Molecular Ecology and Fisheries Genetics Laboratory
I am interested in using contemporary molecular tools to address diverse questions focusing on biodiversity, ecology and evolution. This is a particularly exciting time in the field of molecular ecology, since advances in DNA sequencing throughput have recently offered a paradigm shift in our ability to assess previously intractable functional and taxonomic biodiversity at an unprecedented scale, augmenting existing biodiversity fields and empowering others. Using such technologies, I am testing a range of hypotheses regarding the alpha and beta functional and taxonomic diversity of macro-, meio- and microbial communities (e.g. microbiomes) in space and time. Focal environments include estuarine, coastal, freshwater, terrestrial, the deep sea and whole organisms, in order to understand the drivers of diversity in natural communities and also how diversity is linked with ecological function/disease state. Additional activities include the investigation of transcriptomic responses to environmental peturbation, mitogenomics, population genetics, life history evolution, polyploidy and "second-generation" biomonitoring. These projects facilitate the investigation of links between biodiversity and ecosystem processes, understanding environmental genomic responses to change/adaptive evolution and the advancement of the field of phylogenetics. If you want to find out more, please go to my research page.
Interested in the difference between metagenomics, metagenetics, metabarcoding and metatranscriptomics? Please check out this poster that we recently contributed to a "Systems Ecology" workshop invited by the 2012 British Ecological Society Annual Meeting, Birmingham UK. More in the series available upon request!!
2000 PhD. Molecular phylogeography and venom evolution of Trimeresurus stejnegeri in Taiwan. NERC funded, The University of Wales, Bangor (UWB), UK.
1997 MSc. Ecology (Distinction). NERC funded, UWB.
1992 BSc. (Hons) Applied Biology (2.1). University of Bath, UK.
2005 Teaching in Higher Education Certificate. UWB.
11/12 - present Senior Lecturer in Molecular Ecology - Bangor University
11/11 - 10/12 Lecturer in Molecular Ecology - Bangor University.
11/05 – 10/11 Senior Research Fellow in Molecular Ecology - Bangor University.
07/05 – 10/05 Postdoctoral Research Associate. NERC grant, “Functional and genomic venom diversity of phospholipase A2 (PLA2) genes in Asian pitvipers” UWB.
06/01– 06/05 Postdoctoral Research Associate (named). Wellcome Trust grant, “Reliable molecular phylogenies for medically important venomous snakes: subtropical and tropical Asian vipers” UWB.
09/03 – 09/04 Temporary Lectureship in Zoology. UWB.
01 – 06/01 Postdoctoral Research Associate. Leverhulme Trust grant, “Far-east Asian pitvipers: venom evolution and biodiversity” University of Wales, Bangor.
2012-2015 - FISHPROBIO: Marie Curie Outgoing Fellowship with Martin Llewelyn (290,000 Euros)
2010-2011 - NERC AFI Collaborative Gearing Scheme grant: A second-generation sequencing perspective of the Antarctic bentho-pelagic microbial biosphere
2010-2012 - MARMEDIV: Marie Curie Incoming Fellowship with Frederic Sinniger (174,000 Euros)
2009- Natural Environment Research Council (NERC) Environmental genomics of life in the intertidal: Design and optimization of a gastropod microarray (£8000)
2008-2010 - NERC Post genomic and proteomics grant: Sequencing the meiofaunal metagenome of the marine/freshwater interface in key estuarine ecosystems (£140000)
2008- CoSyst: The Systematics Association, The Linnean Society, Biotechnology and Biological Sciences Research Council (BBSRC), NERC: Advancing mitogenomics via ultrasequencing: A case study within the Araneae (£10200)
2006-2009 - NERC New Investigator Award: Are marine nematodes hyperdiverse? A metagenomic solution (£76000)
2007 - NERC Phylochip development for the rapid identification of littoral meiofaunal communities (£4750)
2004 Joseph B. Slowinski Award for the most distinguished international paper on snake systematics for Creer et al (2003a) ($500)
1997 UWB Llewellyn and Mary Williams Scholarship for PhD funding (£14000)
1996 NERC MSc funding (£3500)
2009- NERC Peer Review College member
2006-2009 Committee member for the Joseph B. Slowinski Award
2005 Instigator of UW Bangor becoming a member organisation of the Consortium for Barcoding of Life
2003-present Recorder for the British Arachnological Society Spider Recording Scheme
2003-present Member of the British Arachnological Society (BAS)
In addition to the above, I review articles for Nature Communications, Systematic Biology, Molecular Ecology, Philosophical Transactions and Proceedings of the Royal Society, Biological Sciences, BMC Evolutionary Biology, Conservation Genetics, Heredity, Journal of Molecular Evolution, Journal of Experimental Marine Biology and Ecology, Journal of Fish Biology, Journal of Zoology, Environmental Microbiology and Marine Ecology Progress Series.
Man-made chemicals that disrupt endocrine function (endocrine dispuptors) contaminate all environments, producing a range of undesirable effects across a wide range of taxa and can cause abnormal development of male and female traits. The female dogwhelk, Nucella lapillus, provides one of the most clearcut examples of anthropogenically induced endocrine disruption in aquatic ecosystems and is used as an “ecological sentinel” to detect the detrimental effect of tributyltin (TBT) in marine ecosystems. Combining second-generation transcriptome sequencing and Agilent 180K feature microarray fabrication, this work aimed to unravel the functional genomic mechanisms underpinning the action of TBT in the imposex response (the superimposition of male sexual characteristics in females) in Nucella. We were able to simultaneously observe the involvement of previously identified pathways, but also discover and confirm the involvement of additional putative PPAR pathways, providing evidence for novel commonality in endocrine disruption signalling pathways between invertebrates and vertebrates. Arising from the PhD program of Dr. Sonia Pascoal and funded by FCT and the NERC NBAF program, this work, published in Molecular Ecology was a great collaboration between MEFGL members, Prof. Andy Cossins and colleagues from the Liverpool Centre for Genomic Research and Carlos Barroso and Sonia Mendo (University of Aveiro, Portugual).
In their natural waterlogged state, peatlands constitute the most important, long-term, terrestrial organic carbon store on our planet. However, it has been shown that under drought conditions the stored carbon is released as atmospheric gaseous CO2 and dissolved organic carbon (DOC) into surrounding waterways, contributing to global warming and the net loss of carbon from peatland ecosystems. Here, funded by the HPC Wales/Fujitsu partnership and partnered with Welsh Water, we will use "metagenetic" and shotgun "metagenomic" approaches to identify both the composition and functional diversity of the microbial communities responsible for drought-driven carbon loss from a range of peatland ecosystems. By understanding the mechanisms associated with carbon loss, we will be able to explore approaches aimed at regulation of key microbial drivers of carbon loss through the geo-engineering of peatlands to regain carbon. Such a multidisciplinary project demands expertise in wetland biogeochemistry and metagenomics and is lead by Caitlin Potter, in collaboration with Prof. Chris Freeman, Prof. Peter Golyshin, Dr. Nathalie Fenner and Dr. James McDonald.
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 and the Environment Agency, 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 biodiversity is important for ecosystem functioning, sustainability and resilience, but the magnitude and composition of marine diversity at a range of spatial and taxonomic scales are undefined. Marine meiofaunal communities are dominated by the potentially hyperdiverse nematodes, accompanied by other small metazoans from 60% of animal phyla, therefore presenting a major fraction of global biodiversity. Despite the abundance and pivotal role in ecosystem functioning, a current estimate of global meiobenthic diversity remains a matter of conjecture. This knowledge gap is the result of the small size and the apparent morphological similarity of microbial metazoans that causes problems in the logistics and accuracy of species identification. Over the past few years myself and collaborators have contributed substantially to the development of a new field of eukaryotic biodiversity identification, that uses "second", or "next" generation sequencing approaches to simultaneously assess the richness of multiple phyla from the marine benthos. Empirical and perspective style papers have been published in Molecular Ecology, Nature Communications, Nucleic Acids Research and Trends in Ecology and Evolution.
This NERC funded project used standard and novel molecular approaches (454 Roche 18S sequencing) and videocapture technology to estimate the actual molecular (and subsequent species) diversity present at different spatial scales throughout littoral communities of UK nematodes and other meiofauna and extrapolate this information to estimates of regional and global species richness. The utilization of second-generation sequencing to quantify molecular biodiversity represents a major advance towards identifying a crucial biological component of the earth's ecosystems and enable further hypotheses to be tested regarding the complex nature of 454 sequencing.
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.
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/).
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 Andy Briscoe, 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.
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.
Lallias, D., Fonseca, V.G., Gaspar, J., Hiddink, J., Sung, W., Neill, S.P., Barnes, N., Ferrero, T., Hall, T., Lambshead, P.J., Packer, M., Thomas, W.K. and Creer, S. 2014. Environmental metabarcoding reveal heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME Journal. In Press, online early open.
Fonseca, V.G., Carvalho, G.R., Nichols, B., Quince, C., Johnson, H., Neill, S., Lambshead, P.J.D., Thomas, W.K., Power, D. and Creer, S. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography. Read the full article.
Bohmann, K., Evans, A., Gilbert, T.A., Carvalho, G.R., Creer, S., Knapp, M., Yu D. and de Bruyn, M. 2014. Environmental DNA for Wildlife Biology and Biodiversity Monitoring. Trends in Ecology and Evolution. 29: 358-367.
Morgan, M. J., Bass, D., Bik, H., Birky, C. W., Blaxter, M., Crisp, M. D., Derycke, S., Fitch, D., Fontaneto, D., Hardy, C. M., King, A. J., Kiontke, K. C., Moens, T., Pawlowski, J. W., Porazinska, D., Tang, C. Q., Thomas, W. K., Yeates, D. K., Creer, S. 2014. A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proceedings of the Royal Society, Series B. 281: no. 1783, 20133076.
Malhotra, A., Creer, S., Harris, J.B., Stocklin, R. Favreau, P. and Thorpe, R.S. 2013. Predicting function from sequence in a large multifunctional toxin family. Toxicon. 72: 113-125
Montes, I., Conklin, D. Albaina, A., Creer, S., Carvalho, G.R., Santos, M., Santos, M. and Estonba, A. 2013. SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing. PLoS One. 10.1371/journal.pone.0070051
Briscoe, A.G., Goodacre, S., Masta, S., Taylor, M.I., Arnedo, M.A., Penney, D., Kenny, J. and Creer, S. 2013. Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). PLoS One. http://dx.plos.org/10.1371/journal.pone.0062404
Pascoal, S., Carvalho, G.R., Vasieva, O., Hughes, R.N., Cossins, A., Fang, Y., Ashelford, K., Olohan, L., Barroso, C., Mendo, S, and Creer, S. 2013. Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. Molecular Ecology. 22: 1589-1608.
Pascoal et al. 2013 was featured in Molecular Ecology's Perspectives: Chapman, R.W. and Guillette Jr, L.J. 2013. Contaminants and impoSEX: transcriptomics of contaminant-induced sex change. Molecular Ecology. 22: 1485-1487.
van Wijk, S.J., Taylor, M.I., Creer, S., Dreyer, C., Rodrigues, F.M., Ramnarine, I.W., van Oosterhout, C. and Carvalho, G.R. 2013. Experimental harvesting of fish populations drives genetically-based shifts in body size and maturation. Frontiers Ecol. Environ. 2013; doi:10.1890/120229; available from: http://www.esajournals.org/toc/fron/0/0
Pascoal S., Carvalho G.R., Creer, S., Mendo S. and Hughes R. 2012. Plastic and heritable variataion in shell thickness of the intertidal gastropod Nucella lapillus associated with risks of crab predation and wave action, and sexual maturation. PLoS One http://dx.plos.org/10.1371/journal.pone.0052134
Matzen da Silva, J., dos Santos, A. Cunha, M.R., Costa, F.O., Creer, S. and Carvalho, G.R. 2012. Investigating the molecular systematic relationships amongst selected Plesionika (Decapoda: Pandalidae) from the Northeast Atlantic and Mediterranean Sea. Marine Ecology, DOI: 10.1111/j.1439-0485.2012.00530.x .
Creer, S. and Sinniger, F. 2012. Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology. 21: 1033-1035.
Bik, H., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R. and Thomas, W.K. 2012. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution. http:/dx.doi.org/10.1016/).tree.2011.11.010
Pascoal, S., Carvalho, G., Creer, S., Rock, J., Kawaii, K., Mendo, S., Hughes, R. 2012. Plastic and heritable components of phenotypic variation in Nucella lapillus: an assessment using reciprocal transplant and common garden experiments. PLoS One 7(1): e30289. doi:10.1371/journal.pone.0030289
Fonseca V.G., Nichols, B., Lallias, D., Quince, C., Carvalho G.R., Power, D.M. and Creer, S. 2012. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research: doi: 10.1093/nar/gks002
Alexandrou, M.A., Oliveira, C. Maillard, M. McGill, R.A.R., Newton, J., Creer, S., and Taylor, M.I. 2011. Competition and phylogeny determine community structure in Mullerian co-mimics. Nature. 469: 84-89.
Matzen, J., dos Santos, A., Cunha M.R., Costa, F.O., Creer, S. and Carvalho, G.R. 2011. Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs. PLoS One. http://dx.plos.org/10.1371/journal.pone.0028233
Fonseca, V.G., Packer, M., Carvalho, G.R., Power, D., Lambshead, P.J.D. and Creer S. 2011. Isolation of marine meiofauna from sandy sediments: from decanting to DNA extraction. Nature Protocol Exchange. doi:10.1038/nprot.2010.157
Matzen, J., Creer, S., dos Santos, A., Costa, A.C., Cunha M.R., Costa, F.O. and Carvalho, G.R. 2011. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One. 6: e19449
Carvalho, G.R., Creer, S., Allen M., Costa F.O., Tsigenopoulos C.S., Le Goff-Vitry M., Magoulas A.M., Medlin L. & Metfies K. 2011. Genomics in the discovery and monitoring of marine biodiversity. In: An Introduction to Marine Genomics, (eds.) Boyen C and Cock, M. Springer-Verlag.
Creer, S. 2011. New technologies. pp. 46-47 in: Marine Benthic Nematode Molecular Protocol Handbook (Nematode Barcoding), eds PJD Lambshead and M. Packer. International Seabed Authority, Jamaica. Read the online version here.
Fonseca, V.G., Carvalho, G.R, Sung, W, Johnson, H.F, Power, D.M, Neill, S.P, Packer, M, Blaxter, ML, Lambshead, PJD, Thomas, WK, & Creer, S (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications. DOI:http://dx.doi.org/10.038/ncomms1095, featured in the Public Library of Science's (PLoS) Biodiversity Hub
Creer, S. 2010. Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Molecular Ecology. 19:2829-2831
Creer, S.*, Fonseca, V.G.*, Porazinska D.L., Giblin-Davies, R.M., Sung, W., Power, D.M., Packer, M., Carvalho, G.R., Blaxter, M.L., Lambshead, P.J.D. and Thomas, W.K. 2010. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology. 19: (Suppl. 1) 4-20. PDF * Joint first authors.
Domingues C.P., Creer S., Taylor MI., Queiroga H., Carvalho GR. Genetic structure of Carcinus maenas withinits native range: larval dispersal and oceanographic variability. Marine Ecology Progress Series 410: 111–123, 2010 DOI: 10.3354/meps08610 PDF
Domingues CP., Creer S., Taylor MI., Queiroga H.,Carvalho GR. Temporal genetic homogeneity among shore crab(Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast. Heredity (2010), 1–9 PDF
Pascoal, S. Creer, S. Taylor, M.I., Queiroga, H., Carvalho, G. and Mendo, S. 2009. Development and application of microsatellites in Carcinus maenas: Genetic differentiation between Northern and Central Portuguese populations. 2009. PLoS One 4: e7268. PDF
Malhotra, A., Creer, S., Pook, C.E. and Thorpe R.S. 2009. Inclusion of nuclear intron sequence data helps to identify the Asian sister group of New World pitvipers. Molecular Phylogenetics and Evolution, 54: 172-178. PDF
Guo, P., Malhotra, A., Creer, S., and Pook, C.E. 2009.An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers. Journal of Zoological Systematics and Evolutionary Research. 47: 378-384. PDF
Guo, P., Malhotra, A., Li, C., Creer, S., Pook, C.E. and Wen, T. 2009.Systematics of the Protobothrops jerdonii complex (Serpentes, Viperidae, Crotalinae) inferred from morphometric data and molecular phylogeny. Herpetological Journal 19: 85-96. PDF
Creer, S. 2007. Choosing and using introns in molecular phylogenetics. Evolutionary Bioinformatics 3: 99-108. PDF
Guo, P., Malhotra, A. Li, P.P., Pook, C.E. and Creer, S. 2007. New evidence on the phylogenetic position of the poorly known Asian pitviper Protobothrops kaulbacki (Serpentes : Viperidae : Crotalinae) with a redescription of the species and a revision of the genus Protobothrops. Herpetological Journal 17: 237-246. PDF
Creer, S., Malhotra, A., Thorpe, R.S., and Pook, C.E. 2006. Optimal intron analyses in the Trimeresurus radiation of Asian pitvipers. Systematic Biology 55: 57-72. PDF
Creer, S. 2005. On the application of molecular barcodes in toxinological research. Toxicon 46: 709-710. PDF
Creer, S., Malhotra, A., and Thorpe, R.S., and Pook, C.E. 2005. Targetting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers. Cladistics 21: 390-395. PDF
Creer, S., Malhotra, A., Thorpe, R.S., Chou, W.-H., and Stenson, A.G. 2004. The utility of AFLPs for corroborating mitochondrial DNA phylogeographical pattern in the Taiwanese bamboo viper, Trimeresurus stejnegeri. Journal of Evolutionary Biology 17: 100-107. PDF
*Creer, S*., Malhotra, A. and Thorpe, R.S. 2003a. Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the Asian pitviper genus Trimeresurus : separate, simultaneous, and conditional data combination analyses. Molecular Biology and Evolution 20: 1240-1251. PDF
Creer, S., Malhotra, A. Thorpe, R.S., Stöcklin, R., Favreau, P., and Chou, W.-H. 2003b. Genetic and ecological correlates of intraspecific variation in pitviper venom composition detected using matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF-MS) and isoelectric focusing. Journal of Molecular Evolution 56: 317-329. PDF
Creer, S., Chou, W.-H., Malhotra, A. and Thorpe, R.S. 2002. Offshore insular variation in the diet of the Taiwanese bamboo viper, Trimeresurus stejnegeri (Schmidt). Zoological Science 19: 907-913. PDF
Creer, S., Malhotra, A. Thorpe, R.S., and Chou, W.-H. 2001. Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan. Molecular Ecology 10: 1967-1981. PDF
Creer, S. 1999. Geographic variation in the venom composition of the Taiwanese bamboo viper (Trimeresurus stejnegeri) in the small, yet environmentally heterogenous island of Taiwan. Toxicon 37. 2. 289-290, from the 13th European Toxinology conference, London.
Fonseca et al. 2010 features artwork from Warren Photographic