Showing papers by "Mark Wilkinson published in 2023"

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

Abstract: We present genome sequences for the caecilians Geotrypetes seraphini (3.8Gb) and Microcaecilia unicolor (4.7Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons the most abundant. We identify 1,150 orthogroups which are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception and immunity amongst others. We discover that caecilian genomes are missing the ZRS enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

Reducing Dietary Acrylamide Exposure from Wheat Products through Crop Management and Imaging

Abstract: The nutritional safety of wheat-based food products is compromised by the presence of the processing contaminant acrylamide. Reduction of the key acrylamide precursor, free (soluble, non-protein) asparagine, in wheat grain can be achieved through crop management strategies, but such strategies have not been fully developed. We ran two field trials with 12 soft (biscuit) wheat varieties and different nitrogen, sulfur, potassium, and phosphorus fertilizer combinations. Our results indicated that a nitrogen-to-sulfur ratio of 10:1 kg/ha was sufficient to prevent large increases in free asparagine, whereas withholding potassium or phosphorus alone did not cause increases in free asparagine when sulfur was applied. Multispectral measurements of plants in the field were able to predict the free asparagine content of grain with an accuracy of 71%, while a combination of multispectral, fluorescence, and morphological measurements of seeds could distinguish high free asparagine grain from low free asparagine grain with an accuracy of 86%. The acrylamide content of biscuits correlated strongly with free asparagine content and with color measurements, indicating that agronomic strategies to decrease free asparagine would be effective and that quality control checks based on product color could eliminate high acrylamide biscuit products.

Mitigating floods and attenuating surface runoff with temporary storage areas in headwaters

Abstract: Temporary storage areas (TSAs) represent a category of soft‐engineered nature‐based solutions that can provide dispersed, small‐scale storage throughout a catchment. TSAs store and attenuate surface runoff, providing new additional storage during flood events. The need for such additional catchment storage will become more urgent as the frequency and magnitude of extreme hydrological events increases due to climate change. Implementation of TSAs in headwater catchments is slowly gaining momentum, but practitioners still require further evidence on how such measures function during flood events. This review focuses on the role of relatively small‐scale (<10,000 m3) TSAs in headwater catchments for flood risk management. It also explores the potential wider benefits for implementing these as part of an integrated catchment management approach. TSA flood mitigation effectiveness is primarily determined by the TSA's available storage prior to the event. At the local scale, this can be represented by the relationship between TSA inputs, outputs and total storage. Factors influencing the local functioning and effectiveness of TSAs are discussed, with potential considerations for optimizing future TSA design and management. Hydrological models have suggested that TSAs could be used to effectively attenuate high magnitude events. However, future considerations should involve addressing the lack of empirical evidence showing TSA catchment scale effectiveness and how local TSA functioning might change in time. Small‐scale headwater TSAs offer a holistic and sustainable approach to catchment management that can deliver both local benefits to landowners and wider flood risk mitigation for society.

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert

Abstract: Abstract Background Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400–4500 m a.s.l.) of the Talabre–Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. Results Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. Conclusions In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

Leveraging Biolink as a FAIR “Rosetta Stone” Between Clinical Semantic Models Provides Emergent Interoperability

Abstract: Interoperability between clinical datasets is challenging due to, in part, the number of data models and vocabularies in use and the variety of implementations. Here we describe the first steps in an ongoing effort to achieve interoperability between two clinical datasets currently being constructed within independent international projects. Both are utilizing the FAIR Principles but have constructed their data models independently and have selected different ontologies. In this initial exploratory experiment, we examined the degree to which a mapping of both models into an independent schema, Biolink, can increase interoperability. Mapping was achieved by categorizing the key nodes in both data models as “types” of concepts in the Biolink schema. We found that with this very thin mapping in place, and without changing either model, queries could be constructed that extracted data from both datasets, demonstrating that at least some degree of interoperability had been achieved. Our results support the use of FAIR-compliant data representations, which are, by nature, more interoperable than legacy clinical data representations, even when the models have not been coordinated upfront.

New postcranial remains from the Lealt Shale Formation of the Isle of Skye, Scotland, showcase hidden pterosaur diversity in the Middle Jurassic

Abstract: The transition between Early to Middle Jurassic was significant in pterosaur evolution, when these volant reptiles exploded in diversity alongside dinosaurs and other animals. It has long been thought, however, that pterosaurs did not develop large wingspans until after the Jurassic, a notion challenged by the recent discovery of Dearc sgiathanach in the Bathonian-aged Lealt Shale Formation of the Isle of Skye, Scotland, whose holotype specimen had an estimated wingspan greater than 2.5 meters. We here report the discovery of a new pterosaur specimen from the Lealt Shale Formation, comprising a tibiotarsus, metatarsal, pedal phalanges, and caudal vertebrae. The elongate tail vertebrae with ossified processes indicate the specimen is a non-pterodactyloid pterosaur, albeit its fragmentary nature makes it difficult to determine whether it belongs to a new taxon. Its metatarsal and caudal vertebrae are considerably larger than corresponding bones in the Dearc holotype, indicating that it belonged to an even larger individual, thus demonstrating that pterosaurs with broad wingspans were not anomalous in the Middle Jurassic. The growing Middle Jurassic pterosaur record of Scotland and England, although mostly represented by isolated and fragmentary fossils, reveals a high diversity of clades, long obscured by the lack of well-preserved skeletons.

Genetic control of grain amino acid composition in a UK soft wheat mapping population.

Abstract: Wheat (Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.

Resistance Is Not Futile: Widespread Convergent Evolution of Resistance to Alpha-Neurotoxic Snake Venoms in Caecilians (Amphibia: Gymnophiona)

Abstract: Predatory innovations impose reciprocal selection pressures upon prey. The evolution of snake venom alpha-neurotoxins has triggered the corresponding evolution of resistance in the post-synaptic nicotinic acetylcholine receptors of prey in a complex chemical arms race. All other things being equal, animals like caecilians (an Order of legless amphibians) are quite vulnerable to predation by fossorial elapid snakes and their powerful alpha-neurotoxic venoms; thus, they are under strong selective pressure. Here, we sequenced the nicotinic acetylcholine receptor alpha-1 subunit of 37 caecilian species, representing all currently known families of caecilians from across the Americas, Africa, and Asia, including species endemic to the Seychelles. Three types of resistance were identified: (1) steric hindrance from N-glycosylated asparagines; (2) secondary structural changes due to the replacement of proline by another amino acid; and (3) electrostatic charge repulsion of the positively charged neurotoxins, through the introduction of a positively charged amino acid into the toxin-binding site. We demonstrated that resistance to alpha-neurotoxins convergently evolved at least fifteen times across the caecilian tree (three times in Africa, seven times in the Americas, and five times in Asia). Additionally, as several species were shown to possess multiple resistance modifications acting synergistically, caecilians must have undergone at least 20 separate events involving the origin of toxin resistance. On the other hand, resistance in non-caecilian amphibians was found to be limited to five origins. Together, the mutations underlying resistance in caecilians constitute a robust signature of positive selection which strongly correlates with elapid presence through both space (sympatry with caecilian-eating elapids) and time (Cenozoic radiation of elapids). Our study demonstrates the extent of convergent evolution that can be expected when a single widespread predatory adaptation triggers parallel evolutionary arms races at a global scale.

Long-term daily stream temperature record for Scotland reveals spatio-temporal patterns in warming of rivers in the past and further warming in the future.

Abstract: Stream temperature is directly and indirectly affected by climate change. To be able to project future changes in stream temperature, historic trends and factors influencing these trends need to be understood. There is a demand for daily data to analyse historical trends and future changes in stream temperature. However, long-term daily stream temperature data are rare and observations of coarse temporal resolution (e.g. once-a-month) do not allow for robust trend analyses. Here, we present a methodology to reconstruct a national long-term daily stream temperature record (1960-2080) from 40 years of once-a-month observations (for 45 Scottish catchments). This involved implementing climatic and hydrological variables in generalized additive models. These models were then used in combination with regional climate projections (UKCP18 Strand 3 - RCP8.5) to predict future spatio-temporal temperature patterns. The results indicate that for the Scottish dataset (i) in addition to air temperature, the dominant environmental controls on stream temperature are unique combinations for each catchment; (ii) a general increase of up to 0.06 °C/year in historic stream temperature over all catchments resulted mainly from increases in spring and summer stream temperatures; (iii) future spatial patterns in stream temperature are more homogenous and differ therefore from the past where temperatures in N Scotland were relatively lower (iv) future changes of up to +4.0 °C in annual stream temperature are strongest in those catchments which show lower stream temperature in the past (NW and W Scotland). These results are important in the context of water quality and stream temperature management. The methodology can be applied to smaller scale sites or to other national/global datasets enabling the analysis of historic trends and future changes at a high temporal resolution.

Geochemical Integrity of Wellbore Cements during Geological Hydrogen Storage

Abstract: Increasing greenhouse gas emissions have put pressure on global economies to adopt strategies for climate-change mitigation. Large-scale geological hydrogen storage in salt caverns and porous rocks has the potential to achieve sustainable energy storage, contributing to the development of a low-carbon economy. During geological storage, hydrogen is injected and extracted through cemented and cased wells. In this context, well integrity and leakage risk must be assessed through in-depth investigations of the hydrogen–cement–rock physical and geochemical processes. There are significant scientific knowledge gaps pertaining to hydrogen–cement interactions, where chemical reactions among hydrogen, in situ reservoir fluids, and cement could degrade the well cement and put the integrity of the storage system at risk. Results from laboratory batch reaction experiments concerning the influence of hydrogen on cement samples under simulated reservoir conditions of North Sea fields, including temperature, pressure, and salinity, provided valuable insights into the integrity of cement for geological hydrogen storage. This work shows that, under the experimental conditions, hydrogen does not induce geochemical or structural alterations to the tested wellbore cements, a promising finding for secure hydrogen subsurface storage.