Improved reference genome of the arboviral vector Aedes albopictus

Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures

Detecting Mediterranean White Sharks with Environmental DNA

The white shark (Carcharodon carcharias) is a globally distributed, ecologically important top predator whose biology and population dynamics are challenging to study. Basic biological parameters remain virtually unknown in the Mediterranean Sea due to its historically low population density, dwindling population size, and lack of substantial sightings. White sharks are considered Critically Endangered in the Mediterranean Sea, and recent analyses suggest that the population has declined by 52% to 96% from historical levels in different Mediterranean sectors (Moro et al., 2020). Thus, white shark sightings dating back to 1860 are being used to estimate population trajectories throughout the entire region. Though the population size is unknown, remaining individuals are thought to be primarily restricted to a handful of hotspots deemed important for their reproduction and foraging. One of these hypothesized hotspots is the Sicilian Channel, which accounts for 19% of total historical sightings

sharkPulse Validation Monitor

Abundance and distribution data of global shark populations is necessary for effective conservation and management. While there are operative direct methods to retrieve such data from scientific surveys and fisheries monitoring, species specific indices of population abundance coming from these sources are rare for most shark species. Yet, there is an abundance of unconventional and unstructured information within social networks that is virtually untapped and has great potential to fill the information gap characterizing shark populations. Social networks such as Flickr and Instagram provide data wells of shark sightings that can be data mined, but must be validated as genuine sightings. Despite its modern surge in popularity, there is little research that implements social media for shark conservation. Here, we show the biological importance of creating an application within sharkPulse to facilitate speedy validation by involving citizen scientists. The Monitor allows users to search a world map for potential shark sightings and fill out forms for popup balloons of these sightings. If it is indeed a shark, they may answer 'yes' and fill out the associative taxonomic information if they are familiar with the common and/or species name. They may also consult a sharkPulse identification guide if they are not familiar. The application was built with RShiny App software. The Validation Monitor can be used by anyone interested in these charismatic group of animals. The application can be found at sharkpulse.cnre.vt.edu/can-you-recognize/.sharkPulseValidationFinalReport.pdf is a PDF version of the final report about our work, including a description of the application. A Word version is in sharkPulseValidationFinalReport.docx. sharkPulseValidationFinalPres.pdf is a PDF version of the final project presentation. A PowerPoint version is in sharkPulseValidationFinalPres.pptx. A video version is in sharkPulse.mp4. An image describing the Monitor is in sharkPulseValidationMonitor.PNG

Ecological Informatics

1. Suitable shark conservation depends on well-informed population assessments. Direct methods such as scientific surveys and fisheries monitoring are adequate for defining population statuses, but species-specific indices of abundance and distribution coming from these sources are rare for most shark species. We can rapidly fill these information gaps by boosting media-based remote monitoring efforts with machine learning and automation. 2. We created a database of 53,345 shark images covering 219 species of sharks and packaged object detection and image classification models into a Shark Detector bundle. We developed the Shark Detector to recognize and classify sharks from videos and images using transfer learning and convolutional neural networks (CNNs). We applied these models to common data-generation approaches of sharks: occurrence records from photographs or taken by the public or citizen scientists, processing baited remote camera footage and online videos, and data-mining Instagram. We examined the accuracy of each model and tested genus and species prediction correctness as a result of training data quantity. 3. The Shark Detector can classify 47 species. It located sharks in baited remote footage and YouTube videos with 89% accuracy, and classified located subjects to the species level with 69% accuracy. The Shark Detector sorted heterogeneous datasets of images sourced from Instagram with 91% accuracy and classified species with 70% accuracy. All data-generation methods were processed without manual interaction. 4. As media-based remote monitoring strives to dominate methods for observing sharks in nature, we developed an open-source Shark Detector to facilitate common identification applications. Prediction accuracy of the software pipeline increases as more images are added to the training dataset. We provide public access to the software on our GitHub page.Accepted versio

Detecting Mediterranean White Sharks with Environmental DNA

The white shark (Carcharodon carcharias) is a globally distributed, ecologically important top predator whose biology and population dynamics are challenging to study. Basic biological parameters remain virtually unknown in the Mediterranean Sea due to its historically low population density, dwindling population size, and lack of substantial sightings. White sharks are considered Critically Endangered in the Mediterranean Sea, and recent analyses suggest that the population has declined by 52% to 96% from historical levels in different Mediterranean sectors (Moro et al., 2020). Thus, white shark sightings dating back to 1860 are being used to estimate population trajectories throughout the entire region. Though the population size is unknown, remaining individuals are thought to be primarily restricted to a handful of hotspots deemed important for their reproduction and foraging. One of these hypothesized hotspots is the Sicilian Channel, which accounts for 19% of total historical sightings.</jats:p

Oceanography

The white shark (Carcharodon carcharias) is a globally distributed, ecologically important top predator whose biology and population dynamics are challenging to study. Basic biological parameters remain virtually unknown in the Mediterranean Sea due to its historically low population density, dwindling population size, and lack of substantial sightings. White sharks are considered Critically Endangered in the Mediterranean Sea, and recent analyses suggest that the population has declined by 52% to 96% from historical levels in different Mediterranean sectors (Moro et al., 2020). Thus, white shark sightings dating back to 1860 are being used to estimate population trajectories throughout the entire region. Though the population size is unknown, remaining individuals are thought to be primarily restricted to a handful of hotspots deemed important for their reproduction and foraging. One of these hypothesized hotspots is the Sicilian Channel, which accounts for 19% of total historical sightings.Published versio

Frontiers in Marine Science

The shortfin mako shark (Isurus oxyrinchus) is a highly mobile, coastal littoral, and epipelagic oceanic species broadly distributed in tropical, subtropical, and temperate seas worldwide (Rigby et al., 2019). In recent years, there has been growing recognition of the impacts of overfishing on shortfin mako populations, and the species is now listed as Endangered by the International Union for the Conservation of Nature (IUCN) (Rigby et al., 2019). The species is listed as Critically Endangered in the Mediterranean Sea due to long-term and continuing exploitation coupled with inadequate management (Walls and Soldo, 2016). Of particular concern is the ongoing capture of juvenile mako sharks in the Central Mediterranean and the Strait of Sicily, which have been identified as potential nursery areas (Walls and Soldo, 2016; Cattano et al., 2023; Mancusi et al., 2023). Even with significant declines in pelagic sharks regionally (Ferretti et al., 2008), sharks continue to be occasionally targeted in the Mediterranean Sea, though the most critical risk to shark populations in the region is bycatch in other fisheries (Bradai et al., 2018; Carpentieri et al., 2021). In the Mediterranean, most fishers typically retain their shark bycatch, with some estimates of shark discard rates as low as 1% (Megalofonou et al., 2005) even for protected species, though discard rates are likely to vary by season and gear (Carpentieri et al., 2021). Despite their imperiled status, shortfin mako sharks remain one of the region’s commonly encountered sharks for fishers, especially for longlines (Carpentieri et al., 2021), and sharks are typically retained despite falling under regional protections such as the Bern Convention, Bonn Convention, and Barcelona Convention (Serena et al., 2014). Of additional concern is the relatively unmonitored recreational fishery, which may additionally encounter high numbers of shortfin mako sharks, many of Frontiers in which are retained, but the scale of this fishery is not well known (Udovičić et al., 2019; Panayiotou et al., 2020). Concerningly, young-of-the-year (YOY) and juvenile specimens comprise the bulk of captured individuals reported in the Mediterranean (Saidi et al., 2019; Udovičić et al., 2019; Panayiotou et al., 2020; Cattano et al., 2023; Mancusi et al., 2023; Scacco et al., 2023). Given the life history of shortfin mako sharks, particularly their advanced age at maturity (Natanson et al., 2020), this frequent and ongoing capture of juvenile sharks represents a severe threat to regional populations, as many sharks will never reach maturity, let alone successfully reproduce. These losses highlight the need for more detailed information regarding the movement patterns and space use of juvenile shortfin mako sharks, for which little is known in the Mediterranean. In recent years, a proliferation of telemetry studies has drastically improved our understanding of themovements and space use of large marine predators like shortfin mako sharks around the globe (Queiroz et al., 2019); however, virtually no study has focused on Mediterranean populations, especially sharks. Here, we report the satellite track from a pop-off archival tag (PAT) deployed on a juvenile shortfin mako shark in the Mediterranean Sea in May 2023. To our knowledge, this track represents the first satellite tag deployed on a shortfin mako shark in the Mediterranean Sea. We describe the horizontal and vertical movements the study shark performed over 54 days at liberty (DAL), discussing potential drivers for the observed movements and the implications of the track for the conservation of shortfin mako sharks regionally.Published versio

SharkTrack: an accurate, generalisable software for streamlining shark and ray underwater video analysis

Elasmobranchs (shark sand rays) are critical components of coral reef ecosystems and are often considered indicators of reef health (Roff et al., 2016). Yet, they are experiencing global population declines and effective monitoring of these populations is essential to their protection. Underwater stationary videos, such as those from Baited Remote Underwater Video Stations (BRUVS), are critical for understanding elasmobranch spatial ecology and abundance. However, processing these videos requires time-consuming manual analysis. To address these challenges, we developed SharkTrack, a semi-automatic underwater video analysis software.SharkTrack uses Convolutional Neural Networks and Multi-Object Tracking to automatically detect and track elasmobranchs and provides an annotation pipeline to manually classify elasmobranch species and compute MaxN, the standard metric of relative abundance. We tested SharkTrack on BRUVS footage collected from threecoral reef locations unseen by the model during training, to demonstrate the model’sadaptability and effectiveness in different reef environments. SharkTrack computedMaxN with 89% accuracy over 207 hours of footage. The semi-automatic SharkTrackpipeline required two minutes of manual classification per hour of video, a 95%reduction of manual analysis time compared to traditional methods, estimated conservatively at 42 minutes per hour of video. These results suggest thatSharkTrack can be utilised to monitor elasmobranch populations across diverse coral reef ecosystems. Furthermore, the software’s flexible pipeline could serve as a blueprint for the development of species classifiers beyond elasmobranchs, enabling more comprehensive monitoring of coral reef biodiversity. We provide public access to SharkTrack, aiming to support future research in coral reef and marine conservation.Submitted versio

Improved reference genome of the arboviral vector Aedes albopictus

Abstract Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures. </jats:sec

Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

International audienc