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Dr Si Creer - Research interests

Enhancing freshwater ecosystem biomonitoring:defining and testing an ecometagenetic DNA identification framework.

Biological indicators are used to estimate the state of the environment and the Environment Agency mandatorily monitors the health of freshwater ecosystems throughout the UK. However, traditional monitoring approaches suffer from the “identification bottleneck” problem (e.g. subjectivity, lack of resolution, labour-intensive traditional taxonomy approaches mismatched with ecosystem diversity). This KESS-funded PhD program, in collaboration with Iliana Bista will populate a DNA reference library for up to 200 macroinvertebrate indicator species and test and test the efficacy of the use of second generation sequencing approaches in enhancing freshwater biomonitoring programs. Chironomid image ©entomart.

 

Marine benthic meiofaunal diversity

Marine benthic meiofaunal communities are dominated by the potentially hyperdiverse nematodes, that play a crucial role in marine ecosystem functioning and services. Nematodes are the most abundant multicellular organisms on earth and in marine sediments they can make up between 50-90% of the multicellular fauna. Despite their abundance and pivotal role in ecosystem functioning, a current estimate of global nematode diversity (c. 1 million species) remains a matter of conjecture. This massive knowledge gap is the result of the small size and the apparent morphological similarity of nematodes that cause problems in the logistics and accuracy of species identification. Accordingly, in the past few years there has been a noticeable move towards the establishment of a molecular operational taxonomic unit (MOTU) scheme for the identification of meiofauna. MOTU studies to date have studied diversity via sequencing molecular barcodes from a limited number of organisms obtained from environmental samples. However, molecular diversity accumulation curves suggest that there are more undiscovered species present in meiofaunal communities.

Sequencing the meiofaunal metagenome of the fresh/saltwater interface.

Estuaries are key transitional habitats that are significantly affected by local and global anthropogenic activities. They are typically considered to be low diversity systems; a taxonomically biased inference drawn from the low alpha diversity of macrofauna. In contrast, meiofaunal diversity is substantial, with most estuaries estimated to be inhabited by approximately 200 species of nematodes, with numbers ranging from 106-108 animals per square metre, contributing to between 50-90% of the metazoan faunal species richness. In collaboration with The Environment Agency, The Thames Estuary Partnership and The Mersey Basin Campaign, this NERC funded project will link large-scale biodiversity appraisals (454 18S sequencing, videocapture and morphology) of environmental samples across ecological gradients with hydrodynamic models and macrofaunal processes.

Mitogenomics and molecular identification of spiders

Spiders are among the oldest and most diverse groups of terrestrial organisms, with a current diversity of over 37,500 described species placed in 3,471 genera and 109 families. From an ecological point of view, spiders are an unequivocally important guild. Furthermore, spiders are model organisms in biochemical (silk proteins and venom), behavioural (especially sexual and web-building behaviours), ecological (foraging, predator-prey systems, integrated pest management), comparative development and speciation research (http://research.amnh.org/atol/files/).

Advancing mitogenomics via ultrasequencing: A case study in the Araneae.

Since the late 1980s, molecular systematics has progressed via the analysis of increasingly larger numbers of genes and characters. At one end of the spectrum, phylogenies are derived from a moderate number of gene partitions, and at the other, genome sequencing and interrogation of expressed sequence tag (EST) libraries are leading to phylogenomic approaches. A compromise between these extremes lies in mitogenomic analyses (the comparative analyses of whole mitochondrial genomes) that have been shown capable of resolving evolutionary relationships among a large range of higher taxa. Although the availability of mitogenomic datasets are increasing, there are still logistical limitations regarding the chain-termination sequencing of c. 15,000 b.p. of sequence data for multiple taxa. A clear solution to this problem lies within ultrasequencing platforms. Despite the ecological and evolutionary significance of the Araneae, our current ability to address comparative phylogenetic hypotheses is severely limited by a lack of a robust phylogenetic framework for the group as a whole. In collaboration with Dr. Sara Goodacre (Nottingham University), Prof. Greg Hurst (University of Liverpool), Dr. Miquel Arnedo (Universitat de Barcelona) and Dr. Susan Masta (Portland State University) this CoSyst-funded project will seek to augment ongoing US AToL endeavours by sequencing and analysing a large number of spider mitogenomes in order to create a robust, family-level phylogenetic framework.

Molecular barcoding in spiders

The cytochrome oxidase I (COI) barcoding of life program (http://www.barcodinglife.org; http://barcoding.si.edu) seeks to use short standardised DNA sequences from a uniform locality on the COI gene for species identification. Barcode databases have the potential to be used to confirm the identity of any life-history stage or body part of an organism, prey item/stomach contents or even discover new and cryptic species. I am currently working towards providing a barcoding framework for a range of marine and terrestrial invertebrates, including European Tetragnathidae and Lycosidae spiders. Spiders are ecologically important, being the dominant predators of insects, and are therefore important biodiversity indicators in natural and agricultural ecosystems. Furthermore, spiders can not usually be identified at the species level until after their final moult and a substantial amount of specialist knowledge and experience is often required to achieve identification of even a small number of families. In addition to providing a valuable ecological resource tool, molecular barcoding European spiders will uncover previously undescribed levels of molecular genetic diversity that exist across a diverse array of species, genera and families. This information will increase our understanding of the relationships between life history strategies and genetic diversity and assist in our understanding of taxonomic relationships among species.