Abstract
Summary
Hidden Markov models (HMMs) and profile HMMs form an integral part of biological sequence analysis, supporting an ever-growing list of applications. The aphid R package can be used ...to derive, train, plot, import and export HMMs and profile HMMs in the R environment. Computationally-intensive dynamic programing recursions, such as the Viterbi, forward and backward algorithms are implemented in C++ and parallelized for increased speed and efficiency.
Availability and implementation
The aphid package is released under the GPL-3 license, and is freely available for download from CRAN and GitHub (https://github.com/shaunpwilkinson/aphid).
Supplementary information
Supplementary data are available at Bioinformatics online.
Small-scale fisheries are responsible for landing half of the world's fish catch, yet there are very sparse data on these fishing activities and associated fisheries production in time and space. ...Fisheries-dependent data underpin scientific guidance of management and conservation of fisheries systems, but it is inherently difficult to generate robust and comprehensive data for small-scale fisheries, particularly given their dispersed and diverse nature. In tackling this challenge, we use open source software components including the Shiny R package to build PeskAAS; an adaptable and scalable digital application that enables the collation, classification, analysis and visualisation of small-scale fisheries catch and effort data. We piloted and refined this system in Timor-Leste; a small island developing nation. The features that make PeskAAS fit for purpose are that it is: (i) fully open-source and free to use (ii) component-based, flexible and able to integrate vessel tracking data with catch records; (iii) able to perform spatial and temporal filtering of fishing productivity by fishing method and habitat; (iv) integrated with species-specific length-weight parameters from FishBase; (v) controlled through a click-button dashboard, that was co-designed with fisheries scientists and government managers, that enables easy to read data summaries and interpretation of context-specific fisheries data. With limited training and code adaptation, the PeskAAS workflow has been used as a framework on which to build and adapt systematic, standardised data collection for small-scale fisheries in other contexts. Automated analytics of these data can provide fishers, managers and researchers with insights into a fisher's experience of fishing efforts, fisheries status, catch rates, economic efficiency and geographic preferences and limits that can potentially guide management and livelihood investments.
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and ...space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of 'snapshots' across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
ABSTRACT
Environmental DNA (eDNA) is increasingly used in biodiversity assessments, but there remain uncertainties regarding its congruence with data based on traditional approaches involving habitat ...sampling and morphological‐based taxonomy. Using eDNA for biomonitoring has several advantages, including improved processing efficiencies and precision of taxonomic identification. In contrast, traditional biomonitoring is time‐consuming and expensive, often limiting the number of sites monitored. Establishing that eDNA‐derived metrics are congruent with their traditional equivalents on a national scale would support its wider use in biomonitoring. Our study compared ecosystem health assessments made by traditional biomonitoring techniques to those using eDNA from 53 sites throughout Aotearoa New Zealand. Because eDNA sampling was not done concurrently with benthic sampling at most sites, we used the average community composition at each site based on previous sampling occasions. We also allocated species identified by eDNA to the traditional level of identification to allow comparisons with eDNA data identified to broader taxonomic groups. We assessed similarities between the three datasets and found a high degree of correlation and convergence between biotic indices calculated from the different methods. eDNA did, however, appear to under‐represent some taxa, reflecting challenges in matching barcodes with an often‐incomplete sequence library. eDNA data did not always perform better in terms of showing the effects of land use on invertebrate community composition, but all datasets produced similar patterns. Multivariate analyses (redundancy analysis and variation partitioning) identified congruent relationships between environmental and spatial variables with the invertebrate community structure described by the three methods. eDNA data replicated the environmental responses and showed the same overall patterns in community composition as the traditionally collected data. We suggest that eDNA biomonitoring can complement traditional methods, and will perform at least as well as traditional data at detecting patterns in invertebrate community composition and ecosystem health at a national scale.
Ecosystem health assessments made by traditional biomonitoring techniques were compared to those made using eDNA at 53 sites throughout New Zealand. We found a high degree of correlation and convergence between biotic indices calculated from traditional biomonitoring techniques and from eDNA. Our results suggest that eDNA biomonitoring complements traditional methods and may be useful in meeting increased demands of future biomonitoring programs.
Cumulative anthropogenic pressures have triggered a global decline in the health of marine ecosystems, and coral reefs, in particular, are in crisis. With climate and population-related pressures ...predicted to intensify in the coming decades, it is increasingly crucial to develop cost-effective and accurate monitoring tools to document changes to these important ecosystems. Environmental DNA (eDNA) coupled with metabarcoding is a powerful tool for surveying a wide variety of biota. Here, we develop a baseline eDNA toolkit targeting scleractinian corals and validate its performance in conjunction with data derived on traditional diver-based visual surveys at the Cocos (Keeling) Islands. Three assays targeting the ITS2 and 16S barcoding regions were designed, which broadly detected diversity within Scleractinia and Porifera. Our eDNA assays recovered 78 ITS2 operational taxonomic units (OTUs) from 25 scleractinian genera which is comparable to the level of diversity recorded on visual surveys (68 species from 26 genera). There were some notable differences in the species detected using eDNA versus visual records that may relate to either misidentifications, intragenic variation, differential assay performance or cryptic species. Our data demonstrate that a multi-assay eDNA analytical approach, applied on surface water collections, represents a powerful and complementary way to survey diversity that can also reveal fine scale spatial differentiation in community composition. With further refinement and improved reference databases, we envisage eDNA to become a powerful complement to visual surveys and to play a key role in monitoring the health and diversity of complex coral reefs ecosystems.
Rising seawater temperatures pose a significant threat to the persistence of coral reefs. Despite the importance of these systems, major gaps remain in our understanding of how thermal stress and ...bleaching affect the metabolic networks that underpin holobiont function. We applied gas chromatography–mass spectrometry (GC–MS) metabolomics to detect changes in the intracellular free metabolite pools (polar and semi-polar compounds) of in hospite dinoflagellate symbionts and their coral hosts (and any associated microorganisms) during early- and late-stage thermal bleaching (a reduction of approximately 50 and 70% in symbiont density, respectively). We detected characteristic changes to the metabolite profiles of each symbiotic partner associated with individual cellular responses to thermal, oxidative and osmotic stress, which progressed with the severity of bleaching. Alterations were also indicative of changes to energy-generating and biosynthesis pathways in both partners, with a shift to the increased catabolism of lipid stores. Specifically, in symbiont intracellular metabolite pools, we observed accumulations of multiple free fatty acids, plus the chloroplast-associated antioxidant alpha-tocopherol. In the host, we detected a decline in the abundance of pools of multiple carbohydrates, amino acids and intermediates, in addition to the antioxidant ascorbate. These findings further our understanding of the metabolic changes that occur to symbiont and host (and its associated microorganisms) during thermal bleaching. These findings also provide further insight into the largely undescribed roles of free metabolite pools in cellular homeostasis, signalling and acclimation to thermal stress in the cnidarian–dinoflagellate symbiosis.
To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with symbiotic dinoflagellates of the family Symbiodiniaceae, but the true diversity of this family remains ...poorly characterised. In this paper, we assess Symbiodiniaceae richness at Atauro Island (Timor-Leste) as well as on reefs of the neighbouring Timor mainland, using direct sequencing of three gene regions:
cob
gene, mitochondrion; ITS2 region, nucleus; and psbA
ncr
region, chloroplast; in addition to a highly multiplexed application of next-generation sequencing. These geographic sites are among the most biodiverse in the world, but have never had their symbiont communities studied. Despite their proximity, our results reveal symbiont richness 1.25 times higher at Atauro Island than the Timor mainland, a result evident in dominant sequences. In contrast, Timor had a significantly richer background sequence diversity. Although sampling was restricted to shallow sites only, symbiont richness at Atauro Island was also higher than comparative reefscapes globally, after standardising for number of taxa sampled. While Atauro and Timor have related symbiont populations, with the same novel types recorded at both sites, there were also clear differences in symbiont composition between the two geographic regions, with Timor displaying a consortium more characteristic of stressed reef environments (proportionally hosting twice as many
Durusdinium
sequences, formerly clade D, as Atauro). These results reveal a symbiont richness that matches the high biodiversity of these reefs, but also potentially negative effects of proximal human populations on Symbiodiniaceae, even when previous studies have shown corals to be largely unaffected.
We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (
). We first established an environmental DNA metabarcoding ...protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.
The ability of corals and other cnidarians to survive climate change depends partly on the composition of their endosymbiont communities. The dinoflagellate family Symbiodiniaceae is genetically and ...physiologically diverse, and one proposed mechanism for cnidarians to acclimate to rising temperatures is to acquire more thermally tolerant symbionts. However, cnidarian-dinoflagellate associations vary in their degree of specificity, which may limit their capacity to alter symbiont communities. Here, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida (commonly referred to as 'Aiptasia'), a model system for the cnidarian-dinoflagellate symbiosis, with simultaneous or sequential mixtures of thermally tolerant and thermally sensitive species of Symbiodiniaceae. We then monitored symbiont success (relative proportional abundance) at normal and elevated temperatures across two to four weeks. All anemones showed signs of bleaching at high temperature. During simultaneous inoculations, the native, thermally sensitive Breviolum minutum colonized polyps most successfully regardless of temperature when paired against the non-native but more thermally tolerant Symbiodinium microadriaticum or Durusdinium trenchii. Furthermore, anemones initially colonized with B. minutum and subsequently exposed to S. microadriaticum failed to acquire the new symbiont. These results highlight how partner specificity may place strong limitations on the ability of certain cnidarians to acquire more thermally tolerant symbionts, and hence their adaptive potential under climate change.
Coral bleaching has devastating effects on coral survival and reef ecosystem function, but many of the fundamental cellular effects of thermal stress on cnidarian physiology are unclear. We used ...label-free liquid chromatography–tandem mass spectrometry to compare the effects of rapidly (33.5 °C, 24 h) and gradually (30 and 33.5 °C, 12 days) elevated temperatures on the proteome of the model symbiotic anemone Aiptasia. We identified 2133 proteins in Aiptasia, 136 of which were differentially abundant between treatments. Thermal shock, but not acclimation, resulted in significant abundance changes in 104 proteins, including those involved in protein folding and synthesis, redox homeostasis, and central metabolism. Nineteen abundant structural proteins showed particularly reduced abundance, demonstrating proteostasis disruption and potential protein synthesis inhibition. Heat shock induced antioxidant mechanisms and proteins involved in stabilizing nascent proteins, preventing protein aggregation and degrading damaged proteins, which is indicative of endoplasmic reticulum stress. Host proteostasis disruption occurred before either bleaching or symbiont photoinhibition was detected, suggesting host-derived reactive oxygen species production as the proximate cause of thermal damage. The pronounced abundance changes in endoplasmic reticulum proteins associated with proteostasis and protein turnover indicate that these processes are essential in the cellular response of symbiotic cnidarians to severe thermal stress.
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