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STRATEGIC SCIENCE ADVISORY PANEL
SUBJECT:
BBSRC : ROLE IN BIODIVERSITY RESEARCH
MEETING: 21 SEPTEMBER 2006
SUMMARY
This paper sets out:
At Annex 1
 Describes BBSRC’s role in Biodiversity Research
 Describes the aspects of biodiversity related research relevant to the BBSRC
mission and particularly to the delivery of its 10 year vision and its strategic plan
At Annex 2
 Describes the BBSRC collaborative scheme for Systematics research (Note – this
is in Draft format as the scheme has still to be approved))
ACTION
The panel members are invited to:
 Note and discuss the role of BBSRC in Biodiversity Research
Dr Alf Game will give an oral presentation on the role of BBSRC in Biodiversity
Research
Science & Analysis Group
September 2006
STRATEGIC SCIENCE ADVISORY PANEL
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THE ROLE OF BBSRC IN BIODIVERSITY RESEARCH
The document at Annex 1 describes BBSRC’s role in biodiversity research. It was
developed in extensive consultation with other UK stakeholders and was the subject of a
public consultation held in Glasgow earlier in the year. It is available on the BBSRC
website at:
1.
http://www.bbsrc.ac.uk/science/areas/gdb/priorities/RBBSRCRoleInBiodiversityResearchFinalVer
sonForWebPublication.pdf.
2.
The BBSRC is about to launch a scheme to encourage collaboration between
systematists and other biological scientists. This will be administered on behalf of
BBSRC by the Linnean Society and the Systematics Association and will fund small
awards to foster collaboration and develop proposals for more substantive funding
through the normal competitive routes. Brief details of this scheme, which has yet to be
finally approved, are at Annex 2.
3.
Responsibility for biodiversity research is distributed over several BBSRC
committees, but policy is coordinated by the Genes & Developmental Biology team.
Contact: Dr Vicky Jackson: vicky.jackson@bbsrc.ac.uk
A G Game
BBSRC
30 August 2006
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THE ROLE OF BBSRC IN BIODIVERSITY RESEARCH
Annex 1
INTRODUCTION
4.
The aim of this document is to explain the role of biodiversity research in the
delivery of the BBSRC mission, and thereby to provide guidance to the scientific
community on the areas of biodiversity research that are appropriate for funding by
BBSRC.
5.
The Convention on Biological Diversity, to which the UK is a signatory, defines
biological diversity as “the variability among living organisms from all sources including,
inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes
of which they are part; this includes diversity within species, between species and of
ecosystems”.
6.
All biodiversity is connected through common ancestry of species (phylogeny).
This provides a framework for studying the patterns of diversity and for comparative
analyses at various hierarchical levels of biological organisation. Because genes interact
with other genes and with the environment, it is important to develop an understanding of
biodiversity in terms of complex adaptive systems, both within and between different
levels of organisation (e.g. molecule, gene, individual, and habitat). In particular, it is
important to identify any generic properties, mechanisms or constraints involved in the
maintenance, evolution, generation or loss of biodiversity.
7.
Mounting evidence that human activity is impacting on ecosystems at the global
scale leaves us no option but to take action to conserve biodiversity. Therefore, research
must operate in the context of managing biodiversity (as defined above) towards
prescribed goals relating to current and future values. Management of biological diversity
towards a set of goals requires an understanding of the processes that sustain the vitality
of ecosystems and give rise to function. Goals might relate to the discovery and
exploitation of biological resources, but they must also relate to the management of
biological diversity to promote as yet undefined future options. The goals are unlikely to
be mutually consistent, so compromise based on a clear set of principles will be required.
8.
Many of the challenges lie clearly within the remit of BBSRC and these are
outlined below. However, many of the most important questions require the integration of
research at the interface between BBSRC, NERC, ESRC, SEERAD and DEFRA. In the
research areas outlined below we provide examples that relate to the missions at the
interface between BBSRC and other research councils. It should be noted that BBSRC’s
interests in biodiversity can be broadly defined as understanding the underlying
mechanisms and processes involved in generating, maintaining and exploiting
biodiversity in managed ecosystems (particularly agriculture). Studies that aim to
improve understanding of natural or unmanaged ecosystems are likely to be more
appropriate for consideration by NERC. However, we strongly encourage the scientific
community to exploit the opportunities of research at the interfaces between Councils,
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and to enter into dialogue with the appropriate programme managers to facilitate this
goal. Research which is within the BBSRC remit but which can also contribute to
ongoing work in existing research agendas, such as the Biodiversity Research Action
Group (BRAG), Environmental Research Funders Forum (ERFF) and the Global
Biodiversity Information Facility (GBIF) is also strongly encouraged. In addition to
9.
fundamental studies on biodiversity aimed at improving basic knowledge of
mechanisms and processes, research is needed to identify, characterise and harness
biodiversity with the objective of enhancing the exploitable potential of organisms with
commercial relevance, or impact, on the health of crops, animals and humans.
10.
One of the three objectives of the CBD, as set out in Article 1, is the 'fair and
equitable use of the benefits arising out of the utilisation of genetic resources, including
by appropriate access to genetic resources and by appropriate transfer of relevant
technologies, taking into account all rights over those resources and to technologies, and
by appropriate funding'. BBSRC expects all those who it funds to honour the letter and
spirit of the CBD. It is also expected that obligations and commitments under other
European Directives and international conventions (including the International Treaty on
Plants genetic Resources for Food and Agriculture (ITPGRFA) to which the UK is party /
signatory will be respected.
11.
There is also substantial public interest in biodiversity, for example in gardening,
conservation and natural history, and this can be used as a conduit to convey appreciation
of how research on biodiversity can impact on everyday lives of the population.
12.
Diversity and functionality emerge as a consequence of processes operating
across different levels of organisation from pathways in cells to the interaction between
ecosystems. Research on biodiversity is about understanding the dynamics of complex
adaptive systems, and the examples provided below emphasise the need to focus on
interactions and the emergence of behaviour across levels of organisation from genes to
ecosystems.
13.
Although biodiversity exists in the continuous spectrum from variation in
molecules and genes to diversity of species within ecosystems, it is easiest to identify
BBSRC’s role in biodiversity research in the context of different ‘levels’, whilst at the
same time recognising that boundaries between levels are not discrete and that overlap
occurs. The role of BBSRC in supporting biodiversity research is outlined below for four
different levels of diversity: molecular diversity, gene and genome diversity, organism
diversity and habitat and ecosystem diversity. It is recognised that effective data and
information handling capabilities are required throughout these levels, and specific
requirements are discussed as a separate topic.
MOLECULAR DIVERSITY
14.
Molecular diversity can be viewed as the diversity present among the primary and
secondary products of genes. This encompasses variation in the chemical composition of
cells and tissues with respect to their transcriptional and translational products and/or
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secondary compounds. BBSRC’s interests in biodiversity relate to managed ecosystems
(particularly agriculture); research focused on understanding natural or unmanaged
ecosystems are likely to fall within the remit of NERC. BBSRC’s interests in molecular
diversity fall in the following areas:
Changes in Molecular Diversity
• Understanding the basic mechanisms and processes resulting in molecular diversity
• Understanding how molecular variation is related to functional and physiological
diversity
• Improving our understanding and manipulation of key pathways
• Comparative studies of key pathways in different organisms, including pathogens
(viruses, bacteria, parasites), to elucidate common and unique pathways that could be
exploited
Exploitation of Molecular Diversity
• Identification and characterisation of diverse products that play a role in interactions
with, and protection against, environmental challenges
• Identification of untapped sources of new and potentially exploitable metabolic and
physiological pathways and natural products
• The significance of variation in cell products for the food chain
• Investigating variation in the protective and interactive roles of metabolites
Conservation of Molecular Diversity
• Identification and characterisation of biotypes with molecular diversity of agroecological significance
Tools and Techniques for Studying Molecular Diversity
• Development of high throughput or novel screening methods for the identification of
products that have commercially exploitable potential
• Enhancement of molecular diversity (e.g. by exploiting mechanisms of
recombination, shuffling and forced / directed evolution)
• Metabolomics studies in the context of food safety
GENE AND GENOME DIVERSITY
15.
Genomes vary in gene organisation and structure, in the composition and
organisation of non-transcribed regions (e.g. hypervariable regions, repetitive DNA,
retroelements), in ploidy level and in karyotypic variation. Gene diversity is the allelic
variation that can be found in structural and regulatory genes. Comparative genomics is
based on the study and comparison of genes and genomes of different organisms, and is
important for understanding evolutionary relationships between organisms in gene
organisation and function. BBSRC’s interests in biodiversity relate to managed
ecosystems (particularly agriculture); research focused on understanding natural or
unmanaged ecosystems are likely to fall within the remit of NERC. BBSRC’s interests in
gene
and
genome
diversity
fall
in
the
following
areas:
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Changes in Gene and Genome Diversity
• Biodiversity genomics, including the evolutionary mechanisms of genome
organisation and genome change
• Understanding the molecular mechanisms and processes of genome change
• Understanding recombination, mutation and rates of evolution and how these are
controlled
• Investigating different mechanisms resulting in genetic exchange and understanding
how genetic information moves around within and between organisms
• Investigating the role of different genetic elements in genome change, genetic
instability and phenotypic plasticity
• Investigating the evolution and generation of diversity in the genomes of organelles
and other extra-chromosomal genomes
• Investigating the role of gene/environment interactions with respect to differential
responses in ageing, nutrition and stress
• Understanding genes under selection during domestication
• The role of human genetic diversity in response to nutritional input, anti-oxidants
and signalling molecules and their impacts on human health
Exploitation of Gene and Genome Diversity
• Understanding and exploiting the genetic basis of diversity in form and function in
animals, plants and microbes
• Elucidating how genome organisation, gene expression and allelic diversity are
related to functional diversity
• Understanding the genetic basis of quantitative variation
• Characterisation and evaluation of gene diversity in germplasm, where this has
strategic or applied context
• Development of approaches using linkage disequilibrium and association studies to
relate specific gene functions and traits
• Investigating the consequences of contrasting adaptive selection pressures in
domesticated versus wild germplasm
• Influence of genome organisation on inheritance/exploitation of genetic variation
Conservation of Gene and Genome Diversity
• Development of models and approaches for the sustainable use of biodiversity
• Identifying and preserving genetic diversity of industrially and medically relevant
microbes, farm animals and crop and useful plant species to maintain potentially
useful traits for breeding purposes
Tools and Techniques for Studying Gene and Genome Diversity
• Efficient tools and techniques for detecting, characterising and analysing
biodiversity
• Development of generic approaches that facilitate high-throughput analysis
• Development of improved statistical procedures for analysing diversity, for studying
evolutionary change and for detecting the influences of selection
• Novel/high-throughput approaches to trait analysis or crop improvement
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Generic methodologies for characterisation or (high-throughput) analysis of large
datasets
• Development of 'pharmacogenomic' techniques for identifying differences between
genotypes
• Developing methods for the identification of rare alleles
•
Development of tools for comparing large or complete nuclear and/or organellar
sequences
•
ORGANISMAL DIVERSITY (INDIVIDUALS, POPULATIONS, SPECIES)
16.
Species diversity is the number and kind of species in an ecosystem. Within
species, diversity may be present among individuals within a population and among
different populations. BBSRC’s interests in biodiversity relate to managed ecosystems
(particularly agriculture); research focused on understanding natural or unmanaged
ecosystems is likely to fall within the remit of NERC. BBSRC’s interests in population
and species diversity fall in the following areas:
Changes in Organismal Diversity
• Systematic (including taxonomic) studies, where there is an intrinsic reason why
improved systematic understanding is needed in order to deliver a hypothesis-driven
objective, or a generic tool or technology for systematics research
• Understanding the genetic and epigenetic underpinnings of major phenotypic shifts
in lineages; the origin and diversification of major clades
• Phylogenetic and phylogeographic approaches to understand the temporal and
environmental context of evolutionary divergence
• Understanding processes leading to population divergence and speciation
• Investigating the evolution of breeding systems
• Understanding the behaviour of genes in populations
• Investigating spatial and temporal dynamics of interacting species
• Understanding mechanisms of co-evolution
• Investigating changes in species or population diversity in some natural
environments of exploitable value or importance to crop, animal or human health and
in artificial (i.e. man-made and man-managed) habitats such as fermenters and
bioreactors
• Understanding the invasiveness and impacts of the release of introduced or GM
organisms on biodiversity
Exploitation of Organismal Diversity
• Investigating natural variation where this leads to potential exploitation (e.g. for
dealing with pollutants and toxins or bioremediation)
• Studies of extremophiles and their mechanisms for dealing with extreme
environments, when these can yield exploitable traits or establish fundamental
mechanisms of adaptation
• Identification of novel variation in natural populations of plants and animals that can
be exploited in crop/useful plant and farm animal genetic improvement
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Investigating population dynamics to increase understanding of fundamental
processes
• Understanding the genetic basis of organismal adaptation to different environments
•
Conservation of Organismal Diversity
• Identification of microbial assemblages that have a key role in sustainable
agriculture
• Conservation and management of soil biodiversity
• Supporting collections of strategic and/or exploitable value
Investigating the maintenance and dispersal of adaptive genes in population
networks
• Selection of new characters in relation to novel types of niche occupancy
•
Tools and Techniques for Studying Organismal Diversity
• Development of tools (e.g. databases) and bioinformatics approaches for managing
and analysing information on biodiversity at the individual, population or species
level
• Development of new approaches for inference of population genetic or evolutionary
parameters
• Methods for rapid species identification and diagnostics including DNA barcoding
approaches
• Using individual-based modelling to improve fundamental understanding of
processes involved in the generation or dynamics of diversity
HABITAT AND ECOSYSTEM DIVERSITY
17.
Habitat and ecosystem diversity is the variation in species within and between
different habitats and ecosystems. BBSRC’s interests in biodiversity relate to managed
ecosystems (particularly agriculture); research focused on understanding natural or
unmanaged ecosystems is likely to fall within the remit of NERC. BBSRC’s interests in
habitat and ecosystem diversity fall in the following areas:
Changes in Habitat and Ecosystem Diversity
• Improving our mechanistic understanding of species diversity and distribution in
managed and semi-natural habitats (e.g. agro-ecosystems)
• Understanding how climate change affects ecosystems, where these studies increase
basic biological understanding or potential for exploitation. This includes the effect of
climate change on artificial ecosystems such as agriculture
• Impact of global climate change on animal and plant health, and the changes in
geographical ranges in which pathogens can survive
• The role of gene flow and horizontal gene transfer
• Evolutionary ecology of soil
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Exploitation of Habitat and Ecosystem Diversity
• Improving our understanding of how management affects the evolution of diversity
as a component of ecosystem functioning in the context of production systems,
including forestry, aquaculture and agriculture
• Exploiting the value of functional biodiversity in sustainable agricultural context
• Understanding the ecological significance of intra-specific variation and interrelationships between inter- and intra-specific variation
• Investigating biodiversity processes in relation to different land-use patterns and
different agricultural systems
Conservation of Habitat and Ecosystem Diversity
• Identification of the mechanisms that promote coexistence of managed and
natural/semi-natural communities, and the conservation of associated habitats and
species
• Understanding the role of genetic diversity in habitat/ecosystem resilience
Improving our understanding of the impact of nitrogen pollution on the biodiversity
of ecosystems
•
Tools and Techniques for Studying Habitat and Ecosystem Diversity
• Development of predictive models capable of relating ecosystem structure to
dynamics and function
• Development of new tools to relate diversity to function (e.g. molecular biological
approaches to characterising functional diversity)
BIODIVERSITY INFORMATICS AND E-SCIENCE
18.
Improved access to biodiversity information underpins the delivery of many of
the above objectives. Key to this is the development of technologies for the digitisation of
large datasets and collections, and for the integrative interoperability of heterogeneous
datasets. This latter objective is particularly dependent on the development of an
electronic catalogue of species names, as the means by which all biological data can be
related within a coherent framework. Modern e-science technologies (e.g. GRID systems)
offer considerable promise for biodiversity informatics.
19.
The BBSRC has a research priority, delivered through its Genes and
Developmental Biology Committee (see Annex 1), to support the development of new
techniques in this area. Other areas in which BBSRC’s interests lie include:
• Methods that link diversity information on metabolomes, transcriptomes and
proteomes
• Development of systems using a common language and common data standards
• Developing effective methods of data storage
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CONCLUDING REMARKS
20.
This document describes the aspects of biodiversity-related research relevant to
the BBSRC mission and particularly to the delivery of its 10-year Vision and its Strategic
Plan (q.v.). BBSRC’s biodiversity research portfolio is complementary to, and developed
and delivered in cooperation with, other Research Councils (particularly NERC) and key
government stakeholders (particularly DEFRA). These organisations have their own
missions and priorities, which also contribute to the overall UK effort in biodiversity
research.
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BIODIVERSITY INFORMATICS
21.
The BBSRC, together with NERC, the Natural History Museum, Kew Gardens
and DEFRA, contributes to the UK subscription to the Global Biodiversity Information
Facility (GBIF): www.gbif.org. Applications which will contribute to the delivery of the
GBIF programmes DADI (data access and database interoperability) and ECAT (the
electronic catalogue of the names of known organisms) are particularly welcomed.
Taxonomically ‘Intelligent’ Systems (also systems for evolutionary data)
22.
Information held in databases may be difficult to compare and use effectively
because of differences in taxonomy or nomenclature. Intelligent systems can compare the
nomenclature used in each database (species names, synonyms, common names, etc) to
identify data that relates to one species, even when represented by different names in
different databases. Applications are sought which develop intelligent systems for dealing
with taxonomic and evolutionary data.
Synthesising Biodiversity Knowledge from Distributed Systems
23.
Because biodiversity is researched worldwide, information about a species is held
in various databases in numerous locations. Knowledge can be gained by combining the
information from these different sources, but this requires interoperable systems that are
capable of identifying and managing relevant data from different sources. Studies that
aim to improve interoperability between databases are encouraged.
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DRAFT
Annex 2
BBSRC Collaborative Scheme for Systematics Research (CoSyst)
Aim
24.
The BBSRC Collaborative Scheme for Systematics Research is designed to provide
short-term funding for new collaborative research in systematics. The initiative is intended
to support preliminary collaborative research that will form the basis of novel responsive
mode proposals with a substantial systematics component. All applicants must be of at least
senior Post-Doctoral status although resources may be sought to support existing junior PostDoctoral Research Assistants, technical and support staff or Post-Graduate Students during
laboratory exchanges, sample acquisition and the generation of preliminary data.
Long-Term Objectives
(1) To stimulate a greater quantity and better quality of systematics-related research
proposals submitted to the UK’s Research Councils.
(2) To firmly establish systematic biology within the UK’s biological research base.
Short-Term Objectives
(1) To attract a minimum of 20 applications to the BBSRC Collaborative Scheme for
Systematics Research each year.
(2) Distribution of the awards will result in at least 25% of the projects being used to
generate a full responsive mode application to either BBSRC or NERC within two
years of the grant being awarded.
25.
Funds of up to £75k per annum for three years will be provided for this scheme by
BBSRC. Grants will be in the range £2–20k, with an indicative range of £5–10k.
26.
The new scheme will be reviewed at the end of its second year, Spring 2009, to
consider its degree of success in meeting the Short-Term Objectives. Assuming that BBSRC
recognises an acceptable level of success, the Panel will submit a bid for renewal of the new
scheme for at least two years beyond the three years already vouchsafed.
27.
Eligibility criteria and application procedures etc will be announced when approved
by the linnean Society and the Systematics Association.
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