MetaCompass: Reference-guided Assembly of Metagenomes.

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.

Plastic pollution transcends marine protected area boundaries in the eastern tropical and south-eastern Pacific.

The Eastern Tropical and South-Eastern Pacific region is of global biodiversity importance. At COP26, the governments of Costa Rica, Panama, Colombia, and Ecuador committed to the expansion of existing MPAs to create a new Mega MPA, safeguarding the Eastern Tropical Pacific Marine Corridor. It offers a profound step forward in conservation efforts but is not specifically designed to protect against the more diffuse anthropogenic threats, such as plastic pollution. We combine published data with our own unpublished records to assess the abundance and distribution of plastic pollution in the region. Macro- and microplastic concentrations varied markedly and were not significantly different when comparing areas inside and outside existing MPA boundaries. These findings highlight the diffuse and complex nature of plastic pollution and its ubiquitous presence across MPA boundaries. Understanding the sources and drivers of plastic pollution in the region is key to developing effective solutions.

Sea surface microplastics in the Galapagos: Grab samples reveal high concentrations of particles <200 µm in size.

Plastic pollution in the oceans is increasing, yet most global sea surface data is collected using plankton nets which limits our knowledge of the smaller and more bioaccessible size fraction of microplastics (<5 mm). We sampled the biodiverse coastal waters of the Galapagos Island of San Cristobal, comparing two different microplastic sampling methodologies; 1 l whole seawater grab samples filtered to 1.2 µm and sea surface plankton tows with a net mesh size of 200 µm. Our data reveal high concentrations of microplastics in Galapagos coastal waters surrounding the urban area, averaging 11.5 ± 1.48 particles l-1, with a four-order of magnitude increase in microplastic abundance observed using grab sampling compared with 200 µm plankton nets. This increase was greater when including anthropogenic cellulose particles, averaging 19.8 ± 1.86 particles l-1. Microplastic and anthropogenic cellulose particles smaller than 200 µm comprised 44 % of the particles from grab samples, suggesting previous estimates of microplastic pollution based on plankton nets likely miss and therefore underestimate these smaller particles. The particle characteristics and distribution of these smaller particles points strongly to a local input of cellulosic fibres in addition to the microplastic particles transported longer distances via the Humbolt current found across the surface seawater of the Galapagos. Improving our understanding of particle characteristics and distributions to highlight likely local sources will facilitate the development of local mitigation and management plans to reduce the input and impacts of microplastics to marine species, not just in the Galapagos but globally.

Microplastic burden in marine benthic invertebrates depends on species traits and feeding ecology within biogeographical provinces.

The microplastic body burden of marine animals is often assumed to reflect levels of environmental contamination, yet variations in feeding ecology and regional trait expression could also affect a species' risk of contaminant uptake. Here, we explore the global inventory of individual microplastic body burden for invertebrate species inhabiting marine sediments across 16 biogeographic provinces. We show that individual microplastic body burden in benthic invertebrates cannot be fully explained by absolute levels of microplastic contamination in the environment, because interspecific differences in behaviour and feeding ecology strongly determine microplastic uptake. Our analyses also indicate a degree of species-specific particle selectivity; likely associated with feeding biology. Highest microplastic burden occurs in the Yellow and Mediterranean Seas and, contrary to expectation, amongst omnivores, predators, and deposit feeders rather than suspension feeding species. Our findings highlight the inadequacy of microplastic uptake risk assessments based on inventories of environmental contamination alone, and the need to understand how species behaviour and trait expression covary with microplastic contamination.

Genetics of yellow-orange color variation in a pair of sympatric sulphur butterflies.

Continuous color polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits. Here we investigated continuous color variation in Colias eurytheme and Colias philodice, two species of sulphur butterflies that hybridize in sympatry. Using quantitative trait locus (QTL) analysis and high-throughput color quantification, we found two interacting large-effect loci affecting orange-to-yellow chromaticity. Knockouts of red Malpighian tubules (red), likely involved in endosomal maturation, result in depigmented wing scales. Additionally, the transcription factor bric-a-brac can act as a modulator of orange pigmentation. We also describe the QTL architecture of other continuously varying traits, together supporting a large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the range of possible genetic architectures that can underpin a continuously varying trait and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.

Evidence for a single, ancient origin of a genus-wide alternative life history strategy.

Understanding the evolutionary origins and factors maintaining alternative life history strategies (ALHS) within species is a major goal of evolutionary research. While alternative alleles causing discrete ALHS are expected to purge or fix over time, one-third of the ~90 species of Colias butterflies are polymorphic for a female-limited ALHS called Alba. Whether Alba arose once, evolved in parallel, or has been exchanged among taxa is currently unknown. Using comparative genome-wide association study (GWAS) and population genomic analyses, we placed the genetic basis of Alba in time-calibrated phylogenomic framework, revealing that Alba evolved once near the base of the genus and has been subsequently maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was then used to verify a putative cis-regulatory region of Alba, which we identified using phylogenetic foot printing. We hypothesize that this cis-regulatory region acts as a modular enhancer for the induction of the Alba ALHS, which has likely facilitated its long evolutionary persistence.

Uptake of microplastics by marine worms depends on feeding mode and particle shape but not exposure time.

The uptake of microplastics into marine species has been widely documented across trophic levels. Feeding mode is suggested as playing an important role in determining different contamination loads across species, but this theory is poorly supported with empirical evidence. Here we use the two distinct feeding modes of the benthic polychaete, Hediste diversicolor (The Harbour Ragworm) (O.F. Müller, 1776), to test the hypothesis that filter feeding will lead to a greater uptake of microplastic particles than deposit feeding. Worms were exposed to both polyamide microfragments and microfibres in either water (as filter feeders) or sediment (as deposit feeders) for 1 week. No effect of exposure time was found between 1 day and 1 week (p > 0.19) but feeding mode was found to significantly affect the number of microfibres recovered from each worm (p < 0.001). When exposed to microfibers, filter feeding worms took up ≈15,000 % more fibres than deposit feeding worms (p < 0.001), whereas when feeding on microfragments there was no difference between feeding modes. Our data demonstrate that both feeding mode and particle characteristics significantly influence the uptake of microplastics by H. diversicolor. Using imaging flow cytometry, filter feeders were found to take up a broader size range of particles, with significantly more smaller and larger particles than deposit feeders (p < 0.05), commensurate with the range of plastics isolated from the guts of ragworms recovered from the environment. These results demonstrate that biological traits are useful in understanding the uptake of plastics into marine worms and warrant further exploration as a tool for understanding the bioaccessibility of plastics to marine organisms.

Microplastic distribution and composition on two Galápagos island beaches, Ecuador: Verifying the use of citizen science derived data in long-term monitoring.

Monitoring beach plastic contamination across space and time is necessary for understanding its sources and ecological effects, and for guiding mitigation. This is logistically and financially challenging, especially for microplastics. Citizen science represents an option for sampling accessible sites to support long term monitoring, but challenges persist around data validation. Here we test a simple citizen science methodology to monitor visible microplastic contamination on sandy beaches using a standard quadrat unit (50 cm × 50 cm x 5 cm depth) sieved to 1 mm, to support the analysis of microplastic on two islands within the marine protected area of the Galápagos Archipelago, Ecuador (San Cristóbal and Santa Cruz islands). High school and university students undertook supervised sampling of two beaches in 2019-2020 collecting over 7000 particles. A sub-sample of the suspected microplastics collected (n = 2,213, ∼30% total) were analysed using FTIR spectrometry, confirming 93% of particles >1 mm visually identified by students were microplastics or rubber, validating this method as a crowd-sourced indicator for microplastic contamination. These data provide important insights into the plastic contamination of Galápagos, revealing plastic abundances of 0-2524 particles m-2 over the two beaches (the highest reported in Galápagos). Strong accumulation gradients were measured parallel to the waterline at Punta Pitt (San Cristobal island) and perpendicular to the waterline at Tortuga Bay (Santa Cruz island), where four-fold higher concentrations were recorded at the sea turtle nesting habitat on the back-beach dune. No significant seasonal trends were measured during one year. These results demonstrate the value of citizen science in filling spatiotemporal knowledge gaps of beach contamination to support intervention design and conservation.

Measuring quality of DNA sequence data via degradation.

We formulate and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the greater the effects of degradation. We demonstrate that this phenomenon is ubiquitous, and that quantified measures of degradation can be used for multiple purposes, illustrated by outlier detection. We focus on identifying outliers that may be problematic with respect to data quality, but might also be true anomalies or even attempts to subvert the database.

Ingestion of plastics by terrestrial small mammals.

The exposure of wildlife to waste plastic is widely recognised as an issue for aquatic ecosystems but very little is known about terrestrial systems. Here, we addressed the hypothesis that UK small mammals are ingesting plastics by examining faecal samples for the presence of plastic using micro Fourier Transform infrared microscopy. Plastic polymers were detected in four out of the seven species examined (European hedgehog (Erinaceus europaeus), wood mouse (Apodemus sylvaticus); field vole (Microtus agrestis); brown rat (Rattus norvegicus)). Ingestion occurred across species of differing dietary habits (herbivorous, insectivorous and omnivorous) and locations (urban versus non-urban). Densities excreted were comparable with those reported in human studies. The prevalence of confirmed plastics in the 261 faecal samples was 16.5 % (95 % CI 13 %, 22 %). Most (70 %) of the 60 plastic fragments were <1 mm (microplastics). Polyester, likely to be derived from textiles, accounted for 27 % of the fragments and was found in all plastic-positive species except for the wood mouse. The high prevalence of polyester in terrestrial ecosystems was unexpected and suggests that evaluation is needed of practices likely to transfer this plastic into the environment (such as sewage sludge application to farmland). Polynorbornene, which is likely to be derived from tyre wear, and polyethylene were also commonly detected polymers. 'Biodegradable' plastics formed 27 % (n = 12) of the particles found in wild mammal faeces, warranting further research to assess their persistence in the environment.

Uptake of microplastics by the snakelocks anemone (Anemonia viridis) is commonplace across environmental conditions.

Microplastics (<1 mm) are ubiquitous in our oceans and widely acknowledged as concerning contaminants due to the multi-faceted threats they exert on marine organisms and ecosystems. Anthozoans, including sea anemones and corals, are particularly at risk of microplastic uptake due to their proximity to the coastline, non-selective feeding mechanisms and sedentary nature. Here, the common snakelocks anemone (Anemonia viridis) was used to generate understanding of microplastic uptake in the relatively understudied Anthozoa class. A series of microplastic exposure and multi-stressor experiments were performed to examine particle shape and size selectivity, and to test for the influence of food availability and temperature on microplastic uptake. All A. viridis individuals were found to readily take up microplastics (mean 142.1 ± 83.4 particles per gram of tissue) but exhibited limited preference between different particle shapes and sizes (n = 32). Closer examination identified that uptake involved both ingestion and external tissue adhesion, where microplastics were trapped in secreted mucus. Microplastic uptake in A. viridis was not influenced by the presence of food or elevated water temperature (n = 40). Furthermore, environmental sampling was performed to investigate microplastic uptake in A. viridis (n = 8) on the coast of southwest England, with a mean of 17.5 ± 4.0 particles taken up per individual. Fibres represented the majority of particles (91%) followed by fragments (9%), with 87% either clear, blue or black in colour. FTIR analysis identified 70% of the particles as anthropogenic cellulosic or plastic polymers. Thus, this study provides evidence of microplastic uptake by A. viridis in both laboratory exposures experiments and in the marine environment. These findings support recent literature suggesting that external adhesion may be the primary mechanism in which anthozoans capture microplastics from the water column and highlights the potential role anemones can play as environmental microplastic bioindicators.

A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies.

Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern United States with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X (or large-Z) effect. Within this chromosome-wide reproductive barrier, linkage mapping indicates that cis-regulatory variation of bric a brac (bab) underlies the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knockout, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results highlight how a genetic switch can regulate a premating signal and integrate with other reproductive barriers during intermediate phases of speciation.

Specified Certainty Classification, with Application to Read Classification for Reference-Guided Metagenomic Assembly.

Specified Certainty Classification (SCC) classifiers whose outputs carry uncertainties, typically in the form of Bayesian posterior probabilities. By allowing the classifier output to be less precise than one of a set of atomic decisions, SCC allows all decisions to achieve a specified level of certainty, as well as provides insights into classifier behavior by examining all decisions that are possible. Our primary illustration is read classification for reference-guided genome assembly, but we demonstrate the breadth of SCC by also analyzing COVID-19 vaccination data.

Plastic contamination of a Galapagos Island (Ecuador) and the relative risks to native marine species.

Ecuador's Galapagos Islands and their unique biodiversity are a global conservation priority. We explored the presence, composition and environmental drivers of plastic contamination across the marine ecosystem at an island scale, investigated uptake in marine invertebrates and designed a systematic priority scoring analysis to identify the most vulnerable vertebrate species. Beach contamination varied by site (macroplastic 0-0.66 items·m-2, microplastics 0-448.8 particles·m-2 or 0-74.6 particles·kg-1), with high plastic accumulation on east-facing beaches that are influenced by the Humboldt Current. Local littering and waste management leakages accounted for just 2% of macroplastic. Microplastics (including anthropogenic cellulosics) were ubiquitous but in low concentrations in benthic sediments (6.7-86.7 particles·kg-1) and surface seawater (0.04-0.89 particles·m-3), with elevated concentrations in the harbour suggesting some local input. Microplastics were present in all seven marine invertebrate species examined, found in 52% of individuals (n = 123) confirming uptake of microplastics in the Galapagos marine food web. Priority scoring analysis combining species distribution information, IUCN Red List conservation status and literature evidence of harm from entanglement and ingestion of plastics in similar species identified 27 marine vertebrates in need of urgent, targeted monitoring and mitigation including pinnipeds, seabirds, turtles and sharks.

Oceanic Hitchhikers - Assessing Pathogen Risks from Marine Microplastic.

As plastic debris in the environment continues to increase, an emerging concern is the potential for microplastic to act as vectors for pathogen transport. With aquaculture the fastest growing food sector, and microplastic contamination of shellfish increasingly demonstrated, understanding any risk of pathogen transport associated with microplastic is important for this industry. However, there remains a lack of detailed, systematic studies assessing the interactions and potential impacts that the attachment of human and animal pathogens on microplastic may have. Here we synthesise current knowledge regarding these distinct microplastic-associated bacterial communities and microplastic uptake pathways into bivalves, and discuss whether they represent a human and animal health threat, highlighting the outstanding questions critical to our understanding of this potential risk to food safety.

Microplastic in the stomachs of open-ocean and deep-sea fishes of the North-East Atlantic.

The presence of microplastic in marine fishes has been well documented but few studies have directly examined differences between fishes occupying contrasting environmental compartments. In the present study, we investigated the gut contents of 390 fishes belonging to three pelagic (blue jack mackerel, chub mackerel, skipjack tuna) and two deep-sea species (blackbelly rosefish, blackspot seabream) from the Azores archipelago, North-East Atlantic for microplastic contamination. Our results revealed that pelagic species had significantly more microplastic than the deep-water species. In all of the species studied, fragments were the most common plastic shape recovered and we found a significant difference in the type of polymer between the pelagic and deep-water species. In deep-sea fish we found almost exclusively polypropylene, whereas in the pelagic fish, polyethylene was the most abundant polymer type. Overall, the proportion of fish containing plastic items varied across our study species from 3.7% to 16.7% of individuals sampled, and the average abundance of plastic items ranged from 0.04 to 0.22 per individual (the maximum was 4 items recovered in one stomach). Despite the proximity of the Azores archipelago to the North Atlantic subtropical gyre, a region of elevated plastic abundance, the proportion of individuals containing plastic (9.49%) were comparable with data reported elsewhere.

Role-Playing Computer Ethics: Designing and Evaluating the Privacy by Design (PbD) Simulation.

There is growing consensus that teaching computer ethics is important, but there is little consensus on how to do so. One unmet challenge is increasing the capacity of computing students to make decisions about the ethical challenges embedded in their technical work. This paper reports on the design, testing, and evaluation of an educational simulation to meet this challenge. The privacy by design simulation enables more relevant and effective computer ethics education by letting students experience and make decisions about common ethical challenges encountered in real-world work environments. This paper describes the process of incorporating empirical observations of ethical questions in computing into an online simulation and an in-person board game. We employed the Values at Play framework to transform empirical observations of design into a playable educational experience. First, we conducted qualitative research to discover when and how values levers-practices that encourage values discussions during technology development-occur during the design of new mobile applications. We then translated these findings into gameplay elements, including the goals, roles, and elements of surprise incorporated into a simulation. We ran the online simulation in five undergraduate computer and information science classes. Based on this experience, we created a more accessible board game, which we tested in two undergraduate classes and two professional workshops. We evaluated the effectiveness of both the online simulation and the board game using two methods: a pre/post-test of moral sensitivity based on the Defining Issues Test, and a questionnaire evaluating student experience. We found that converting real-world ethical challenges into a playable simulation increased student's reported interest in ethical issues in technology, and that students identified the role-playing activity as relevant to their technical coursework. This demonstrates that roleplaying can emphasize ethical decision-making as a relevant component of technical work.

The sea urchin Paracentrotus lividus as a bioeroder of plastic.

It is increasingly recognised that plastic pollution of the marine environment is highly dynamic in nature. Larger plastic items are fragmented or eroded into smaller and smaller pieces as its moves through marine ecosystems and small particles can be fouled or flocculate into larger aggregates. Whilst physical processes play a major part in photo- and oxidative degradation of plastic debris, biological process may also contribute to the breakdown of larger plastic items into smaller particulates, yet this has not been studied well to date. Here, we demonstrate the potential for the sea urchin Paracentrotus lividus to act as bioeroders of macroplastics. We found that urchins readily graze on a plastic surface, with this grazing activity generating microplastics, when held in experimental systems together. On average each urchin produced 91.7 (±33.8 pieces) smaller plastic pieces (118-15,797 µm) from one macroplastic item over a ten day period. This plastic fragmentation by the urchins grazing activity was strongly influenced by the additional availability of natural food and by the presence of fouling of the macroplastic surface. Fragmentation of macroplastic by urchins dropped by 97% when urchins were exposed to virgin plastic in the presence of natural food (kelp). However, when macroplastic was biofouled urchins acted to fragment this plastic irrespective of the presence of additional food. The majority of fragments produced were negatively buoyant due to both the biofouling process and indeed the fouling by faecal matter, sinking to the bottom of the exposure systems. This smaller size range of plastic would then bioavailable to a much wider suite of species than the original macroplastic item; hence this bioerosion process has the potential to contribute to the transfer plastic fragments through benthic food webs.

Particle characteristics of microplastics contaminating the mussel Mytilus edulis and their surrounding environments.

We investigated the environmental partitioning and particle characteristics of macro-, meso- and microplastics and their uptake into the mussel, Mytilus edulis. Sediment samples, overlying seawater and mussels from 9 intertidal locations in the South West of England were analysed for abundance and type of microplastic. Micro- and mesoplastic-like particles were found in 88.5% of the 269 mussels sampled, ranging from 1.43 to 7.64 items per mussel. Of these plastic particles, 70.9% were identified as semi-synthetic (mainly modified-cellulose). Mussel microplastic abundance, but not polymer type, was correlated with that of their surrounding sediment, but not with sea-surface microplastic concentration or mussel size for our study sites. We found significant differences in the relative abundance of polymer types and particle sizes between seawater, sediment, and mussels, with mussels over-representing modified-cellulose fibre abundance but under-representing polyvinyl. Mussels contained significantly smaller plastic fragments than their surrounding sediment and shorter fibres than their overlying seawater.

Lateral eyes direct principal eyes as jumping spiders track objects.

One way of circumventing the functional tradeoffs on eye design [1,2] is to have different eyes for different tasks. For example, jumping spiders (Salticidae), known for elaborate, visually guided courtship and predatory behavior [3], view the same object simultaneously with two of their four pairs of eyes: the antero-lateral eyes (ALEs) and the principal eyes (reviewed in [2]; Figure 1A). The ALEs, with immobile lenses and retinas, wide fields of view, and hyperacute sensitivity to moving stimuli [4], are structurally distinct from the principal eyes, which have the best spatial acuity known for terrestrial invertebrates and can discern fine details of stationary objects [5]. Behind the immobile corneal lenses of the principal eyes are miniature, boomerang-shaped retinas with correspondingly small fields of view (Figure 1B). The principal-eye visual fields are greatly expanded and overlap because of eye movements: these retinas are at the proximal ends of long, moveable tubes within the spider's cephalothorax [6]. By designing and using a specialized eyetracker, we tested whether principal-eye gaze direction is influenced by what the ALEs see. The principal eyes scanned stationary objects regardless of whether the ALEs were masked, but only when the ALEs were unmasked did the principal eyes smoothly track moving disks. The principal eyes, with high acuity but a narrow field of view, can thus precisely target moving stimuli, but only with the guidance of the secondary eyes.