more southern shores where the same regional biota occurs

Species richness and diversity in different functional groups across environmental stress gradients: A model for marine rocky shores

We present a model predicting how the species richness and diversity within benthic functional groups should vary across the full environmental stress gradient across which a regional biota from marine rocky shores can occur. Built upon previous models, our model makes predictions for sessile species (macroalgae and filter feeders), herbivores, and carnivores. We tested some of its predictions by surveying vertical (intertidal elevation) and horizontal (wave exposure and ice scour) stress gradients in northern Nova Scotia, Canada. Because of harsh winter conditions, these coasts only depict approximately intermediate-to-high yearly levels of stress that the cold-temperate, rocky intertidal biota from the northwestern Atlantic can experience. The observed trends matched predictions for sessile species in 75% of the studied gradients, and showed a moderate agreement for herbivores and carnivores only when they were combined as mobile consumers. Agreement meant that both richness and diversity increased from the most stressful to the most benign habitats that can be found in northern Nova Scotia. Also as predicted, sessile species generally showed a faster rate of increase in richness than mobile consumers. Our model also predicted a higher overall richness for sessile species than for mobile consumers, which was true by a factor of 3. Therefore, our model may constitute a useful tool to understanding community composition as a function of abiotic stress, which may in turn facilitate studies on community functioning. Model predictions for lower stress ranges could be tested on more southern shores where the same regional biota occurs

DataSheet_1_Use of satellite imagery to estimate distribution and abundance of Cumberland Sound beluga whales reveals frequent use of a glacial river estuary.docx

Limiting disturbance in critical habitats is an important part of ensuring the well-being and sustainability of populations at risk, such as Cumberland Sound beluga whales (Delphinapterus leucas). Using non-disruptive Very High Resolution (VHR) satellite imagery, an emerging tool in cetacean monitoring, we aimed to estimate summer abundance and identify critical habitat for Cumberland Sound beluga whales. Specifically we looked in fiords that comprise their summer distribution, such as Clearwater Fiord where there is a large estuary, an important habitat to many beluga populations. Satellite images of the area were collected in 2020 and 2021, at 30 cm resolution, and in 2022 at 50 cm resolution. We evaluated beluga whale distribution using Kernel density, and identified critical habitats as areas consistently part of the beluga whale core distribution across years. Clearwater Fiord abundance estimates were corrected for whales that were too deep to be identified in the images. The estimates were significantly lower in 2021 (197 whales, 95%CI: 180-216) and 2022 (194 whales, 95%CI: 172-218) compared to 2020 (393 whales, 95%CI: 366-422). Other fiords were only imaged in 2021 and 2022, resulting in average corrected abundance estimates for all fiords of 462 (95% CI: 425-502) and 252 (95%CI: 226-280) beluga whales, respectively. Downsampling of 30 cm images to 50 cm resulted in up to 45% fewer whales detected. The only critical habitat identified within the summer distribution was in Clearwater Fiord, in or near the estuary freshwater plume and in a bay to the west of the plume. The identified critical habitats should be areas of consideration in the continued discussion on the protection and sustainability of the Cumberland Sound beluga whale population.</p

Estimating abundance of Eastern Canada-West Greenland bowhead whales using genetic mark-recapture analyses

The Eastern Canada-West Greenland (EC-WG) bowhead whale (Balaena mysticetus) population is widely distributed across the eastern Canadian Arctic and across Baffin Bay to the western coast of Greenland. Their vast distribution makes obtaining population estimates via aerial surveys difficult, as coverage over their entire range is not possible. Genetic mark recapture analyses address this issue, as biopsy samples can be collected at various locales across the EC-WG bowhead whale population’s distribution and microsatellites can be analyzed to identify unique individuals. EC-WG bowhead whales were subject to intense commercial whaling pressure between the early 1700 s and early 1900 s, after which a moratorium on commercial whaling was put in place in 1915. We used available genetic samples from EC-WG bowhead whales in mark recapture models to estimate population abundance from 2012 to 2021 to gain insight on population dynamics ∼100 years post commercial whaling. The preferred model, using a Jolly-Seber structure, estimated the total abundance as 5173 individuals (CI: 3436–7788). Since the cessation of commercial whaling, the population has been thought to be rebounding, which is reflected by gradually increasing abundance estimates, from the low hundreds in the 1970 s and 1980 s, to ∼6000 in the early 2000 s, but our present estimate suggests population abundance may be plateauing well below the pre-commercial whaling carrying capacity estimate. This population estimate for EC-WG bowhead whales is required to update the population dynamics for conservation efforts

Reproductive Parameters for Female Beluga Whales (Delphinapterus leucas) of Baffin Bay and Hudson Bay, Canada

Monitoring marine mammal populations and their habitats is crucial for assessing population status and&nbsp;defining realistic management and conservation goals. Environmental and anthropogenic changes in the Arctic have prompted the pursuit for improved understanding of female beluga whale (Delphinapterus leucas) spatial and temporal reproductive patterns. There are relatively few estimates for female reproductive parameters of beluga whale populations across the Arctic, and those few that are available are outdated. Here we summarize female reproductive data from samples collected through Inuit subsistence hunts of three eastern Canadian Arctic beluga populations: High Arctic/Baffin Bay (HA), Western Hudson Bay (HB), and Cumberland Sound (CS) from 1989 to 2014. We grouped the CS and HA populations into a Baffin Bay region (BB) population based on similar body growth patterns and genetic similarity. Asymptotic body length of BB beluga whales (370.9 cm) was greater than HB whales (354.4 cm) as established from Gompertz growth curves fitted for whales ranging in age from 1 – 89 y. We did not detect a significant difference in average number of pseudocervices (8.6) between regions. Differences in average age of sexual maturity (ASM) and length at sexual maturity (LSM) were identified, with evidence of BB females maturing earlier than females from HB (probability method BB = 9.9 y versus HB = 11.0 and logistic method ASM50% HB = 9.99 and BB unresolved). BB females were also longer than HB females at maturing age (logistic LSM50%: BB = 314.5 cm vs HB = 290.3). Total corpora counts were strongly correlated with age, although the number of corpora (≥ 10 mm) suggests reproductive senescence between 40 and 50 y. Improved understanding of female reproductive patterns and knowledge of changes in the spatial and temporal timing of reproductive processes are fundamental for effective conservation&nbsp;and sustainable management of beluga whale populations.La surveillance des populations de mammifères marins et de leurs habitats joue un rôle crucial dans l’évaluation&nbsp;de l’état d’une population ainsi que dans la formulation d’objectifs réalistes en matière de gestion et de conservation. Dans l’Arctique, les changements environnementaux et anthropiques incitent à mieux comprendre les tendances spatiales et temporelles de reproduction du béluga femelle (Delphinapterus leucas). Il existe relativement peu d’estimations des paramètres de reproduction des femelles au sein des populations de bélugas de l’Arctique, et celles qui existent ne sont plus à jour. Nous résumons ici les données de reproduction des femelles en fonction d’échantillons recueillis à partir des chasses de subsistance d’Inuits parmi trois populations de bélugas de l’est de l’Arctique canadien : Extrême-Arctique et baie de Baffin (HA), ouest de la baie d’Hudson (HB) et détroit de Cumberland (CS), de 1989 à 2014. Nous avons regroupé les populations de CS et de HA dans une population de la région de la baie de Baffin (BB) en fonction de tendances de croissance corporelle semblables et de similarité génétique. La longueur corporelle asymptotique des bélugas de BB (370,9 cm) était plus grande que celle des baleines de HB (354,4 cm), ainsi déterminée à l’aide des courbes de croissance de Gompertz adaptées aux baleines, dont l’âge varie de un an à 89 ans. Nous n’avons pas détecté de différence importante dans le nombre moyen de « pseudo-cols de l’utérus » (8,6) entre les régions. Des différences dans l’âge moyen de la maturité sexuelle (ASM) et dans la longueur à la maturité sexuelle (LSM) ont été décelées, avec preuve que les femelles de BB arrivaient plus vite à maturité que les femelles de HB (méthode de probabilité de BB = 9,9 ans par opposition à HB = 11,0 et une méthode de logistique d’ASM50% HB = 9,99 et de BB non résolue). Par ailleurs, les femelles de BB étaient plus longues que les femelles de HB à l’âge de la maturité (logistique LSM50% : BB = 314,5 cm par opposition à HB = 290,3). Le nombre total de corps jaunes était fortement corrélé à l’âge, bien que le nombre de corps jaunes (≥ 10 mm) suggère une sénescence reproductive variant entre 40 et 50 ans. Une meilleure compréhension des tendances de reproduction des femelles et de meilleures connaissances des changements spatiaux et temporels des processus de reproduction revêtent une importance fondamentale pour la conservation efficace et la&nbsp;gestion durable des populations de bélugas

Scaling whale monitoring using deep learning: A human-in-the-loop solution for analyzing aerial datasets

To ensure effective cetacean management and conservation policies, it is necessary to collect and rigorously analyze data about these populations. Remote sensing allows the acquisition of images over large observation areas, but due to the lack of reliable automatic analysis techniques, biologists usually analyze all images by hand. In this paper, we propose a human-in-the-loop approach to couple the power of deep learning-based automation with the expertise of biologists to develop a reliable artificial intelligence assisted annotation tool for cetacean monitoring. We tested this approach to analyze a dataset of 5334 aerial images acquired in 2017 by Fisheries and Oceans Canada to monitor belugas (Delphinapterus leucas) from the threatened Cumberland Sound population in Clearwater Fjord, Canada. First, we used a test subset of photographs to compare predictions obtained by the fine-tuned model to manual annotations made by three observers, expert marine mammal biologists. With only 100 annotated images for training, the model obtained between 90% and 91.4% mutual agreement with the three observers, exceeding the minimum inter-observer agreement of 88.6% obtained between the experts themselves. Second, this model was applied to the full dataset. The predictions were then verified by an observer and compared to annotations made completely manually and independently by another observer. The annotating observer and the human-in-the-loop pipeline detected 4051 belugas in common, out of a total of 4572 detections for the observer and 4298 for our pipeline. This experiment shows that the proposed human-in-the-loop approach is suitable for processing novel aerial datasets for beluga counting and can be used to scale cetacean monitoring. It also highlights that human observers, even experienced ones, have varied detection bias, underlining the need to discuss standardization of annotation protocols