• Environmental impacts of the deep-water oil and gas industry: a review to guide management strategies

      Cordes, EE; Jones, DOB; Schlacher, TA; Amon, Diva; Bernardino, AF; Brooke, S; Carney, R; DeLeo, DM; Dunlop, KM; Escobar-Briones, EG; et al. (Frontiers, 2016-09-16)
      The industrialization of the deep sea is expanding worldwide. Increasing oil and gas exploration activities in the absence of sufficient baseline data in deep-sea ecosystems has made environmental management challenging. Here, we review the types of activities that are associated with global offshore oil and gas development in water depths over 200 m, the typical impacts of these activities, some of the more extreme impacts of accidental oil and gas releases, and the current state of management in the major regions of offshore industrial activity including 18 exclusive economic zones. Direct impacts of infrastructure installation, including sediment resuspension and burial by seafloor anchors and pipelines, are typically restricted to a radius of ~100 m on from the installation on the seafloor. Discharges of water-based and low-toxicity oil-based drilling muds and produced water can extend over 2 km, while the ecological impacts at the population and community levels on the seafloor are most commonly on the order of 200–300 m from their source. These impacts may persist in the deep sea for many years and likely longer for its more fragile ecosystems, such as cold-water corals. This synthesis of information provides the basis for a series of recommendations for the management of offshore oil and gas development. An effective management strategy, aimed at minimizing risk of significant environmental harm, will typically encompass regulations of the activity itself (e.g., discharge practices, materials used), combined with spatial (e.g., avoidance rules and marine protected areas), and temporal measures (e.g., restricted activities during peak reproductive periods). Spatial management measures that encompass representatives of all of the regional deep-sea community types is important in this context. Implementation of these management strategies should consider minimum buffer zones to displace industrial activity beyond the range of typical impacts: at least 2 km from any discharge points and surface infrastructure and 200 m from seafloor infrastructure with no expected discharges. Although managing natural resources is, arguably, more challenging in deep-water environments, inclusion of these proven conservation tools contributes to robust environmental management strategies for oil and gas extraction in the deep sea.
    • Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments

      Fenton, IS; Pearson, PN; Dunkley Jones, T; Purvis, A; Gillikin, DP (2016-11-16)
    • Epidemiological Interactions between Urogenital and Intestinal Human Schistosomiasis in the Context of Praziquantel Treatment across Three West African Countries

      Knowles, SCL; Webster, BL; Garba, A; Sacko, M; Diaw, OT; Fenwick, A; Rollinson, D; Webster, JP; Raso, G (2015-10-15)
    • Erratum to: Development of novel multiplex microsatellite polymerase chain reactions to enable high-throughput population genetic studies of Schistosoma haematobium

      Webster, BL; Rabone, M; Pennance, T; Emery, AM; Allan, F; Gouvras, A; Knopp, S; Garba, A; Hamidou, AA; Mohammed, KA; et al. (2015-12)
    • Estimating crime scene temperatures from nearby meteorological station data

      Hofer, IMJ; Hart, AJ; Martín-Vega, D; Hall, MJR (Elsevier BV, 2019-10-30)
      The importance of temperature data in minimum postmortem interval (minPMI) estimations in criminal investigations is well known. To maximise the accuracy of minPMI estimations, it is imperative to investigate the different components involved in temperature modelling, such as the duration of temperature data logger placement at the crime scene and choice of nearest weather station to compare the crime scene data to. Currently, there is no standardised practice on how long to leave the temperature data logger at the crime scene and the effects of varying logger duration are little known. The choice of the nearest weather station is usually made based on availability and accessibility of data from weather stations in the crime scene vicinity. However, there are no guidelines on what to look for to maximise the comparability of weather station and crime scene temperatures. Linear regression analysis of scene data with data from weather stations with varying time intervals, distances, altitudes and microclimates showed the greatest goodness of fit (R2), i.e. the highest compatibility between datasets, after 4–10 days. However, there was no significant improvement in estimation of crime scene temperatures beyond a 5-day regression period. The smaller the distance between scene and weather station and the higher the similarity in environment, such as altitude and geographical area, resulted in greater compatibility between datasets. Overall, the study demonstrated the complexity of choosing the most comparable weather station to the crime scene, especially because of a high variation in seasonal temperature and numerous influencing factors such as geographical location, urban ‘heat island effect’ and microclimates. Despite subtle differences, for both urban and rural areas an optimal data fit was generally reached after about five consecutive days within a radius of up to 30 km of the ‘crime scene’. With increasing distance and differing altitudes, a lower overall data fit was observed, and a diminishing increase in R2 values was reached after 4–10 consecutive days. These results demonstrate the need for caution regarding distances and climate differences when using weather station data for retrospective regression analyses for estimating temperatures at crime scenes. However, the estimates of scene temperatures from regression analysis were better than simply using the temperatures from the nearest weather station. This study provides recommendations for data logging duration of operation, and a baseline for further research into producing standard guidelines for increasing the accuracy of minPMI estimations and, ultimately, greater robustness of forensic entomology evidence in court.
    • Eutrophication erodes inter-basin variation in macrophytes and co-occurring invertebrates in a shallow lake: combining ecology and palaeoecology

      Salgado, J; Sayer, CD; Brooks, SJ; Davidson, TA; Okamura, B (Springer, 2017-03-13)
      Aquatic biodiversity is commonly linked with environmental variation in lake networks, but less is known about how local factors may influence within-lake biological heterogeneity. Using a combined ecological and multi-proxy palaeoecological approach we investigated long-term changes in the pathways and processes that underlie eutrophication and water depth effects on lake macrophyte and invertebrate communities across three basins in a shallow lake—Castle Lough, Northern Ireland, UK. Contemporary data allow us to assess how macrophyte assemblages vary in composition and heterogeneity according to basin-specific factors (e.g. variation in water depth), while palaeoecological data (macrophytes and co-occurring invertebrates) enable us to infer basin-specific impacts and susceptibilities to nutrient-enrichment. Results indicate that variability in water depth promotes assemblage variation amongst the lake basins, stimulating within-lake macrophyte assemblage heterogeneity and hence higher lake biodiversity. The palaeo-data indicate that eutrophication has acted as a strong homogenising agent of macrophyte and invertebrate diversities and abundances over time at the whole-lake scale. This novel finding strongly suggests that, as eutrophication advances, the influence of water depth on community heterogeneity is gradually eroded and that ultimately a limited set of eutrophication-tolerant species will become homogeneously distributed across the entire lake.
    • Eutrophication homogenizes shallow lake macrophyte assemblages over space and time

      Salgado, J; Sayer, CD; Brooks, SJ; Davidson, TA; Goldsmith, B; Patmore, IR; Baker, AG; Okamura, B (Ecological Society of America, 2018-09-11)
      Eutrophication is commonly implicated in the reduction in macrophyte species richness in shallow lakes. However, the extent to which other more nuanced measures of macrophyte diversity, such as assemblage heterogeneity, are impacted concurrently by eutrophication over space and time and the joint influences of other factors (e.g., species invasions and connectivity) remains relatively poorly documented. Using a combination of contemporary and paleoecological data, we examine how eutrophication influences macrophyte assemblage heterogeneity and how nutrient enrichment interacts with watercourse connectivity, lake surface area, and relative zebra mussel abundance over space (within and among lakes) and time (decades to centuries) at the landscape scale. The study system is the Upper Lough Erne, Northern Ireland, UK, which is composed of a large main lake and several smaller satellite lakes that vary in their hydrological connectivity to the main lake. By applying homogeneity analysis of multivariate dispersions and partial redundancy analysis, we demonstrate that contemporary lake macrophyte heterogeneity and species richness are reduced in lakes with intensified eutrophication but are increased in lakes with greater zebra mussel abundance and lake surface area. Watercourse connectivity positively influenced assemblage heterogeneity and explained larger proportions of the variation in assemblage heterogeneity than local environmental factors, whereas variation in species richness was better related to local abiotic factors. Macrophyte fossil data revealed within- and among-lake assemblage homogenization post-1960, with the main lake and connected sites showing the highest rates of homogenization due to progressive eutrophication. The long-term and contemporary data collectively indicate that eutrophication reduces assemblage heterogeneity over time by overriding the importance of regional processes (e.g., connectivity) and exerts stronger pressure on isolated lakes. Our results suggest further that in connected lake systems, assemblage heterogeneity may be impacted more rapidly by eutrophication than species richness. This means that early effects of eutrophication in many systems may be underestimated by monitoring that focuses solely on species richness and is not performed at adequate landscape scales.
    • Evaluation of DNA barcode libraries used in the UK and developing an action plan to fill priority gaps

      Price, BW; Briscoe, AG; Misra, Raju; Broad, G (Natural England, 2020-10)
      There are approximately 76,000 eukaryote species recognised in the UK, and while we know some of them in great detail, the majority of these species are poorly known, and hundreds of new species are discovered each year. DNA barcoding uses a short, standardised segment of an organism’s genome for identification by comparison to a reference library; however, the UK lags behind several countries in Europe and North America in that we lack trusted, reliable and openly accessible reference sequences for key UK taxa. This report is the first step in rectifying this by engaging diverse stakeholders to facilitate collaboration and coordination; providing robust stakeholder-based and independent assessment of the current state of reference libraries available for all known UK taxa; and prioritising key taxa. A survey was developed and shared with the UK research and end user community, receiving 80 responses from a wide range of stakeholders and covering the focal taxa / assemblages and habitats; the DNA reference libraries in use, their quality assurance and perceived coverage. A formal gap analysis of the public DNA data in major DNA reference libraries highlighted that an estimated 52% of UK species have publicly available DNA data of some sort; however, coverage in gene specific reference libraries varies greatly (eg 2 – 52%), as does the associated quality assurance. Priority taxa highlighted by end users had coverage in reference libraries ranging from almost complete, in the case of known invasive non-native species, to significant coverage (71%) for taxa with conservation designations. However, these data also vary by kingdom and reference library, as does the associated quality assurance. If taking a strict requirement of DNA data provided by UK specimens and held in UK repositories, for robust QC and QA, then the proportion of UK species with public DNA data in reference libraries falls to less than 4% in the largest reference library assessed (BOLD). While standard genes for DNA-based identification have essentially been established, more work is required to establish the priority taxa required for regulatory delivery in contrast to taxa that are surveyed in a non-regulatory framework. Several barriers to the development of barcode libraries were highlighted, the most relevant being sustained large scale funding, expertise, capacity, laboratory skills and equipment, quality control and assurance, collecting logistics (eg permits and access) and communication. Significant opportunities identified include a large network of interested experts, several organisations with significant delivery capabilities, current large-scale projects and funding opportunities, emerging technologies and the economy of scale for DNA sequencing. Following a stakeholder workshop, we have outlined a concise action plan to provide reliable, open access reference sequences, linked to open access vouchers, identified by known experts, to facilitate UK academic and regulatory aims.
    • Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications

      Georgieva, MN; Taboada, Sergio; Riesgo, A; Díez-Vives, C; De Leo, FC; Jeffreys, RM; Copley, JT; Little, Crispin; Ríos, P; Cristobo, J; et al. (Frontiers Media SA, 2020-07-24)
      The peripheral areas of deep-sea hydrothermal vents are often inhabited by an assemblage of animals distinct to those living close to vent chimneys. For many such taxa, it is considered that peak abundances in the vent periphery relate to the availability of hard substrate as well as the increased concentrations of organic matter generated at vents, compared to background areas. However, the peripheries of vents are less well-studied than the assemblages of vent-endemic taxa, and the mechanisms through which peripheral fauna may benefit from vent environments are generally unknown. Understanding this is crucial for evaluating the sphere of influence of hydrothermal vents and managing the impacts of future human activity within these environments, as well as offering insights into the processes of metazoan adaptation to vents. In this study, we explored the evolutionary histories, microbiomes and nutritional sources of two distantly-related sponge types living at the periphery of active hydrothermal vents in two different geological settings (Cladorhiza from the E2 vent site on the East Scotia Ridge, Southern Ocean, and Spinularia from the Endeavour vent site on the Juan de Fuca Ridge, North-East Pacific) to examine their relationship to nearby venting. Our results uncovered a close sister relationship between the majority of our E2 Cladorhiza specimens and the species Cladorhiza methanophila, known to harbor and obtain nutrition from methanotrophic symbionts at cold seeps. Our microbiome analyses demonstrated that both E2 Cladorhiza and Endeavour Spinularia sp. are associated with putative chemosynthetic Gammaproteobacteria, including Thioglobaceae (present in both sponge types) and Methylomonaceae (present in Spinularia sp.). These bacteria are closely related to chemoautotrophic symbionts of bathymodiolin mussels. Both vent-peripheral sponges demonstrate carbon and nitrogen isotopic signatures consistent with contributions to nutrition from chemosynthesis. This study expands the number of known associations between metazoans and potentially chemosynthetic Gammaproteobacteria, indicating that they can be incredibly widespread and also occur away from the immediate vicinity of chemosynthetic environments in the vent-periphery, where these sponges may be adapted to benefit from dispersed vent fluids.
    • Evolution Is Linear: Debunking Life's Little Joke

      Jenner, RA (Wiley, 2017-12-16)
      Linear depictions of the evolutionary process are ubiquitous in popular culture, but linear evolutionary imagery is strongly rejected by scientists who argue that evolution branches. This point is frequently illustrated by saying that we didn't evolve from monkeys, but that we are related to them as collateral relatives. Yet, we did evolve from monkeys, but our monkey ancestors are extinct, not extant. Influential voices, such as the late Stephen Jay Gould, have misled audiences for decades by falsely portraying the linear and branching aspects of evolution to be in conflict, and by failing to distinguish between the legitimate linearity of evolutionary descent, and the branching relationships among collateral relatives that result when lineages of ancestors diverge. The purpose of this article is to correct the widespread misplaced rejection of linear evolutionary imagery, and to re‐emphasize the basic truth that the evolutionary process is fundamentally linear.
    • Evolution of reproductive strategies in the species-rich land snail subfamily Phaedusinae (Stylommatophora: Clausiliidae)

      Mamos, Tomasz; Uit de Weerd, Dennis; von Oheimb, Parm Viktor; Sulikowska-Drozd, Anna (Elsevier, 2020-12-28)
      Most of the present knowledge on animal reproductive mode evolution, and possible factors driving transitions between oviparity and viviparity is based on studies on vertebrates. The species rich door snail (Clausiliidae) subfamily Phaedusinae represents a suitable and unique model for further examining parity evolution, as three different strategies, oviparity, viviparity, and the intermediate mode of embryo-retention, occur in this group. The present study reconstructs the evolution of reproductive strategies in Phaedusinae based on time-calibrated molecular phylogenetics, reproductive mode examinations and ancestral state reconstruction. Our phylogenetic analysis employing multiple mitochondrial and nuclear markers identified a well-supported clade (including the tribes Phaedusini and Serrulinini) that contains species exhibiting various reproductive strategies. This clade evolved from an oviparous most recent common ancestor according to our reconstruction. All non-oviparous taxa are confined to a highly supported subclade, coinciding with the tribe Phaedusini. Both oviparity and viviparity occur frequently in different lineages of this subclade that are not closely related. During Phaedusini diversification, multiple transitions in reproductive strategy must have taken place, which could have been promoted by a high fitness of embryo-retaining species. The evolutionary success of this group might result from the maintenance of various strategies.
    • Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

      Solà, E; Álvarez-Presas, M; Frías-López, C; Littlewood, T; Rozas, J; Riutort, M; Escriva, H (2015-03-20)
    • Evolutionary Ecology of Fish Venom: Adaptations and Consequences of Evolving a Venom System.

      Harris, RJ; Jenner, RA (MDPI, 2019-01-22)
      Research on venomous animals has mainly focused on the molecular, biochemical, and pharmacological aspects of venom toxins. However, it is the relatively neglected broader study of evolutionary ecology that is crucial for understanding the biological relevance of venom systems. As fish have convergently evolved venom systems multiple times, it makes them ideal organisms to investigate the evolutionary ecology of venom on a broader scale. This review outlines what is known about how fish venom systems evolved as a result of natural enemy interactions and about the ecological consequences of evolving a venom system. This review will show how research on the evolutionary ecology of venom in fish can aid in understanding the evolutionary ecology of animal venoms more generally. Further, understanding these broad ecological questions can shed more light on the other areas of toxinology, with applications across multiple disciplinary fields.
    • Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

      Chaves, Jaime A; Martinez-Torres, Pedro J; Depino, Emiliano A; Espinoza-Ulloa, Sebastian; García-Loor, Jefferson; Beichman, Annabel; Stervander, Martin (MDPI, 2020-11-12)
      The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.
    • Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

      Burguera, D; Marquez, Y; Racioppi, C; Permanyer, J; Torres-Mendez, A; Esposito, R; Albuixech-Crespo, B; Fanlo, L; D'Agostino, Y; Gohr, A; et al. (2017-12)
      Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.