The closing date for applications to the 2011/12 round was 31st January 2012 and the following projects were funded.
- Okamura and Bass (Natural History Museum, London)
Unexplored parasite diversity and fisheries disease risk
The main systematic component of this project is to investigate unexplored diversity of two understudied parasitic groups that cause important diseases in freshwater and marine fisheries – the Myxozoa and Ascetosporea. Novel small subunit ribosomal RNA genes of these groups detected in environmental gene libraries will improve understanding of their taxonomy and systematics through new, more comprehensive and highly resolved phylogenies. The project will also entail descriptions of new taxa with information on host identity and potential lifecycle via an integrated approach (molecular techniques, microscopy, host response, pathology) in collaboration with the Centre for Environment, Fisheries & Aquaculture Science (Cefas).
- Boxshall and Huys (Natural History Museum, London)
Essential sequencing and systematics for sealice
Sealice (ectoparasitic copepods of the family Caligidae) are a major problem in commercial aquaculture, but our understanding of their host relationships and developmental patterns is hampered by uncertainty over the validity of genera, relationships between genera, and the boundaries of the family. This project will generate a systematic and taxonomic framework for caligids based on a molecular phylogenetic backbone. It will help stabilise their classification and provide a foundation for an improved understanding of sealice biology. Sequence data generated will be published on-line boosting available sequences on sealice, enhancing comprehensive taxonomic analysis, and allowing rapid diagnosis of important pest species.
- Rossiter (Queen Mary University of London) and Bates (Harrison Zoological Museum)
The diversification of horseshoe bats: sorting the trees from the phylogenetic forest
Rapid gains in throughput and cost-effectiveness of Next Generation Sequencing mean that phylogenomic approaches will become increasingly important in taxonomy and systematics. Yet as the volume of available sequence data rises, so will the frequency of phylogenetic discordance between genes. Resolving species relationships using NGS data will necessitate correcting for this problematic phenomenon, demanding appreciation of the nature, causes and consequences of discordance in a range of evolutionary contexts. To achieve this and also distinguish between conflicts caused by noise versus real evolutionary processes, we will develop a method for rapid gene-by-gene screening and classification of discordance at a genome-scale.
- Day (Natural History Museum, London) and Gharbi (The University of Edinburgh, The GenePool)
Untangling the systematics of soda lake cichlids using a genomic approach
Cichlid fishes are model organisms in speciation research. It is therefore surprising that African soda lake cichlids, inhabiting one of the most hostile environments on Earth supporting fish life have been overlooked. To elucidate mechanisms promoting and maintaining diversification in such extreme conditions, the systematics of this young, ecomorpholgically variable species-flock need to be resolved. This is only now possible with the advent of new sequencing technology and phylogenetic methods. Here, we propose to generate SNP data using the genotyping-by-sequencing approach of RAD-tags, applying a Bayesian modelling approach, to untangle the diversity and systematics of this unique adaptive radiation.
- Jungblut (Natural History Museum, London) and Edwards (Aberystwyth University)
Taxonomic evaluation of cryoconite cyanobacteria: barcoding keystone taxa on glaciers
The project will provide the first comprehensive taxonomic assessment of the cyanobacteria of meltwater habitats on Arctic, Antarctic and alpine glaciers. It will provide cultured isolates for whole genome phylogenetics that will improve resolution of evolutionary relationships of glacier-dwelling cyanobacteria and their position within the phylum Cyanobacteria. The results will assist determining the importance of glacial systems for microbial taxonomic diversity in permanently cold environments. The impacts of climate change are amplified in the cryosphere, particularly the Polar Regions, so the taxonomic results will provide baseline data essential to studying the effects of climatic change on biodiversity in glacial ecosystems.
- Glover (Natural History Museum, London)
Systematics of Antarctic scaleworms: adaptive radiation in an extreme environment
Systematics and taxonomy completely underpins our project; without a comprehensive systematics of this group it would be completely impossible to test these important globally-relevant hypotheses with regard how marine taxa have responded to a warming Antarctic both over recent geological time (the last 15 Ka) and in recent ecological time as a result of anthropogenic influences. Our project, publications and follow-on grant, will also highlight the importance of systematics and we will utilise the outreach potential of the NHM in delivering these messages to key stakeholders, including both the general public, research councils and government.
- Hall (University of Liverpool) and Jackson (Wellcome Trust Sanger Institute)
Inside the Trojan horse: systematics of Acanthamoeba spp. and their endosymbionts
Acanthamoeba spp. are free-living, unicellular eukaryotes that have a natural ability to sustain a diverse microflora of primary and secondary bacterial endosymbionts, which can include potent Human pathogens. There is a clear need for robust systematics of both Acanthamoeba spp. and their endosymbionts, which is currently lacking. We believe that the known microbial interactions among Acanthamoeba spp. are a fraction of the reality. Our vision is to systematically survey Human and natural environments to reveal the scale and diversity of these associations, creating an engine for the discovery of novel microorganisms and so substantially increase our knowledge of microbial taxonomy.
- Hudson and Gharbi (University of Edinburgh)
Testing RAD sequences for phylogenetics in the young genus Antirrhinum
Relationships between young or rapidly radiated taxa are often obscured by lineage sorting and hybridisation. Comparing multiple nuclear loci offers a potential solution, but requires amplifying many genes individually or whole-genome sequencing. Here we will test a cost-effective alternative restriction-site associated DNA (RAD) sequencing developed recently for intraspecific studies. Applying it to the young Mediterranean genus Antirrhinum (snapdragons), we will (a) test RAD in different methods of phylogenetic reconstruction, (b) possibly resolve a robust phylogeny for Antirrhinum and (c) examine whether adaptive loci have a different evolutionary history to the bulk of the nuclear genome.
- Brodie (Natural History Museum, London) and Yallop (University of Bristol)
A taxonomic discovery system for macroalgal microbiomes
This project proposes to develop a microbial diversity assessment system for marine macroalgae and is therefore dependent on a robust taxonomy in order to be able to discover and describe the microbiomes of the chosen species, the red calcifying red alga Corallina officinalis, and from which spatial and temporal comparisons can be made. It will also enable the exploration of microbiome cryptic diversity and will enable more complete phylogenies to be made of less-well known taxonomic groups and in doing so contribute to improving our understanding of evolutionary relationships of these organisms.
- Vorontsova and Forest (Royal Botanic Gardens, Kew)
Reconstructing Madagascar grassland history using the three-awn grasses
Madagascar grassland species richness and endemism are currently impossible to assess due to lack of species knowledge. Species delimitation of Aristida and Sartidia in Madagascar will be carried out using traditional micromorphological methods measuring spikelet parts from selected herbarium specimens. Delimitation of endemic species will provide a platform for DNA based lineage history reconstruction. The taxonomic revision of Aristida and Sartidia in Madagascar, distribution maps, and identification keys will provide a baseline information source on Madagascar Aristidoideae. This project will form the first part of PI’s work towards the Grass Flora of Madagascar.
- Pressel (Natural History Museum, London) and Duckett (Queen Mary University of London) Scratching the surface: a morphological framework to understanding cuticle origin and evolution
We have the long-term goal of searching for novel morphological characters to resolve early land plant phylogeny. Our proposal for detailed characterization of the cuticle throughout life cycles will provide much needed ontogenetic and ultra-structural data to support or challenge molecular phylogenies. We will also generate new morphological and biochemical characters to evaluate links between early land plants and algal lineages, and for the interpretation of paleobotanical cuticle deposits. Finally systematic descriptions of the cuticle will yield insights into the early function of the cuticle in desiccation biology, and the origin of this most important land plant innovation.