RSS 1.0Welcome to The Natural History Museum repository
The Natural History Museum is an international leader in the study of the natural world. Our science describes the diversity of nature, promotes an understanding of its past, and supports the anticipation and management of the impact of human activity on the environment.
The Museum's repository provides free access to publications produced by more than 300 scientists working here. Researchers at the Museum study a diverse range of issues, including threats to Earth's biodiversity, the maintenance of delicate ecosystems, environmental pollution and disease. The accessible repository showcases this broad research output.
The repository was launched in 2016 with an initially modest number of journal publications in its database. It now includes book chapters and blogs from Museum scientists.
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Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)The ability to identify and quantify the constituent plant species that make up a mixed‐species sample of pollen has important applications in ecology, conservation, and agriculture. Recently, metabarcoding protocols have been developed for pollen that can identify constituent plant species, but there are strong reasons to doubt that metabarcoding can accurately quantify their relative abundances. A PCR‐free, shotgun metagenomics approach has greater potential for accurately quantifying species relative abundances, but applying metagenomics to eukaryotes is challenging due to low numbers of reference genomes. We have developed a pipeline, RevMet (Reverse Metagenomics) that allows reliable and semi‐quantitative characterization of the species composition of mixed‐species eukaryote samples, such as bee‐collected pollen, without requiring reference genomes. Instead, reference species are represented only by ‘genome skims’: low‐cost, low‐coverage, short‐read sequence datasets. The skims are mapped to individual long reads sequenced from mixed‐species samples using the MinION, a portable nanopore sequencing device, and each long read is uniquely assigned to a plant species. We genome‐skimmed 49 wild UK plant species, validated our pipeline with mock DNA mixtures of known composition, and then applied RevMet to pollen loads collected from wild bees. We demonstrate that RevMet can identify plant species present in mixed‐species samples at proportions of DNA ≥ 1%, with few false positives and false negatives, and reliably differentiate species represented by high versus low amounts of DNA in a sample. RevMet could readily be adapted to generate semi‐quantitative datasets for a wide range of mixed eukaryote samples. Our per‐sample costs were £90 per genome skim and £60 per pollen sample, and new versions of sequencers available now will further reduce these costs.
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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samplesAdaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic mock community and construct sequencing libraries with a range of mean read lengths. Enrichment is up to 13.87-fold for the least abundant species in the longest read length library; factoring in reduced yields from rejecting molecules the calculated efficiency raises this to 4.93-fold. Finally, we introduce a mathematical model of enrichment based on molecule length and relative abundance, whose predictions correlate strongly with mock and complex real-world microbial communities.
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Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methodsWhile DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output. Several DNA extraction and library build methods that are designed to work with degraded DNA have been developed, although the ability to implement these methods at scale and at low cost has yet to be formally addressed. Here, the performance of widely used DNA extraction and library build methods are compared using museum specimens. We find that while our selected DNA extraction methods do not significantly differ in DNA yield, the Santa Cruz Reaction (SCR) library build method is not only the most effective at retrieving degraded DNA from museum specimens but also easily implemented at high throughput for low cost. Results highlight the importance of lab protocol on data yield. An optimised “sample to sequencing” high-throughput protocol which incorporates SCR is included to allow for easy uptake by the wider scientific community.
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A new euarthropod from the Soom Shale (Ordovician) Konservat‐Lagerstätte, South Africa, with exceptional preservation of the connective endoskeleton and myoanatomyA new exceptionally preserved euarthropod, Keurbos susanae gen. et sp. nov. from the Upper Ordovician Soom Shale Konservat‐Lagerstätte of South Africa, is described herein. Two specimens exhibit an unusual preservation style such that the cuticular exoskeleton is preserved in low relief but retains high‐fidelity details, whereas the internal anatomy is preserved in three dimensions and includes myoanatomy and aspects of the connective inter‐ and intrasegmental endoskeleton. The trunk has 46 homonomous segments and tapers towards the posterior. The dorsal surface comprises the posterior margins of tergites that form rounded paratergal folds at their lateral margins. Sternal morphology is seen from an internal view of the fossils and includes axial sternites and associated ovoid plates, both with fringing setae along their posterior margins. Patchy, incomplete preservation of the appendages is consistent with the ‘reversed’ taphonomy of these fossils in which sclerotized elements that project beyond the body margin, such as lamellae with vascular channels and pits, are preserved, whereas those inside the body margins are absent or poorly expressed. Euarthropod characters include an arthrodized tergal and sternal exoskeleton, and a segmental connective endoskeleton. Recent depopulation of the euarthropod stem group has witnessed conspicuously arthrodized fossils formerly placed in the stem group being shifted into the crown, increasing the likelihood that <jats:italic>Keurbos</jats:italic> is likewise a crown‐group euarthropod. Comparison with a phylogenetically disparate suite of similarly homonomous, multisegmented taxa indicates no convincing synapomorphies. The grouping of relevant middle Palaeozoic exemplars as ‘enantiopod’ pancrustaceans could suggest that Keurbos might be allied.
