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2024-03-19T19:51:42ZDiversity and Phylogeny of Novel Cord-Forming Fungi from Borneo
http://hdl.handle.net/10141/623077
Diversity and Phylogeny of Novel Cord-Forming Fungi from Borneo
Foster, R; Hartikainen, Hanna; Hall, Andie; Bass, David
Cord-forming (CF) fungi are found worldwide; however, tropical CF fungi are poorly documented. They play an essential role in forest ecosystems by interconnecting nutrient resources and aiding in the decomposition of plant matter and woody litter. CF fungi samples were collected from two forest conservation sites in the Sabah region of Malaysian Borneo. Sequencing and phylogenetic analysis of the ribosomal rRNA gene array 18S to 28S region from cords collected placed all of the collected specimens in Agaricomycetes (Basidiomycetes), specifically within the orders Trechisporales, Phallales, Hymenochaetales, Polyporales, and Agaricales. Comparison of the cord-derived sequences against GenBank and UNITE sequence databases, as well as phylogenetic analyses, revealed they were all novel sequences types. Many of these novel lineages were found to be closely related to other basidiomycetes commonly found in tropical forests, suggesting a large undiscovered tropical fungal diversity in Borneo that has been detected independently of sampling fruiting bodies. We show how these sequence types relate to the morphologies of the cords from which they were sampled. We also highlight how rapid, small-scale sampling can be a useful tool as an easy and relatively unbiased way of collecting data on cord-forming fungi in difficult-to-access, complex forest environments, independently of locating and sampling sporophores.
2022-01-22T00:00:00ZTwo new sympatric species of the pirate spider genus Ero C.L. Koch, 1836 from the cloud forest of Saint Helena Island, South Atlantic Ocean (Araneae: Mimetidae)
http://hdl.handle.net/10141/623076
Two new sympatric species of the pirate spider genus Ero C.L. Koch, 1836 from the cloud forest of Saint Helena Island, South Atlantic Ocean (Araneae: Mimetidae)
Sherwood, Danniella; Henrard, Arnaud; Peters, Martina; Price, BW; Hall, Andie; White, Oliver W; Grignet, Virginie; Wilkins, Vicky
A remarkable morphologically and genetically distinct species of the genus Ero C.L. Koch, 1836 is described based on both sexes from the cloud forest of the island of Saint Helena: Ero lizae sp. nov. Another new species, Ero natashae sp. nov., is also described on the basis of morphological differences in the male and female genitalia. Both species were initially reported a single species, Ero aphana (Walckenaer, 1802), from the island by Unzicker (1977).
2024-02-02T00:00:00ZUnprecedented frequency of mitochondrial introns in colonial bilaterians
http://hdl.handle.net/10141/623075
Unprecedented frequency of mitochondrial introns in colonial bilaterians
Jenkins, Helen Louise; Graham, Rachael; Porter, Joanne Sara; Vieira, Leandro Manzoni; de Almeida, Ana Carolina Sousa; Hall, Andrea; O’Dea, Aaron; Coppard, Simon Edward; Waeschenbach, A
Abstract
Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.
2022-06-28T00:00:00ZEvaluation of genome skimming to detect and characterise human and livestock helminths
http://hdl.handle.net/10141/623074
Evaluation of genome skimming to detect and characterise human and livestock helminths
PAPAIAKOVOU, MARINA; Fraija-Fernández, Natalia; James, Katherine; Briscoe, AG; Hall, Andie; Jenkins, Timothy P; Dunn, Julia; Levecke, Bruno; Mekonnen, Zeleke; Cools, Piet; Doyle, Stephen R; Cantacessi, Cinzia; Littlewood, DTJ
The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.
2023-01-11T00:00:00ZReconstructing the feeding ecology of Cambrian sponge reefs: the case for active suspension feeding in Archaeocyatha
http://hdl.handle.net/10141/623073
Reconstructing the feeding ecology of Cambrian sponge reefs: the case for active suspension feeding in Archaeocyatha
Gibson, Brandt M; Chipman, Max; Attanasio, Paolo; Qureshi, Zaid; Darroch, Simon AF; Rahman, Imran A; Laflamme, Marc
Sponge-grade Archaeocyatha were early Cambrian biomineralizing metazoans that constructed reefs globally. Despite decades of research, many facets of archaeocyath palaeobiology remain unclear, making it difficult to reconstruct the palaeoecology of Cambrian reef ecosystems. Of specific interest is how these organisms fed; previous experimental studies have suggested that archaeocyaths functioned as passive suspension feeders relying on ambient currents to transport nutrient-rich water into their central cavities. Here, we test this hypothesis using computational fluid dynamics (CFD) simulations of digital models of select archaeocyath species. Our results demonstrate that, given a range of plausible current velocities, there was very little fluid circulation through the skeleton, suggesting obligate passive suspension feeding was unlikely. Comparing our simulation data with exhalent velocities collected from extant sponges, we infer an active suspension feeding lifestyle for archaeocyaths. The combination of active suspension feeding and biomineralization in Archaeocyatha may have facilitated the creation of modern metazoan reef ecosystems. The attached file is the published version of the article.
2023-11-22T00:00:00ZA multi-taxon analysis of European Red Lists reveals major threats to biodiversity
http://hdl.handle.net/10141/623072
A multi-taxon analysis of European Red Lists reveals major threats to biodiversity
Hochkirch, Axel; Bilz, Melanie; Ferreira, Catarina C; Danielczak, Anja; Allen, David; Nieto, Ana; Rondinini, Carlo; Harding, Kate; Hilton-Taylor, Craig; Pollock, Caroline M; Seddon, Mary; Vié, Jean-Christophe; Alexander, Keith NA; Beech, Emily; Biscoito, Manuel; Braud, Yoan; Burfield, Ian J; Buzzetti, Filippo Maria; Cálix, Marta; Carpenter, Kent E; Chao, Ning Labbish; Chobanov, Dragan; Christenhusz, Maarten JM; Collette, Bruce B; Comeros-Raynal, Mia T; Cox, Neil; Craig, Matthew; Cuttelod, Annabelle; Darwall, William RT; Dodelin, Benoit; Dulvy, Nicholas K; Englefield, Eve; Fay, Michael F; Fettes, Nicholas; Freyhof, Jörg; García, Silvia; Criado, Mariana García; Harvey, Michael; Hodgetts, Nick; Ieronymidou, Christina; Kalkman, Vincent J; Kell, Shelagh P; Kemp, James; Khela, Sonia; Lansdown, Richard V; Lawson, Julia M; Leaman, Danna J; Brehm, Joana Magos; Maxted, Nigel; Miller, Rebecca M; Neubert, Eike; Odé, Baudewijn; Pollard, David; Pollom, Riley; Pople, Rob; Presa Asensio, Juan José; Ralph, Gina M; Rankou, Hassan; Rivers, Malin; Roberts, Stuart PM; Russell, Barry; Sennikov, Alexander; Soldati, Fabien; Staneva, Anna; Stump, Emilie; Symes, Andy; Telnov, Dmitry; Temple, Helen; Terry, Andrew; Timoshyna, Anastasiya; Swaay, Chris van; Väre, Henry; Walls, Rachel HL; Willemse, Luc; Wilson, Brett; Window, Jemma; Wright, Emma GE; Zuna-Kratky, Thomas
Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.
2023-11-08T00:00:00Z