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Plant materials and genome sequencingFresh leaves of a wild P. koreana plant in the Changbai Mountains of Jilin province in China were collected, and the total genomic DNA was extracted using the CTAB method. For the Illumina short-read sequencing, paired-end libraries with insert sizes of 350 bp were constructed and sequenced using an Illumina HiSeq X Ten platform. For the long-read sequencing, the genomic libraries with 20-kbp insertions were constructed and sequenced using the PromethION platform of Oxford Nanopore Technologies (ONT). For the Hi-C experiment, approximately 3 g of fresh young leaves of the same P. koreana accession was ground to powder in liquid nitrogen. A sequencing library was then constructed by chromatin extraction and digestion, DNA ligation, purification, and fragmentation53 and was subsequently sequenced on an Illumina HiSeq X Ten platform.Genome assembly and scaffoldingThe quality-controlled reads were first corrected via a self-align method using the NextCorrect module in the software NextDenovo v2.0-beta.1 (https://github.com/Nextomics/NextDenovo) with parameters “reads_cutoff=1k (filter reads with length 20, percent of unqualified bases More

Ground-truth surveys of seagrass habitatTo obtain georeferenced field data on benthic cover levels from habitats of the Bahama Banks, we employed two similar, in-water survey and image approaches: (1) swimmer-based photo-transects; and (2) tow board photo transects (Supplementary Fig. 6), resulting in a total of 2542 surveys.For (1), free-divers swam over the bottom of the seafloor at a fixed height with a digital camera (Canon 5D mIV, GoPro Hero) set to capture images manually. Photographs were captured using automatic settings in a 1.0 m × 1.0 m footprint, 1.5 m above the seafloor following [39]. A center console vessel was used to run the transects at distances of 5–7 km, whereby the free-diver would capture successive photos at a horizontal distance of between 400–800 m, and the location was logged using either a handheld GPS (Garmin GPS 73) or a boat-mounted GPS with a depth sounder (Garmin EchoMap DV). Transect locations were chosen based on a priori local expert knowledge of varying benthic cover in the region. Surveyed areas included: southern New Providence (24.948862°, −77.387834°), southeast of New Providence (24.980265°, −77.229168°), south of Rose Island (25.066268°, −77.160063°), the middle Great Bahama Bank (24.735355°, −77.212998°), and the northern Exumas (24.729973°, −76.889488°). For (2), snorkeling observers were pulled from a research vessel on tow boards affixed with underwater action cameras (GoPro Hero 3+) traveling at ~1 m/s. The start and end of a tow were delineated with either a handheld GPS (Garmin eTrex 30) or a boat mounted GPS with depth-finder (Garmin EchoMap DV), and tows proceeded in a straight line recorded by the GPS. Cameras recorded images at 0.5 Hz throughout the tow, starting in conjunction with creating a waypoint. Samples (i.e., paired image and geolocated point) were sub-selected from the tow once movement began, at the midpoint of a tow, and immediately before movement stopped. Images were manually quality controlled such that if a selected image contained obstructions or was out of focus, the nearest clear image was selected to replace it. If no images within 10 s were clear (i.e., 10 m maximum spatial error), the sample was discarded. If the GPS track contained gaps or segments larger than 10 m, only images/point pairs at the start and end waypoints were sampled.Surveys focused on historical fishing grounds for queen conch (Lobatus gigas) between 2015 and 2018 following the sampling design and methods of ref. 32. A stratified random design was used to allocate 6000 m2 of observation effort into each cell of a 1’ by 1’ grid placed over each fishing ground. This effort was split into multiple tows between 200 and 1000 m in length, thus images were separated by at least 100 m.Fishing grounds extended from the edge of a deepwater sound to between 7 and 10 km up the bank and were limited to the depths used by freediving fishers. Surveyed fishing grounds included: the Exumas (24.382207°, −76.631058°), the southwestern Berry Islands (25.455529°, −78.014214°), south of Bimini (25.375592°, −79.187609°), the Grassy Cays (23.666864°, −77.383547°), the Joulter Cays (25.321297°, −78.109251°) and the southeast tip of the Tongue of the Ocean (23.376417°, −76.621943°). For details on image processing, see section on remote sensing below.Sediment coringTo gather the sediment cores analyzed for organic carbon content on the Bahama Banks, we collected samples from various benthic habitats that included varying densities of seagrass habitat (Thalassia testidinum and Syringodium filiforme). We percussed, via SCUBA, an acrylic cylinder tube perpendicular to the seafloor into marine sediment until rejection at various penetration depths up to 30 cm. The sample was then extracted vertically from the marine sediment and capped at the bottom to avoid loss of material. This sample was then transported vertically through the water column to a research vessel where it was removed from the coring device and immediately capped on top with an air-tight cap. Compression rates were negligible (~5 cm) across the first 5 cores, and as such were not subsequently measured. The samples were then labeled, photographed, geotagged, and the first 30 centimeters of each core was extruded. To complete the extrusion process, we placed each sample on top of a capped piston device in the same orientation as collection (deepest portion of collected sediment still on the bottom). The bottom cap was removed to thread the acrylic cylinder tube onto the piston device and then was lowered to various measured lengths to collect corresponding depth sections of the sediment core. These sections were sliced (every 1–5 centimeters), labeled, and placed into whirl pack bags to collect the wet weight of each sample. All samples were then frozen and stored for future laboratory analyses. All samples were dried in a laboratory oven at 55 °C for 48 h until constant dry weights were reached. The samples were then weighed to collect their corresponding dry weights. The dry bulk density (DBD) was calculated by diving the sample dry weight (g) by the sample volume (cm3). The samples were then further ground with a mortar and pestle until a homogeneous fine grain size was achieved. Sediment samples collected from the Exuma Cays (142 samples from 16 cores) were analyzed for Corg content. Sediment samples were weighed accurately into silver capsules and acidified with 4% HCl until no effervescence was detected in two consecutive cycles. The samples were then dried in a 60 °C oven overnight, encapsulated into tin capsules and analyzed using an Organic Elemental Analyzer Flash 2000 (Thermo Fisher Scientific, Massachusetts, USA). We then conducted a standard loss on ignition (LOI) methodology at our laboratory facility (Braintree, Massachusetts, USA) for all the samples. Each sample was subsequently sub sampled with 5–15 grams of representative material and placed into a ceramic crucible to collect its mass. The crucibles were then loaded into a separate muffle laboratory oven and heated at 550 °C for 6 h. Upon completion of this muffle, the crucibles were then immediately weighed to collect the LOI of organic material from each sample, defined as the weight lost in the muffle (g) divided by the subsample dry weight (g). A fitted regression between the Corg and LOI from the Exuma Cays cores was generated (Supplementary Fig. 7), and then used to predict the sediment Corg contents from LOI measurements in the Grand Bahama cores. Sediment Corg stocks were quantified by multiplying Corg and DBD data by soil depth increment (1–5 cm) of the sampled soil cores. The cores from the Exuma Cays (15 cm) and Grand Bahama (30 cm) were collected with different depths, we therefore fitted a regression between Corg stock in 15 cm-depth and Corg stock in 30 cm-depth for the Grand Bahama cores (Supplementary Fig. 8) and used this regression to extrapolate Corg stock of the Exuma Cays cores into 30 cm-depth. Moreover, to allow direct comparison among other studies27, the Corg stock per unit area was standardized to 1 m-thick deposits by multiplying 100/30.Tiger shark taggingThe research and protocols conducted in this study complies with relevant ethical regulations as approved by the Carleton University Animal Care Committee. The shark data used in this paper were collected as part of a multi-year, long-term research program evaluating the interannual behavior and physiology of large sharks throughout the coastal waters of The Commonwealth of The Bahamas23. All sharks were captured using standardized circle-hook drumlines33 on the Great and Little Bahama Banks throughout the country, focusing efforts in three primary locations: off New Providence Island, the Exuma Cays, and off West End, Grand Bahama, from 2011–2019. All sharks were secured alongside center console research vessels and local dive boats, where their sex, morphometric measurements, and blood samples were taken. A mark-recapture identification tag was applied to the shark at the base of the dorsal fin. Some of the sharks sampled in the present study were also tagged with a coded acoustic transmitter which was surgically implanted ventrally into the peritoneal cavity and then sutured, as part of a concurrent study on shark habitat use and residency within the region23.Pop-off archival satellite tags were affixed to eight tiger sharks (seven female, one male; 298 ± 28 cm total length; mean ± SD) in The Bahamas from 2011–2019, permitting measurements of swimming depth and water temperature recorded at either 4-min (Sea-Tag MODS, Desert Star Systems LCC, USA) or 10-s intervals (miniPAT tags, Wildlife Computers, USA). Pop-off satellite tags were inserted into the dorsal musculature of the sharks using stainless steel anchors and tethers. All pop-off satellite tags were either recovered manually, permitting access to the full time-series, or popped-off and transmitted their data to an Earth-orbiting Argos satellite, resulting in a subset of the full time-series (transmission frequencies: 2.5 min [miniPAT], 10 min [PSATGEO], daily average [Sea-Tag MOD]). Tiger shark positions were estimated from the satellite data using tag-specific proprietary state space algorithms from Wildlife Computers (GPE3; based on ref. 34) and Desert Star Systems35. With miniPAT tags, positions were further filtered to remove the least reliable positions ( More

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The success of biological control agents — organisms used to reduce the success of other, usually non-native invasive species — is complicated by ongoing climate change. Chosen for their host-specificity and introduced into new locations, biological agents can succumb to both direct and indirect climate-related stressors, compromising their biology and activity against target organisms. Adding to this is the fact that environmental stressors often occur in concert, making it hard to predict the efficacy of biological control programs. More

Lerato Shikwambana from the South African National Space Agency and the University of the Witwatersrand, South Africa, and colleagues also from South Africa compared the wildfire emissions of a strong El Niño event in 2015–2016 and a pronounced La Niña event in 2010–2011. They find that both a strong El Niño and La Niña event can increase emissions from wildfires compared with average years, but they affect different regions, with the effect of La Niña reaching farther south than El Niño. Overall, emissions are stronger during the El Niño phase, mainly driven by higher air temperatures. ENSO variability is expected to increase with future warming, which would also make strong El Niño events more likely. Therefore, these findings indicate that the exposure to wildfire air pollution could grow in southern Africa. More