ALBERT

Description: We used remote underwater stereo-video footage and AI driven object tracking to assess the functional foraging traits and movement trajectories of benthic herbivorous fishes on a degraded model coral reef. Sampling took place on the reef in front of the Inter-University Institute for Marine Sciences (IUI) (29°30'7.0"N, 34°55'3.7"E) in Eilat (Israel, Gulf of Aqaba) between 8th and 14th of March 2018. In preparation for the surveys, calibrated stereo-video setups, each consisting of 2 GoPro (4 x Hero 5 and 2 x Hero 4) cameras, were mounted on a total of 3 racks (Neuswanger et al. 2016, doi:10.1139/cjfas-2016-0010). For each sampling day, racks were sequentially installed at a depth of between 2 to 3 m and set to record continuously. Setting up the cameras was the sole purpose of a dive to minimize the disturbance caused to the site. Sites were chosen based on the criteria that a variety of grazable substratum (not just live coral) must be present, as there are a range of micro-habitats within the grazable substrate for fishes that require specific categorisation (Green & Bellwood, 2009, https://repository.library.noaa.gov/view/noaa/926). Therefore, sites with a heterogenous mixture of available benthic substrate cover such as live coral and epilithic algal turf (EAT) on standing dead coral, bare rocks, coral rubble and sand were generally preferred. Because grazing rates in surgeonfishes are highest during midday, the majority of our filming was; conducted between 11:00 – 15:00 (Montgomery et al. 1989 (doi:10.1016/0022-0981(89)90127-5); Fouda and El-Sayed 1994). The analysable video was accumulated from 15 rack placements and comprised 22.9 hrs of footage in total. At the beginning of each recording, we placed a 1 x 1 m PVC quadrat in front of the cameras. We quantified the substrate cover of each quadrat by taking a long shot photograph. These images were uploaded to the program SketchAndCalc Version 1.1.2 (iCalc Inc), in which the 1 x 1 m quadrat was calibrated so each transformed image contained roughly the same number of cells. This equated to ~1000 cells per image, each being around 5 cm². The images with the canvas imprinted upon them were subsequently exported and annotated with each form of substratum having a corresponding colour. Annotated cells were counted and relative substrate cover (in %) was calculated. We then proceeded to measure fish total length (mm), bite rate (bites per min), and the distance between each consecutive bite (bite distance, in mm) only within the delimited quadrat area during the entirety of the recorded video footage. In total, we recorded 2,386 bites by 23 different fish species (from 11 families). We calculated individual fish mass according to the following formula: mass = aTL^b, where a and b for each species were informed from FishBase (www.fishbase.org). The initial 15-min of each video, however, were discarded to allow for the fishes to resume normal behaviour after the quadrat was removed and divers left the site. To standardize against time, only the subsequent 45-min of recording were used for analysis of feeding traits in all species (https://doi.org/10.1594/PANGAEA.932686). Foraging traits in the three most common surgeonfishes were determined in the entirety of the recorded footage after the initial acclimation period (https://doi.org/10.1594/PANGAEA.957631). The time at which a single fish entered the quadrat to take bites from substrates until the time when it exited constituted a feeding event. For each feeding event, all bites were collated and then standardized to obtain bites per minute. Further, for each feeding event we averaged the distances between consecutive bites to obtain bite distance. We conducted all measurements in VidSync Version 1.661 (Neuswanger et al. 2016, doi:10.1139/cjfas-2016-0010). For the two surgeonfish species we calculated Manly's feeding ratios (Manly et al. 2002), which illustrate an individual's use of each substrate category (number of bites) in relation to the availability of substrate type across the entire reef. We achieved AI driven fish detection, identification and tracking from stereo-video by performing several steps. Firstly, we calibrated the system in Matlab (TheMathWorks) using a checkboard pattern recorded with both cameras. Next, we performed stereorectification using OpenCV (Open Source Computer Vision Library) to locate pixels in both images and triangulate the depth of the scene. Using this method of calibration we obtained an overall mean [±SD] absolute reprojection error of 0.9 [±1.9] mm which corresponds to 0.45% of the true value. For object detection, we employed the You Only Look Once (YOLO) convolutional neural network (CNN) (Bochkovskiy et al. 2020), which we retrained with background images from the recorded videos to improve its performance. We then used the bounding boxes produced by the detection algorithm as input data for the classifier and stereo matching. To classify the detected fish species, we utilized science-grade location invariant images of identified fish species from iNaturalist (www.inaturalist.org) to train the CNN (Van Horn et al. 2018, doi:10.1109/CVPR.2018.00914; Shepley et al. 2021, doi:10.1002/ece3.7344). However, the iNaturalist dataset had limited images, and therefore we employed transfer learning using weights computed from a previously recorded dataset from Mayotte as a starting point (Villon et al. 2018, doi:10.1016/j.ecoinf.2018.09.007). Finally, we implemented the Deep SORT framework - an enhanced version of the Simple Online and Realtime Tracking (SORT) algorithm - for multi-object tracking (Wojke et al. 2017, doi:10.48550/arXiv.1703.07402). This framework tracked each bounding box in both the left and right videos. Triangulation was performed to retrieve the 3D coordinates of the fish relative to the left camera, and we applied de-noising to remove any erroneous data points. Overall, our approach enabled reliable and automatic object detection and tracking from stereo-video, providing valuable data for studying the behaviour and ecology of the two focal species in their natural habitats. We extracted XYZ coordinates from a subgroup of 16 Acanthurus nigrofuscus and 23 Zebrasoma xanthurum individuals whose automatically measured lengths fell within the manually determined length frequency distribution. These individuals had automatically generated tracks that were precisely cut down to 700 frames, ensuring a standardized and consistent observation period.

Description: We sampled the archaeological and modern-day snapper otoliths used for this analysis from sites in the Hauraki Gulf, on the east coast of the North Island of New Zealand. Long Bay (AL) samples were radiocarbon dated using Bayesian modelling to between 1430-1485 AD, while the Omaha (AO) samples were dated to between 1530-1640 AD (Campbell et al. 2004, 2019). For comparison we acquired modern samples from as close as possible to the archaeological middens. Kawau Island (MO, 2016 AD) served as the modern comparison to the Omaha midden and outside of the current Long Bay marine reserve (ML, 2020 AD) provided samples to compare with the Long Bay midden. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis was conducted to measure Barium (138Ba) and Strontium (88Sr) compositions along an ablation path though the core to the proximal tip of each otolith. For each of the four sites, ten sagittal otoliths were transverse-sectioned and then mounted on a geological slide for laser ablation. Instrumentation was an Applied Spectroscopy RESOlution M-50 laser ablation system powered by a Coherent 193 nm ArF excimer laser and an Agilent 7900 quadrupole ICP-MS, located in the Centre for Trace Element Analysis in the Department of Chemistry, University of Otago (Dunedin, New Zealand). Slides with mounted otoliths were placed in an ablation cell in an atmosphere of pure helium to minimize any possibilities of experiencing re-condensation of ablated materials and elemental fractionations (Eggins et al. 1998). The video imaging system had suitable magnification to identify the core and was used for mapping transect pathways. Prior to obtaining measurements the 75 µm diameter transects were pre-ablated from core to the edge of the otolith to remove surface contaminants. The spot size employed for the transects was selected as a compromise between spatial sensitivity and detection power of the overall system (Taddese et al. 2019). The ablation with a laser firing frequency of 10 Hz and an on-sample fluence of 2.5 J/cm2 was operated along the pre-ablated transects with the sample stage moving at 10 µm/s, for determining elemental concentrations in correspondence to life cycle of the fish. The ICP-MS instrument was tuned to minimize oxide formation, double charge formation and mass fractionation. Signal intensities of Ba and Sr were maximized after carrying out gas tuning processes on software-controlled gas flows of He and N2 along with ICP-MS controlled Ar. Standards were run regularly with NIST610, NIST 612 and MACS3 used for instrument calibration, verification and matrix matched quality control respectively. Data reduction of the raw count data to molar ratios (element of interest/Ca) was conducted using Iolite 3.63 (School of Earth Sciences, University of Melbourne) which subtracts gas backgrounds and corrects for any drift in instrument response (Paton et al. 2011). Accuracy and precision of the analyses were assessed using NIST 612 and the MACS-3 otolith reference material (United States Geological Survey - USGS). For the glass control precision was excellent RSD 〈3% and the accuracy was within ± 5% for all elements. For the otolith reference material precision was better than 5% with recoveries percentages of 97% and 96% for Sr and Ba, respectively.

Description: In plants, the mechanism for ecological sympatric speciation (SS) is little known. Here, after ruling out the possibility of secondary contact, we show that wild emmer wheat, at the microclimatically divergent microsite of “Evolution Canyon” (EC), Mt. Carmel, Israel, underwent triple SS. Initially, it split following a bottleneck of an ancestral population, and further diversified to three isolated populations driven by disruptive ecological selection. Remarkably, two postzygotically isolated populations (SFS1 and SFS2) sympatrically branched within an area less than 30 m at the tropical hot and dry savannoid south-facing slope (SFS). A series of homozygous chromosomal rearrangements in the SFS1 population caused hybrid sterility with the SFS2 population. We demonstrate that these two populations developed divergent adaptive mechanisms against severe abiotic stresses on the tropical SFS. The SFS2 population evolved very early flowering, while the SFS1 population alternatively evolved a direct tolerance to irradiance by improved ROS scavenging activity that potentially accounts for its evolutionary fate with unstable chromosome status. Moreover, a third prezygotically isolated sympatric population adapted on the abutting temperate, humid, cool, and forested north-facing slope (NFS), separated by 250 m from the SFS wild emmer wheat populations. The NFS population evolved multiple resistant loci to fungal diseases, including powdery mildew and stripe rust. Our study illustrates how plants sympatrically adapt and speciate under disruptive ecological selection of abiotic and biotic stresses.

Description: Synthesis of liquid fuels (C5+hydrocarbons) via CO2hydrogenation is very promising. Hydrogenation of CO2to liquid hydrocarbons usually proceeds through tandem catalysis of reverse water gas shift (RWGS) reaction to produce CO, and subsequent CO hydrogenation to hydrocarbons via Fischer–Tropsch synthesis (FTS). CO2is a thermodynamically stable and chemically inert molecule, and RWGS reaction is endothermic and needs a higher temperature, whereas FTS reaction is exothermic and is thermodynamically favored at a lower temperature. Therefore, the reported technologies have some obvious drawbacks, such as high temperature, low selectivity, and use of complex catalysts. Herein we discovered that a simple Co6/MnOxnanocatalyst could efficiently catalyze CO2hydrogenation. The reaction proceeded at 200 °C, which is much lower than those reported so far. The selectivity of liquid hydrocarbon (C5to C26, mostlyn-paraffin) in total product could reach 53.2 C-mol%, which is among the highest reported to date. Interestingly, CO was hardly detectable during the reaction. The in situ Fourier transform infrared characterization and13CO labeling test confirmed that the reaction was not via CO, accounting for the eminent catalytic results. This report represents significant progress in CO2chemistry and CO2transformation.

Description: MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors that shape CD1 diversity remain unclear. In mice, two homologous genes, CD1D1 and CD1D2, encode the CD1d protein, which is essential to the development and function of natural killer T (NKT) cells. However, it remains unclear whether both CD1d isoforms are equivalent in their antigen presentation capacity and functions. Here, we report that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells. Intriguingly, the T cell antigen receptor repertoire and phenotype of CD1d2-selected type I NKT cells in CD1D1−/− mice differed from CD1d1-selected type I NKT cells. The structures of CD1d2 in complex with endogenous lipids and a truncated acyl-chain analog of α-galactosylceramide revealed that its A′-pocket was restricted in size compared with CD1d1. Accordingly, CD1d2 molecules could not present glycolipid antigens with long acyl chains efficiently, favoring the presentation of short acyl chain antigens. These results indicate that the two CD1d molecules present different sets of self-antigen(s) in the mouse thymus, thereby impacting the development of invariant NKT cells.