PeerJ

Journal: PeerJ

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PeerJ

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PeerJ

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2167-8359

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Publications1 - 10 of 29

Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms
Priest, Taylor; Orellana, Luis H.; Huettel, Bruno; et al. (2021)
PeerJ
The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2–3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.
Multimodal system for recording individual-level behaviors in songbird groups
Rüttimann, Linus; Wang, Yuhang; Rychen, Jörg; et al. (2025)
PeerJ
The implicit goal of longitudinal observations of animal groups is to identify individuals and to reliably detect their behaviors, including their vocalizations. Yet, to segment fast behaviors and to extract individual vocalizations from sound mixtures remain challenging problems. Promising approaches are systems that record behaviors with multiple cameras, microphones, and animal-borne wireless sensors. Good systems extract from such multimodal signals perfectly synchronized data streams. In this vein, we designed a modular system (BirdPark) for simultaneously recording small animals wearing custom low-power frequency-modulated radio transmitters. Our custom software-defined radio receiver makes use of a multi-antenna demodulation technique that eliminates data losses due to radio signal fading and that increases the signal-to-noise ratio of the received radio signals by 6.5 dB compared to demodulation from the best single-antenna. Digital acquisition of all data streams relies on a single clock, which offers accurate cross-modal redundancies that can be used to dissect rapid behaviors on time scales well below the video frame period. We demonstrate this feat by reconstructing the wing-stroke phases of free-flying songbirds and by separating the vocalizations among up to eight vocally interacting birds. In conclusion, our work paves the way for automatically dissecting complex social behaviors.
Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
Rollin, Johan; Bester, Rachelle; Brostaux, Yves; et al. (2023)
PeerJ
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
Goats favour personal over social information in an experimental foraging task
Baciadonna, Luigi; McElligott, Alan G.; Briefer, Elodie F. (2013)
PeerJ
Animals can use their environments more efficiently by selecting particular sources of information (personal or social), according to specific situations. Group-living animals may benefit from gaining information based on the behaviour of other individuals. Indeed, social information is assumed to be faster and less costly to use than personal information, thus increasing foraging efficiency. However, when food sources change seasonally or are randomly distributed, individual information may become more reliable than social information. The aim of this study was to test the use of conflicting personal versus social information in goats (Capra hircus), in a foraging task. We found that goats relied more on personal than social information, when both types of information were available and in conflict. No effect of social rank was found on the occasions when goats followed other demonstrator goats. Goats are selective browsers/grazers and therefore relying on personal rather than social information could be the most efficient way to find patchily distributed resources in highly variable environments. Studies testing specific assumptions regarding the use of different sources of information can extend our understanding of decision making, including observed patterns of social learning.
Adaptive Metropolis-coupled MCMC for BEAST 2
Müller, Nicola F.; Bouckaert, Remco R. (2020)
PeerJ
With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Metropolis-coupled Markov chain Monte Carlo (MCMC) has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Metropolis-coupled MCMC essentially runs multiple MCMC chains in parallel. All chains are heated except for one cold chain that explores the posterior probability space like a regular MCMC chain. This heating allows chains to make bigger jumps in phylogenetic state space. The heated chains can then be used to propose new states for other chains, including the cold chain. One of the practical challenges using this approach, is to find optimal temperatures of the heated chains to efficiently explore state spaces. We here provide an adaptive Metropolis-coupled MCMC scheme to Bayesian phylogenetics, where the temperature difference between heated chains is automatically tuned to achieve a target acceptance probability of states being exchanged between individual chains. We first show the validity of this approach by comparing inferences of adaptive Metropolis-coupled MCMC to MCMC on several datasets. We then explore where Metropolis-coupled MCMC provides benefits over MCMC. We implemented this adaptive Metropolis-coupled MCMC approach as an open source package licenced under GPL 3.0 to the Bayesian phylogenetics software BEAST 2, available from https://github.com/nicfel/CoupledMCMC.
Short-termed changes in quantitative ultrasound estimated bone density among young men in an 18-weeks follow-up during their basic training for the Swiss Armed Forces
Strässle, Michael; Grossmann, Jonas; Eppenberger, Patrick; et al. (2023)
PeerJ
Background: Quantitative Ultrasound (QUS) methods have been widely used to assess estimated bone density. This study aimed to assess changes in estimated bone density in association with changes in body composition, physical activity, and anthropometry. Methods: We examined changes in anthropometry, body composition, and physical activity associated with changes in estimated bone mineral density (measured using quantitative ultrasound with a heel ultrasound device indicating broadband ultrasound attenuation BUA and speed of sound SOS) in a follow-up sample of n = 73 young men at the beginning and again 18 weeks later at the end of basic military training. Results: At the end of the basic training, the subjects were on average significantly heavier (+1.0%), slightly taller (+0.5%) and had a higher fat mass (+6.6%) and grip strength (+8.6%). A significant decrease in mean physical activity (−49.5%) and mean estimated bone density calculated with BUA (−7.5%) was observed in the paired t-test. The results of the multivariable linear regressions (backward selection) show that changes in skeletal muscle mass (delta = 2nd measurement minus 1st measurement) have negative and body weight (delta) have positive association with the speed of sound SOS (delta), while fat mass (delta) and physical activity (delta) had the strongest negative associations with estimated bone mineral density (delta). In particular, we found a negative association between fat mass (delta) and estimated bone mineral density (delta, estimated with BUA). Conclusion: Our study suggests that estimated bone density from the calcaneus can change within a few months even in young and mostly healthy individuals, depending upon physical activity levels and other co-factors. Further studies including other troop types as control groups as well as on women should follow in order to investigate this public health relevant topic in more depth. To what extent the estimated bone density measurement with quantitative ultrasound is clinically relevant needs to be investigated in further studies.
Geo-referencing bird-window collisions for targeted mitigation
Winton, R. Scott; Ocampo-Peñuela, Natalia; Cagle, Nicolette (2018)
PeerJ
Bird collisions with windows are an important conservation concern. Efficient mitigation efforts should prioritize retrofitting sections of glass exhibiting the highest mortality of birds. Most collision studies, however, record location meta-data at a spatial scale too coarse (i.e., compass direction of facing façade) to be useful for large buildings with complex geometries. Through spatial analysis of three seasons of survey data at a large building at a university campus, we found that GPS data were able to identify collision hotspots while compass directions could not. To demonstrate the broad applicability and utility of this georeferencing approach, we identified collision hotspots at two additional urban areas in North America. The data for this latter exercise were collected via the citizen science database, iNaturalist, which we review for its potential to generate the georeferenced data necessary for directing building retrofits and mitigating a major source of anthropogenic bird mortality.
A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia
Romilio, Anthony; Hacker, Jorg M.; Zlot, Robert; et al. (2017)
PeerJ
The abundant dinosaurian tracksites of the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia, form an important part of the West Kimberley National Heritage Place. Previous attempts to document these tracksites using traditional mapping techniques (e.g., surface overlays, transects and gridlines combined with conventional photography) have been hindered by the non-trivial challenges associated with working in this area, including, but not limited to: (1) the remoteness of many of the tracksites; (2) the occurrence of the majority of the tracksites in the intertidal zone; (3) the size and complexity of many of the tracksites, with some extending over several square kilometres. Using the historically significant and well-known dinosaurian tracksites at Minyirr (Gantheaume Point), we show how these issues can be overcome through the use of an integrated array of remote sensing tools. A combination of high-resolution aerial photography with both manned and unmanned aircraft, airborne and handheld high-resolution lidar imaging and handheld photography enabled the collection of large amounts of digital data from which 3D models of the tracksites at varying resolutions were constructed. The acquired data encompasses a very broad scale, from the sub-millimetre level that details individual tracks, to the multiple-kilometre level, which encompasses discontinuous tracksite exposures and large swathes of coastline. The former are useful for detailed ichnological work, while the latter are being employed to better understand the stratigraphic and temporal relationship between tracksites in a broader geological and palaeoecological context. These approaches and the data they can generate now provide a means through which digital conservation and temporal monitoring of the Dampier Peninsula’s dinosaurian tracksites can occur. As plans for the on-going management of the tracks in this area progress, analysis of the 3D data and 3D visualization will also likely provide an important means through which the broader public can experience these spectacular National Heritage listed landscapes.
Assigning confidence scores to homoeologs using fuzzy logic
Glover, Natasha M.; Altenhoff, Adrian; Dessimoz, Christophe (2019)
PeerJ
n polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna
Aguirre-Fernández, Gabriel; Jost, Jürg; Hilfiker, Sarah (2022)
PeerJ
The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins)OMMassemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale.

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