We aim to understand how the diversity of form in the animal kingdom evolved. The focus of our research is the connection between the evolution of animal genome organisation and development, with a particular concentration on the homeobox-containing genes. The Hox gene cluster is established as a corner-stone of Evolutionary Developmental Biology, but much about the evolution of its organisation and mode of operation remains unknown. Also the Hox cluster is not unique as a homeobox gene cluster controlling animal development, further clusters being the ParaHox and NK clusters, all of which evolved within larger arrays of homeobox genes (the Mega-cluster and Super-Hox cluster). We utilize a variety of organisms in our research (including amphioxus, sea squirts, polychaetes and priapulids), chosen from key points in the phylogeny of the animals to enable reconstruction of the ancestral conditions at major nodes in the animal kingdom; the origin of bilaterians, protostomes, deuterostomes, chordates and vertebrates. 

My research interests are aimed at determining the effect that contaminant and pathogen exposure has on the risk of mortality and morbidity in marine mammals, both seals and cetaceans.  I am particularly interested in the role of these factors in determining an animals early survival and reproductive capability and in how they interact with the species immune and endocrine systems.  This interest has also led to more fundamental questions about how the immune system may be shaped by the life history strategy of marine mammals.  

I am also now very interested in the physiolgical adaptations of mammals to a marne existence, particularly at the molecular level; such as the respiratory adaptations and strategies that allow animals to forage at depth and their adaptations to cope with long periods of fasting.

Genomic and physiological approaches are being used to investigate muscle growth and adaptation in teleost fish.  Skeletal muscle fibres are produced during the embryonic, larval and adult stages. The genetic mechanisms controlling the production of muscle fibres and their subsequent hypertrophy are being studied. Several novel genes have been discovered that may inhibit myotube formation in adult fish and future research will elucidate their function.  microRNAs are short noncoding RNAs with largely uncharacterized regulatory roles that  represent a considerable part of the transcriptional output of animal and plant genomes. Our research with model species (pufferfish and zebrafish) has discovered some new miRNAs and is investigating changes in miRNA expression patterns with growth and environmental adaptation.  Several miRNAs have been identified that change in expression when myotube production becomes inhibited. The gene targets and function of these miRNAs is being elucidated. Other research interests include the role of maternally transmitted messenger RNAs in early development and developmental plasticity. The temperature of embryonic development has been shown to have persistent effects on muscle growth in adult stages and both the genetic mechanisms and physiological consequences at the whole animal level are being investigated.

Animal Physiology

Muscle action and performance during locomotion in molluscs, fishand amphibians. The implications of body size for muscle functionin vivo. The evolution of muscle performance characteristics inrelation to environmental temperature with particular referenceto sub-Antarctic and Antarctic Notothenioid fishes and bivalvemolluscs. The phenotypic plasticity of muscle to temperature changeduring ontogeny: molecular and cellular mechanisms and evolutionarysignificance. Laboratory and field studies on muscle developmentand growth regulation in fish, with particular reference to temperature.The effects of ploidy manipulation and sex-reversal on musclegrowth characteristics in fish.

Plant evolutionary biology, genealogical reconstruction and analysis (likelihood-based paternity and parentage analysis), quantitative genetics, sexual dimorphism, linkages between molecular variation and phenotypic evolution, ecological and genetic bases for population differentiation and speciation, conservation biology and biodiversity, risk assessment of gene flow and its consequences in genetically modified organisms, public understanding of science.

My research interests are in parentage analysis, quantitative genetics, phenotypic evolution, sexual dimorphism, evolutionary genomics of plants, and societal applications of science

Research Group

Doctoral Students

• 2007-present  Ms Malin Rivers. Conservation status and conservation genetics of Delonix in Madagascar.
• 2003-2007 Dr. Mark Looseley. A Comparative investigation of nuclear DNA content and its phenotypic impacts in Silene marizii and S. latifolia. 
• 1994-2000 Dr. Jessica Wright . The effects of positive and negative selection on floral characters in natural population of Silene latifolia. Currently a Conservation Geneticist, USFS, University of California, Davis, CA, USA
• 1990-1997 Dr. Elizabeth Elle. Sex allocation and reproductive success in a perennial hermaphrodite, Solanum carolinense. Currently Associate Professor, Department of Biology, Simon Fraser University
• 1989-1995 Dr. Deborah Sheely . The ecological impact of genetic diversity on seedling recruitment in a tropical tree Campnosperma brevipetiolata (Anacardiaceae). Currently a Program Officer with USDA Competitive Grants.
• 1998-1993 Dr. Diane Byers . The genetic consequences of rarity in Eupatroium resinosum. Currently an Associate Professor at Illinois State University.

Postdoctoral Fellows

• 2005-2006 Dr. Rebecca Yahr , Ph.D. Duke University (advisors Dr. R. Vilgalys and Dr P. Depriest) population biology and genetics of lichen symbioses. Research Fellow, RBGE.
• 2000-2004 Dr. Christine Vassiliadis , Ph.D. University of Lille (advisors Dr. P. Vernet and Dr Saumitou-Laprade) evolution and maintenance of androdioecy. Lecturer, University of Orsay
• 1990-1994 Dr. Denise E Costich , Ph.D. University of Iowa (advisor, Dr. H. F. Howe) evolution of dioecy in plants. Cornell University/Boyce Thompson Institute
• 1989 Dr. Lynda F. Delph . Ph.D. University of Canterbury, New Zealand (advisor Dr. D. G. Lloyd) gender specific resource allocation in plants Associate Professor, Indiana University.

Parentage analysis & quantitative genetics

I have a long-standing interest in the application of statistical methods of genealogical inference to the analysis of the structure and genetic dynamics of natural populations. Applying likelihood methods that originated in forensic analysis of human paternity, the assignment of male parentage in plant populations provides information on gene flow and impacts of specific phenotypic traits on male reproductive success. Specific contributions in this area have included development of likelihood models for paternity analysis, application of such models to understating the structure of a range of plant populations, and the delelopment of a Windows-based software package, PatQuest, for conducting such analyses. Present work in this area includes development of statistical methods for the integration of likelihood-based paternity inference with REML estimation of quantitative genetic parameters, to be applied to natural populations where standard multigenerational quantitative genetics experiments are not practical. In addition, models for investigating gene flow, based on approaches derived from paternity analyses, have been applied to investigation of gene flow in transgenic cultivars.

• Meagher TR (1986) Analysis of paternity within a natural population of Chamaelirium luteum . I. Identification of most-likely male parents. American Naturalist . 128: 199-215.
• Meagher TR, Thompson EA. (1987) Identification of parentage for seedlings within a natural population of Chamaelirium luteum . Ecology 68: 803-812.
• Thompson EA, Meagher TR (1998) Genome sharing and the estimation of pairwise relationship. Theoretical and Applied Genetics 97: 857-864.
• Smouse PE, Meagher TR, Kobak CJ (1999) Parentage analysis in Chamaelirium luteum (L.) Gray (Liliaceae): why do some males have disproportionate reproductive contributions. Journal of Evolutionary Biology 12: 1069-1077.
• Elle E, Meagher TR (2000) Sex allocation and reproductive success in the andromonoecious perennial, Solanum carolinense (Solanaceae). II. Paternity and functional gender. American Naturalist 156: 622-636.
• MeagherTR, Vassiliadis C (2003) Spatial geometry determines gene flow in plant populations. Hails RS, Beringer JE, Godfray HCJ (eds.) Genes in the environment. Pp. 76-90.
  Oxford, UK, Blackwell Science Ltd. Meagher T., Belanger FC, Day PR (2003) Using empirical data to model transgene dispersal. Trans. Royal Society (London) B 358: 1157-1162.

Sexual dimorphism and sex-specific selection

Reproductive success as male or female parents in plants is based on very different pathways, subject to sex-specific processes of selection. In dioecious species, long-term consequences of such sex-specific selection can lead to sexual dimporphism in a wide range of traits, from the molecular level to the ecological. My interest in this area began with an investigation of resource allocation and life history impacts of such in Chamaelirium luteum (Liliaceae, pictured above), a flowering plant that exhibits extreme sexual dimorphism in inflorescence structure. More recent work on this phenomenon has focused on floral dimorphism in the dioecious Silene latifolia , which has a well-established genetic basis for sex determination, and a shorter life-span that is more amenable to genetic investigation.

• Meagher TR (1984) Sexual dimorphism and ecological differentiation of male and female plants. Annals Missouri Botanical Garden 71: 254-264.
• Meagher TR (1994) The quantitative genetics of sexual dimorphism in Silene latifolia . II. Responses to sex-specific selection. Evolution 48: 939-951.
• Delph LF, Meagher TR (1995) Sexual dimorphism masks life history trade-offs in the dioecious plant Silene latifolia . Ecology 76: 775-785.
• Meagher TR, Delph LF (2001) Individual flower demography, floral phenology, and life history in Silene latifolia . Evolutionary Ecology Research 3: 845-860.
• Costich DC, Meagher TR (2001) Impacts of floral gender and whole-plant gender on floral evolution in Ecballium elaterium (Cucurbitaceae). Biological Journal of the Linnean Society 74: 475-487.
• Wright JW, Meagher TR (2004) Selection on floral characters of natural Spanish populations of Silene latifolia . Journal of Evolutionary Biology , in press.
   

Evolutionary genomics and phenotypic evolution

My investigations into the genetic basis of floral dimorphism in flower size in Silene latifolia have inexorably led to a more detailed analysis of the genetic basis of flower size in general. As this is a quantitative trait, initial investigations involved quantitative genetics approaches. More recently, a link has been established between quantitative variation in flower size and genome size/organization. This latter discovery has led to a phylogenetic investigation of the relationship between genome size and flower size evolution across related taxa, and a joint QTL analysis of flower size and DNA content.

Present work in this area is exploring the possible role of specific repetitive sequences, such as retrotransposons, in DNA content variation associated with flower size evolution. We are also investigation the role of such DNA content variation in contributing to reproductive isolation between species.

• Meagher TR, Costich DE (1994) Sexual dimorphism in nuclear DNA content within and between populations of Silene latifolia . American Journal of Botany 81: 1198-1204.
• Meagher TR, Costich DE (1996) Nuclear DNA content and floral evolution.Proceedings of the Royal Society (London), Series B 263: 1455-1460.
• Meagher TR (1999) The quantitative genetics of sexual dimorphism. In Sexual dimorphism in plants , M. Geber, T. Dawson, and L. Delph, eds. Springer-Verlag New York.

Societal applications of science

Science is conducted within a broader societal context, and indeed is based on support derived from that context in the form of government financing. As a practicing scientist, one has an obligation to identify connections between basic research and potential application to societal needs. My activities in this area have been several fold. First, I have applied methods of paternity analysis and other analytical tools from evolutionary biology to the issue of gene flow from transgenic cultivars to adjacent ruderal populations. On a science policy level, I was a co-chair of a US national initiative on Evolution, Science and Society, which was directed towards outlining the importance of scientific contributions of evolutionary biology, I have served as a founding and current member of the Society for the Study of Evolution 's Education Committee, and I am presently a member of the Science Advisory Council of the UK Department of Environment, Food and Rural Affairs.

• Meagher TR (1999) Evolution and today's society. BioScience 49: 923-925.
• Meagher TR, Futuyma DJ (eds) (2001) Evolution, Science and Society: evolutionary biology and the national research agenda. California Journal of Science Education 1: 19-32.
• Meagher TR, Futuyma DJ (2001) Executive document: Evolution, science, and society - Foreword: Evolution in the century of biology. American Naturalist 158: 1-46 Suppl. S.
   

Science is conducted within a broader societal context, and indeed is based on support derived from that context in the form of government financing. As a practicing scientist, one has an obligation to identify connections between basic research and potential application to societal needs. My activities in this area have been several fold. First, I have applied methods of paternity analysis and other analytical tools from evolutionary biology to the issue of gene flow from transgenic cultivars to adjacent ruderal populations. On a science policy level, I was a co-chair of a US national initiative on Evolution, Science and Society, which was directed towards outlining the importance of scientific contributions of evolutionary biology, I have served as a founding and current member of the

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Evolutionary Biology and Speciation

His major research field concenrs the evolutionary genetics of behaviours which influence sexual isolation, and other approaches to speciation. Main research projects involve analyses of the inheritance and geographic variation of courtship signals and preferences of Drosophila and bushcrickets. Also, quantitative trait loci analysis of interspecific differences in song and pheromones of Drosophila, and phylogeographic analysis of the bushcricket Ephippiger. A particular interest is developing model systems for the accurate quantification and analysis of female mating preferences. Other projects include population and phylogenetic analyses of Mexican fish and empid flies.

Overview of Research Interests:

The Ritchie laboratory takes a broad approach to studies of the origin of species. Behaviours involved in sexual isolation are characterised and their genetic control studied, using both quantitative and molecular approaches to behaviour genetics, as well as phylogeographic studies of variation in behaviour. 

Current Research Projects:

Analysing genes influencing Drosophila behaviour

We have used Quantitative Trait Locus techniques to localise the genomic location of genes influencing behaviour in flies. Now that several genomes are available, it is possible to move into ‘postgenomic’ studies of patterns in the evolution of these genes, and to begin looking at the expression and variation of candidate genes

Variation in female mate preferences

Female preferences are very important to sexual selection and speciation, but are difficult to measure and quantify. We measure preference variation in different species of Drosophila and other insects such as bushcrickets.

Phylogeography and behaviour

Studies of geographic variation in a range of organisms, including Mexican fish and cannibalistic crickets, explore the importance of variation in behaviour to population genetic structure and the role of sexual selection in speciation.

MPhil/PhD project opportunities:

Please contact me directly to discuss potential postgraduate opportunities.

For more information, please visit my research pages: Complex Biological Neworks.

My research uses computational methods to analyse complex biological networks, and evaluates the computational methods through both computer simulation and biological intervention. I concentrate on networks in three types of biological systems: neuronal networks, gene regulatory networks, and species interaction networks.

Current Projects

Neural information flow

We have for the first time applied and validated a Bayesian network (BN) inference algorithm for recovering neural information flow. BNs are an advance over prior methods, as they can handle the known non-linearity present in neural systems. We applied a BN to multi-unit electrode array recordings from the songbird auditory system, and found that recovered networks were appropriately constrained to anatomical connections, matched physiological features of the system, and were consistent with measure dynamics of the system.  As part of the CARMEN (Code Analysis, Repository, and Modelling for e-Neuroscience) neuroinformatics consortium, we are expanding Bayesian network theory to enable recovering neural information flow from single-unit neural recordings. We are analysing place cells recorded from the rat hippocampus, to understand network-level information coding of location and other variables.

Gene regulation

We develop BN inference algorithms for recovering gene regulatory networks from gene expression data, with special attention paid to overcoming the difficulty of handling biologically realistic small amounts of data.  Yeast, Saccharomyces cerevisiae, is used as a model system to develop and test these algorithms.  As regulation  occurs at the step of protein translation as well as mRNA transcription, the genes which code for proteins involved in this type of regulation also have a part in the gene regulatory network. We also focus on methods to incorporate this type of regulation into the network inference task.

Ecological systems

We are pioneering the use of BN algorithms for the analysis of interspecific and species-habitat interactions within ecosystems, using species abundance and habitat data.

MPhil/PhD project opportunities:

• PhD projects - PhD projects are available in (1) Bayesian network analysis of neuronal networks and information coding, (2) incorporation of additional genomic information to recover gene regulatory networks, and (3) development of Bayesian network techniques for ecological analysis.
   
• MPhil projects - Proposals for MPhil projects in any of the above areas are welcome; particular projects may include: simulation based studies of Bayesian networks for revealing neural information flow, investigation of Bayesian networks' representation of ecological networks, and recovery of gene regulatory networks using publicly available data.

Comparative and evolutionary immunology

Innate immunity in invertebrates and lower vertebrates. Antibacterial proteins in crustaceans, ascidians, cnidarians, teleosts , elasmobranchs and marine mammals. Plasticity within the innate responses of these animals. Immune development in fish and marine invertebrates and effect of environment. Complement phylogeny. Virus diseases and antiviral immunity in crustaceans. Marine invertebrate blood cell culture. Development of molecular probes for disease diagnosis in marine shellfish. Effects of environmental factors on immune capability in marine animals. Wastewater treatment by marine micro-algae. Antibacterial compounds from micro-algae.

General areas of research: Comparative immunology and marine microbiology

Innate immunity in invertebrates, lower vertebrates and marine mammals.
Antibacterialproteins in crustaceans, ascidians, cnidarians, teleosts and pinniped seals.
Plasticity within the innate responses of marine animals.
Immunedevelopment in fish and marine invertebrates and effect of environment on immune function.
Complement phylogeny.
Virus diseases and antiviral immunity incrustaceans.
Marine invertebrate blood cell culture.
Developmentof molecular probes for disease diagnosis in marine shellfish.
Antibacterialproducts from marine micro-algae and cyanobacteria.

Analysis of cellular and subcellular compartmentation and control of metabolism in plants. This includes a programme aimed at identifying control mechanisms involved in regulating mitochondrial division and fusion. Cellular and subcellular level studies of plant responses to the environment, with particular interest in nitrogen nutrition and light (including ultraviolet B radiation). Studies of the response of Antarctic plants to enhanced UV-B radiation and drought stress, including their susceptibility to DNA-damaging stresses and their associated ability to repair DNA damage. Technical approaches include: analysis of plant proteins and DNA; metabolite analysis; plant growth analysis; subcellular studies (isolation of plant cell organelles).

Research interests: Plant Cell Physiology. Understanding how plants assimilate nitrogen. Identification and localization of genes involved in ammonium assimilation in plants. Plant organelles – development and specialization of plastids in photosynthetic and non-photosynthetic cells. Proteomics analysis of isolated plastids. The mechanisms controlling mitochondrial division and specialization. Metabolic interactions between organelles in developing leaves. exposure.

More detail

Current research is into nitrogen assimilation and protein remobilisation during grain filling in barley. We are investigating the genes that encode glutamine synthetase, the enzyme responsible for ammonium assimilation into the first organic product, glutamine. Partitioning of nitrogen during the grain-filling stage is an important determinant of the crop's value for food and for malting. The expression and location of the 4 genes for glutamine synthetase are currently under investigation in my laboratory, with the aim of modifying the grain content of carbon and nitrogen in this major cereal crop.

We also study the development and division of mitochondria in plants, using green fluorescent protein as a marker that enables us to view mitochondria in living cells. Our work has led to the identification of a number of mutants of mitochondrial form and distribution in plants, with subsequent work leading to the isolation of candidate genes

We have developed novel techniques for isolating plastids from leaf epidermal cells and use proteomics methods to start to characterise their metabolic potential. Our work has identified structural and functional differences between these plastids and those of the photosynthetically active mesopyll cells.

 Cellular and subcellular level studies of plant responses to the environment, with particular interest in nitrogen nutrition and light (including ultraviolet B radiation). Studies of the response of Antarctic plants to enhanced UV-B radiation and drought stress, including their susceptibility to DNA-damaging stresses and their associated ability to repair DNA damage.

Technical approaches include: production of transgenic plants; in situ hybridisation and immunolocalisation for gene and protein expression; confocal and fluorescence microscopy and real-time imaging of living mitochondria; analysis of plant proteins and DNA; proteomics and metabolomics analysis; plant growth analysis; subcellular studies, particularly the isolation of plant cell organelles.

Currently-funded projects

Isolation and functional analysis of genes encoding glutamine synthetase isoforms in barley. A particular focus of this research is the identification of genes involved in nitrogen incorporation and protein production in the developing barley grain.

Personnel:

Dr Pankaj Kumar (Postdoctoral research fellow)

Mr Andrew Goodall (PhD student)

Recent funded projects

1. Identifying genes controlling mitochondrial shape, size and number (BBSRC-funded project). The aim of this work is to identify genes controlling mitochondrial shape, size and number. The basis of the project is the identification of unique mutants in Arabidopsis with altered mitochondrial shape/size/distribution. Plants expressing GFP in the mitochondria are used to screen for mutants with altered mitochondrial form.

Personnel

Dr David Logan (Postdoctoral research fellow)

Mr Iain Scott (PhD student)

Relevant Publications:

Scott I, Tobin AK, Logan DC (2006) BIGYIN, an orthologue of human and yeast FIS1 genes functions in the control of mitochondrial size and number in Arabidopsis thaliana  Journal of Experimental Botany 57 (6): 1275-1280.

Logan DC, Scott I, Tobin AK (2004) ADL2a, like ADL2b, is involved in the control of higher plant mitochondrial morphology. Journal Experimental Botany 55 (397) 783-785

Logan DC, Scott I and Tobin AK (2003) The genetic control of plant mitochondrial morphology and dynamics. The Plant Journal36: 500-509.

2. Proteomic analysis of leaf plastids in Arabidopsis (BBSRC-funded with Dr Caroline Bowsher, University of Manchester).

The project aims to identify and to separate distinct populations of plastids from different cells within Arabidopsis leaves. Although extensive research has been carried out into the metabolic properties of chloroplasts, little is known about the metabolic capacity of non-photosynthetic plastids in leave. This project will take a proteomic approach to analysing metabolic potential in these plastids

Personnel

Dr Peter Chovanec (Postdoctoral research fellow)

Relevant Publications

Chovanec P, Tobin A K, Thornton DJ, Bowsher CG (2005) Proteomic analysis of leaf plastids isolated from different cell types of Arabidopsis thaliana. Comparative Biochemistry and Physiology 141: S253

Tobin AK & Bowsher CG (2004) Subcellular Fractionation of Plant Tissues: Isolation of Plastids and Mitochondria . In . 'Methods in Molecular Biology, Protein Purification Protocols' ed P Cutler, Humana Press Inc., Totowa NJ, USA

Bowsher, C.G. & Tobin, A.K. (2001) Compartmentation of metabolism within mitochondria and plastids. Journal of Experimental Botany 51, 513-527.

Tobin, A.K. & Yamaya T (2001) Cellular compartmentation of ammonium assimilation in rice and barley Journal of Experimental Botany 51, 591-604.

3. Ultraviolet-B radiation and DNA damage

The impact of desiccation and UV-B radiation on DNA damage and repair in the moss, Ceratodon purpureus.

Relevant Publications

Robinson SA, Wasley JA, Tobin AK (2003) Living on the edge- plants and global change in continental and maritime Antarctica. Global Change Biology 9: 1681-1717

Tobin AK (2003) UVB effects on crops. Modern Trends in Applied Terrestrial Ecology, ed. RS Ambasht, Kluwer/Plenum Press, New York, USA

Hall RSB, Paulsson M, Duncan K, Tobin AK, Widell S, Bornman JF (2003) Water- and temperature-dependence of DNA damage and repair in the fruticose lichen Cladonia arbuscula ssp mitis exposed to UV-B radiation. Physiologia Plantarum 118 (3): 371-379

Hopkins L, Bond MA and Tobin AK (2002) Ultraviolet B radiation reduces the rates of cell division and elongation in the primary leaf of wheat (Triticum aestivum L. cv Maris Huntsman). Plant Cell & Environment 25 (5): 617-624