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Collaborative Scheme for Systematics Research
This scheme has now finished
The Systematics and Taxonomy (SynTax) research scheme is designed to provide short-term funding for preliminary research that will form the basis of novel responsive mode proposals with a substantial systematics/taxonomy component. The scheme is supported by BBSRC and NERC research councils and the scheme aims to stimulate high quality taxonomy and systematics-related research proposals to the UK's Research Councils. The scheme follows on from the Collaborative Systematics (CoSyst) scheme, through which a number of projects have gone on to receive responsive mode funding. Please note that the SynTax scheme has now finished.
The closing date for applications to the 2011/12 round was 31st January 2012 and the following projects have been 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.
The closing date for applications to the 2010/11 round was 31st January 2011 and the following projects have been funded.
- Collins (University of York) and Barnes (Royal Holloway, University of London)
Collagen: the barcode of death
By developing a tool for routine identification of samples, and providing a means to infer the evolutionary relationships of novel palaeontological specimens, the project is inherently taxonomic and systematic. The proposed case studies deal with evolutionary histories of three poorly resolved groups of taxa, and will substantially enhance our understanding of evolution, adaptation, radiation and convergence, whilst also improving collections management for Quaternary fossil material.
- Purvis (Imperial College London) and Darling (University of Edinburgh)
Species limits in planktonic foraminifera
Planktonic foraminifera have probably the best fossil record of any group, making them a model system for macroevolutionary research. However, genetic evidence indicates that many of the extant species recognised from morphology contain deep divergences, at least some of which probably delimit good genetic species. We propose two linked investigations. (1) We will apply a recently-developed analytical approach to demarcate the genetic species statistically; this will also estimate their ages. (2) We will use non-destructive computer tomography (CT) scans of sequenced specimens on four morphospecies, with the aim of identifying morphological criteria for diagnosing the genetic species.
- Bass (Natural History Museum) and Neuhauser (University of Innsbruck)
Phytomyxids: A hidden world of parasites and symbionts
Phytomyxid protists are very poorly known rhizarian parasites/symbionts of plants, algae, and oomycetes. Recent molecular environmental studies suggest that they are much more diverse, and have a wider range of host species, than previously known. These studies have also begun to reveal related but highly distinct lineages about which nothing else is known. This project will sample phytomyxids and their relatives from environmental samples in a much more targeted way than previously attempted, and will use ecological, phylogenetic, and morphological (microscopy and culture-based) techniques to strongly advance knowledge of this group and their position on the eukaryote tree of life.
- Purnell (University of Leicester)
Taphonomic bias in taxonomic and systematic analysis of fossils
Recent work has reaffirmed the importance of fossils, especially those representing non-biomineralised animals, in systematic and evolutionary biology (see Background and Rationale). This research will have a direct bearing on the taxonomy and phylogenetic systematic analysis of non-biomineralised fossils, particularly phyllocarids and potential stem malacostracans (crustaceans). It will allow us to understand how taphonomic processes of decay and preservation distort and bias the taxonomic and systematic information content of exceptionally-well-preserved fossils. Without this understanding such fossils cannot realise their true potential.
- Falcon-Lang (Royal Holloway University of London)
Early angiosperm diversity and ecology: seeing the trees from the wood
This project addresses Charles Darwin's "abominable mystery": the origin, evolution and ecology of the earliest angiosperms. Specifically, it focuses on fossil wood, which has received little attention in earlier studies of angiosperm evolution. Using morphometrics and multivariate character analysis, I plan to identify Cretaceous (140-65 million year old) fossil wood assemblages with greater taxonomic precision than previously possible to improve knowledge of angiosperm diversity during a crucial evolutionary phase. This 'proof of concept' study will be used as a springboard for a NERC Standard Grant application.
- Wills (University of Bath) and Wilkinson (The Natural History Museum)
Building the arthropod supertree interactively: Malacostracan crustaceans as a test case
We will produce MRP and other supertrees of malacostracan species, synthesising 200+ primary trees from the literature. Rather than generate this as a one-off, all of the data and trees will be made available online. This will be searchable using numerous tags (e.g., source data type, publication year, authors, tree and node support metrics) and linked to embedded software enabling inexperienced users to generate error-free supertrees to any specifications. In addition, the project will embed taxonomic knowledge, ensuring standard and repeatable best practice. This will constitute a proof of principle pilot for a proposed interactive supertree database of all arthropods.
- Sands and Griffiths (British Antarctic Survey)
Systematics and taxonomy of Antarctic ophiuorids: a next-gen holistic approach
We propose to refine and demonstrate the application of genomics using next generation sequencing technology to facilitate morphology based systematics and taxonomy of individual specimens. We will address a complex taxonomic issue present in Antarctic ophiuroids involving potential generic synonyms and species complexes by sequencing thousands of gene regions for each individual, determining allelic variation of each gene, and co-analysing both phylogeny and multi-locus genotype clustering using a user-friendly bioinformatic pipeline. The holistic approach we propose will radically alter and reduce to laboratory time and costs of molecular evolutionary studies, while greatly increasing the amount of data and its applicability.
- Wüster and Mulley (School of Biological Sciences, Bangor University)
Cryptic reptile diversity in a floristic biodiversity hotspot
Effective conservation of biodiversity hotspots requires information on the diversity of all major groups of organisms. The southern African Cape Floristic Region (CFR) has been recognised primarily for its floral diversity, but early data suggest that it may be of hitherto underestimated importance for faunal diversity. We seek to develop and use microsatellite markers to investigate and redefine species limits in four species of CFR reptile showing strong phylogeographic structure, with the aim of uncovering cryptic species, and as a prelude to wider-ranging studies on the patterns and processes of reptile speciation in the CFR.
- Wilkinson (The Natural History Museum) and Day (University College London)
History and Future of the Seychelles Herpetofauna
The research is on diversity and its causes at a number of temporal scales and is thus broadly systematic. Seychellean caecilians are monophyletic with currently six species in three genera. Previous taxonomic treatments, the most recent more than 50 years ago, have disagreed on genera and on whether island populations of the six currently recognised species, which show some morphological differences, represent distinct taxa. We will test species and generic concepts using molecules and morphology and provide a comprehensive taxonomic review of the group. Revisionary taxonomy will also underpin the planned comparative broadening of this study to other taxa.
- Pennington (Royal Botanic Garden Edinburgh) and Coley (Department of Biology, University of Utah)
Chemistry, taxonomy and diversification in tropical plants: a case study of Inga
Inga is one of the most important tree genera in the rain forests of Latin America. It is species-rich, abundant, and economically important because of its edible fruits and rapid growth, which make it widely used as a multipurpose tree in agroforestry (e.g., as coffee shade). This proposal will deliver bespoke DNA markers for Inga that can improve species delimitation, provide a resolved species phylogeny, and investigate intraspecific genetic variation. An improved taxonomy and phylogeny will underpin future applied research on Inga species and be a springboard to understanding the processes that have led to its high diversity.
- Dentinger (Royal Botanic Gardens, Kew) and McLaughlin (University of Minnesota)
Molecular systematics of the enigmatic attine-ant mutualistic coral mushroom family Pterulaceae
The attine ant-fungus mutualism is a classic coevolutionary system. Recent evidence suggests one small group of attines in the genus Apterostigma switched fungal cultivars twenty million years ago from gilled to coral mushrooms (Pterulaceae), a remarkable event that remains unexplained. This project will improve our systematic knowledge of the Pterulaceae by identifying phylogenetically informative loci and improving taxon sampling. The results will provide the foundation for a contemporary systematic revision of a poorly known group of fungi, allowing for the formal taxonomic classification of the unusual coral mushroom ant cultivars for the first time.
- Scotland (University of Oxford) and Carine (Natural History Museum, Dept of Botany)
Foundation Monographs - accelerating the pace of taxonomy
This research project is fundamentally taxonomic in scope and content.
- Leitch (Queen Mary University of London) and Leitch (Jodrell Laboratory)
Status of homoploid hybrids in a model genus for sympatric speciation
Interspecific hybridization events differ in their propensity to produce new hybrid species, both at the allopolyploid and homoploid level. Factors affecting these propensities are poorly understood, partly due to a lack of alpha-taxonomy on homoploid hybrids. The plant genus Tragopogon L. (Asteraceae) includes classic models species for the study of allopolyploid speciation in the USA. The genus also contains many European homoploid hybrids. These hybrids have not been investigated despite the valuable insight it will give to our understanding of related allopolyploid species. We will characterize their parentage and stability and to determine whether incipient speciation is occurring.
- Shaw (Centre for research in Ecology) and Emerson (Biological Sciences,
University of East Anglia)
A molecular taxonomic approach to resolving species boundaries within British members of the genera Lepidocyrtus and Entomobrya (Arthropoda: Pancrustacea: Collembola).
We intend to use mitochondrial and nuclear DNA to validate species boundaries in two widespread genera of UK Collembola; Lepidocyrtus and Entomobrya. Existing taxonomy in both is colour-based and suspect. Recent work around the Mediterranean basin has shown the same morphospecies of Lepidocyrtus that occur in the UK to contain multiple unrelated clades. It is unclear whether most UK records of Entomobrya nivalis are valid or mixed with E. intermedia. We will collect these surface-active Collembola from multiple habitats either side of the Devensian borderline, seeking to establish the genetic validity of species boundaries as currently defined.
The closing date for applications to the 2009/10 round was 31st January 2010 and the following projects have been funded.
- Dr van Veen (University of Exeter)
Resolving Alloxystini taxonomy to facilitate the geographic comparison of insect food webs
This project has a strong taxonomic focus within an ecological context. It will catalogue all currently known species of Alloxystini wasps, including the many currently undescribed and unnamed ones. It will produce an easily accessible identification resource based on an extensive image library and a database of morphological measurements. This will build on the phylogenetic structure of an aphid-based food web, which includes the construction of a molecular phylogeny of the Alloxystini.
- Dr Nichols (Queen Mary University of London) and Dr Garner (Institute
of Zoology, London)
Laying the taxonomic foundations for the study of UK ranaviruses (DEFRA funded)
British amphibian populations are experiencing a wave of infection by ranaviruses. The taxonomic status of these viruses is unclear, consequently their origins have not been determined - hence it is difficult to devise control strategies. Furthermore, there appear to be biological differences between viruses infecting different species of amphibian, but without a sound understanding of the viral taxonomy and origins it has proved difficult to establish which species are infecting which other. The viruses are a serious threat to UK BAP priority species.
- Dr Glover (Natural History Museum, London) and Dr Dahlgren (Göteborg
Dispersal in the deep: molecular systematics and population connectivity of deep-sea annelids
This project will undertake taxonomic descriptions and molecular systematic analysis on at least 10 new species of poorly-studied, but potentially species-rich deep-sea annelids. The generic clades that these species belong to have global distributions, but the patterns at the species level and the degree of genetic structuring with distance are unknown. The results will have important consequences for our understanding of dispersal in the oceans, population connectivity, and the drivers of biodiversity in the deep sea.
- Dr McDonald (Bangor University) and Dr Flint (University of Aberdeen/
The Rowett Institute of Nutrition and Health)
Determination of the phenotypic taxonomy of the bacterial phylum Fibrobacteres
This project will provide the first assessment of the diversity, global distribution, phenotype, phylogeny and taxonomy of novel lineages belonging to the poorly studied bacterial phylum, Fibrobacteres, using a combined molecular/genomic and cultivation-based approach. Significant outputs would include a completely revised taxonomy of the Fibrobacteres phylum and the environmental distribution of its component taxa, and for the first time, a collection of cultivated strains with phenotypic profiles. These taxonomic data will make a much-needed contribution to the characterisation of a potentially novel cellulase system, and the provision of evidence for a role of fibrobacters in global carbon cycling.
- Dr Richards (University of Exeter) and Dr Bass (Natural History Museum,
Global evolutionary complexity of freshwater alveolates: a new threat to frogs? (DEFRA funded).
This project uses environmental DNA, phylogenetics, microbial culture isolation, and microscopy to identify the evolutionary complexity, biogeography, and comparative taxonomy of a novel group of parasitic alveolate protists that appear to infect tadpoles. The project aims include a formal taxonomic description of these novel protists and an assessment of their distribution within UK environments.
- Dr Perotti (University of Reading) and Dr Desch (University of Connecticut)
Follicular mites of primates: taxonomy and molecular markers for further co-evolutionary studies.
This project focuses on the description, for the first time, of the follicular mite species (Acari, Demodecidae) of great and lesser apes. Few mite species from New World monkeys and lemurs are known so far. The project includes a systematic approach by producing molecular markers of the mites and will also include phylogenetic and co-phylogenetic studies of the mites and their primate hosts.
- Dr Olson (Natural History Museum, London) and Dr Berriman (Wellcome
Trust Sanger Institute, Cambridge).
Toward phylogenetic resolution of parasitic flatworms through comparative analysis of complete genomes
This project proposes a novel application of whole-genome data to resolve a critical question in the evolution and systematics of parasitic flatworms (Platyhelminthes). It will serve as an example for how large-scale genomic data can be used in Systematics, and makes phylogenetically informative characters publicly available for a wider range of taxa within the phylum.
- Dr Hofreiter and Dr Missa (University of York).
Systematics of Oribius weevils (Coleoptera, Curculionidae) in New Guinea
This project proposes to work on the systematics and biogeography of Oribius weevils, a genus endemic to the island of New Guinea. Fifty-eight species are currently recognised, including a number of very serious pests to agriculture, which threaten the food security of this developing nation. Despite its economic importance, the genus has not received any taxonomic attention for over 50 years. The intended project will therefore be of immediate practical value for pest identification and management. It will also allow us to reconstruct the evolutionary history of this diverse genus and elucidate the exact role that geology played in its diversification.
- Dr Vogel (The Natural History Museum, London) and Dr Hollingsworth
(Royal Botanic Garden, Edinburgh).
The War of Bluebells
This project focuses on Hyacinthoides which comprises 11 species, including the British bluebell (H. non-scripta). The genus shows examples of recent origins of localised endemic species, and also evidence for narrow stable hybrid zones between H. hispanica and H. non-scripta in Iberia where both species are native, and extensive introgression in the UK where H. non-scripta is native but H. hispanica is introduced. Understanding species limits and the dynamics of hybridisation and diversification will shed light into the mechanisms underpinning recent speciation/maintaining species boundaries, and will also provide information to assess the threat level to the native British bluebell from hybridisation by H. hispanica.
- Dr Helgason (University of York)
Taxonomic diversity and biogeography of the arbuscular mycorrhizas
SSU rRNA gene analysis of environmental samples suggests much higher diversity of Glomeromycotan fungi in nature than can currently be cultured. This project will yield an understanding of the taxonomic diversity present in the unculturable species in the Phylum. In addition, it is becoming clear that phylogeny of other genes does not support the SSU rRNA phylogeny of this phylum. This proposal will develop an actin gene marker for use in field systems that will more accurately reflect both the identity and phylogenetic relationships within the unculturable component of this important group of fungi.
- Dr Williams (Natural History Museum, London) and Dr Goulson (University
Resolving cryptic bumblebees of the lucorum-group
Bumblebee species closely related to Bombus lucorum dominate north temperate pollinator assemblages and are also key commercial pollinators, making their accurate identification important for pure and applied biology. However, traditional species identification based on colour patterns is impossible for many individuals and is often wrong according to recent genetic data. Pilot work suggests that global sampling and genetic analysis may produce new, morphologically diagnosable groups. This project will combine this broad global approach with a local in-depth study to clarify the taxonomy, distribution, ecology, and conservation status of this important group world-wide and in the UK.
- Dr Glover (University of Cambridge) and Dr Rudall (Royal Botanic Gardens,
Molecular control of petal spot evolution in Cape Flora daisies
This project combines plant systematics and development to study the molecular drivers of petal spot evolution within a species complex. Geographically distinct populations of the South African daisy Gorteria have distinct petal spot phenotypes, allowing us to investigate the molecular changes that underlie the morphological evolution between populations of a single species. Determining the direction of petal spot evolution within the context of a detailed phylogenetic analysis and identifying the genes encoding the regulators of petal spot morphology will provide a complete picture of the molecular evolution of a key trait central to morphological differentiation and speciation.