Molecular Ecology and
Fisheries Genetics Laboratory
http:// biology.bangor.ac.uk/research/mefgl
Job Description
Post Title
POSTDOCTORAL
RESEARCH
MOLECULAR ECOLOGY
Faculty/Section
BIOLOGICAL SCIENCES
Reporting to
DR SIMON CREER
Duration
6 MONTHS
Grade
7
OFFICER
IN
Summary of the Post
Six-month NERC-funded postdoctoral research position in the Molecular
Ecology
and
Fisheries
Genetics
Laboratory
(http://biology.bangor.ac.uk/research/mefgl/), School of Biological Sciences,
Bangor University. The successful candidate will investigate links between
454 benthic meiofaunal biodiversity with morphological taxonomy,
macroinvertebrate community processes, sediment granulometry and
environmental factors.
Main Duties
 Perform single organismal (nematodes) and bulk community DNA
extractions (following Ludox flotation of target communities) and
polymerase chain reaction amplifications of benthic estuarine meiofaunal
communities and manage outsourcing of chain termination and 454
sequencing.
 In collaboration with bioinformaticians at Liverpool University, analyse two
454 metagenetic sequencing plate outputs (tagged amplicons),
corresponding to two ecosystems and 20 sampling stations per estuary.
Data will be quality controlled, preprocessed to identify unique reads and
BLASTed prior to downstream clustering and ecological analyses.
 To liaise with co-investigators to share datasets to facilitate the testing of
hypotheses of meio- and macrofaunal community diversity in relation to
bioturbation and hydrodynamic flows.
 To liaise with a partner PDRA in the Natural History Museum to share
sequencing and videocapture editing data to facilitate links between DNA
and morphological taxonomy.
 To test hypotheses of meiofaunal community diversity in relation to salinity
and sediment granulometry profiles.
 To publish lead-authored and participate in the publishing of co-authored
original research articles in high impact journals in a timely and effective
manner.
 To assist in the completion of report(s) associated with the project.
Person Specification
The successful applicant will ideally have:
 A PhD based upon the use of molecular ecological markers (preferentially
sequence data) in ecology or evolution.
 Experience, or an interest in benthic ecosystem biodiversity and/or
marine/estuarine ecosystem biodiversity.
 Experience in molecular biology techniques (including cloning), and in
particular PCR optimization and sequencing. Experience of 454 amplicon
sequencing will clearly be an advantage, although is not expected, given
the novelty of the analyses. Experience of next generation sequencing
bioinformatics (e.g. using Linux bioinformatics platforms and general
computing competency) and advanced BLAST searching would also be
desirable, however, training will be provided for the appointed candidate.
 Experience of phylogenetic/clustering analyses of sequence data.
 A willingness and record of timely publication of research articles.
 Good statistical skills including general statistical methods.
 In good physical health without restrictions on travel to partner institutions.
 Good time-management skills, and ability to maximise personal research
output.
 Demonstrated interpersonal and communication skills, including willingness
to coordinate with others and the ability to work as part of a team.
 Demonstrate an understanding of the bilingual nature of the institution and
area.
School of Biological Sciences, Bangor University
POSTDOCTORAL RESEARCH OFFICER IN MOLECULAR ECOLOGY
(ref: 08-8/29)
ADDITIONAL INFORMATION
Linking 454 DNA and morphological taxonomy with meio- and
macrobenthic biodiversity of the estuarine ecosystem.
Summary. Meiofaunal biodiversity plays a pivotal role in sediment ecosystem
processes, but quantifying community structure using standard morphological
approaches requires highly-skilled taxonomists and is prohibitively time
consuming. Not only does this restrict the analysis of meaningful sample sizes
in ecological studies, but the small size and morphological conservatism of
meiofaunal organisms have led to severe doubts regarding the reliability of
morphological taxonomic approaches. As a result of these constraints,
synergies between traditional taxonomy and modern molecular identification
methods are emerging for meiofaunal biodiversity assessments. Here, we will
use combinations of 454 massively parallel sequencing and morphological
taxonomy to elucidate relationships between meiofaunal biodiversity,
macrofaunal processes (bioturbation) and abiotic processes (e.g. flow rates)
and parameters (e.g. salinity ranges) throughout a range of substrate types in
estuarine ecosystems characterized by ongoing (Mersey) and recovering
(Thames) industrial and municipal pollutant regimes. Both of the latter
ecosystems have been studied extensively in the past using morphological
taxonomy of the dominant meiofaunal organisms. The project is funded by
NERC’s Post Genomics and Proteomics Directed Programme and is in
collaboration with Drs. Jan Hiddink and Simon Neill (School of Ocean
Sciences), Prof. Neil Hall (Liverpool University) and Prof. John Lambshead and
Dr. Tim Ferrero (Natural History Museum). Although the target organisms are
meiofauna, we expect the approaches to facilitate research into generalized
models of total eukaryotic biodiversity from freshwater to marine ecosystems.
Environmental Sciences at UWB
Bangor University (BU) includes one of the largest concentrations of
natural and environmental scientists within any UK university. BU is a
traditional university established in 1884 with ca 8500 students in six
academic Colleges (College of Arts & Humanities; College of Business, Social
Sciences & Law; College of Education and Lifelong Learning; College of
Natural Sciences; College of Health & Behavioural Sciences; College of
Physical
&
Applied
Sciences).
Biological
Sciences
(http://www.bangor.ac.uk/biology/) is part of the College of Natural Sciences
(CNS), together with the Schools of Environment and Natural Resources
(http://www.senr.bangor.ac.uk/)
and
Ocean
Sciences
(http://www.sos.bangor.ac.uk/). A recent BU initiative is the establishment of
the Environment Centre Wales (ECW), a partnership venture between Bangor
University and the Natural Environment Research Council's Centre for
Ecology & Hydrology (CEH). The Centre will function with a strong emphasis
on training and innovative science within the context of sustainability and
conservation of natural resources, an important strategic priority of many
national and international funding bodies. The Molecular Ecology and
Evolution research Group, including the MEFGL, is housed within new
purpose-bulit molecular laboratories on the third floor of ECW. Integral to the
ECW is the Wales Environment Research Hub (WERH) which is funded by
Welsh Assembly, Countryside Council for Wales, Environment Agency Wales,
Forestry Commission Wales, Bangor University, and the Centre for Ecology
and Hydrology. The objective of the Hub is to improve collaboration and
effectiveness of environmental science in Wales to support delivery of the
Welsh Environment Strategy. The overall impact of the ECW initiative is to
facilitate research collaborations across the University, to increase the critical
mass of environmental scientists, and to enhance engagement with external
environmental agencies.
The School of Biological Sciences (http://biology.bangor.ac.uk/) has 30
academic staff, 50 research technicians, research assistants and postdoctoral staff, a teaching support team of 9 and a central administration team
of 7. The School has an undergraduate and postgraduate student population
of approximately 500. It is a research active school with a range of
competitively funded research projects that provides training and research
opportunities to a spectrum of levels including Postdoctoral Research
Officers.
Molecular Ecology at BU
The School of Biological Sciences (SBS) supports a vigorous research
base in molecular ecology and evolution. The Molecular Ecology and
Evolution Group is currently organized into two main groups: The Molecular
Ecology and Fisheries Genetics Laboratory, and the Evolution of Reptiles
Unit. Both laboratories share common molecular facilities, group meetings
and office space. The wider Group focuses on an interdisciplinary approach to
understanding the processes of behaviour, population structure and
divergence, adaptation and speciation through to the broader-scale evolution
of organisms and genomes. A wide range of organisms are studied, but there
is particular expertise in the molecular ecology of aquatic animals
(invertebrates and fish) and lower vertebrates such as island lizards and
medically important venomous snakes (and their venoms). We are housed in
purpose built accommodation and laboratories on the third floor of the new, £8
million ECW . Our well-equipped laboratories have recently benefitted from
SRIF3 funding, the Research Council UK has provided a
Fellowship/Lectureship in Fisheries Genetics and Conservation, the EU has
supported three Marie-Curie Fellows in the last 2 years, and the £10.9 million
research partnership between Bangor and Aberystwyth has funded the newly
established Chair in Environmental Genomics, with which we interact. Our
main project funding comes from the NERC, BBSRC, EU, Environment
Agency, Royal Society, DEFRA, Wellcome Trust, Nuffield Foundation, and
Leverhulme Trust. The appointee will have access to a suite of fully integrated
molecular laboratories (coordinated by graduate technicians) including a 96
lane ABI automated sequencer/genotyper and a Beckman-Coulter capillary
sequencer, an Applied Biosystems- 7900HT Fast Real-Time PCR system,
wide range of thermal cyclers and associated support, and a new dedicated
ancient DNA facility. Technical skills include mtDNA, mitogenomic and
nuclear intron sequencing via chain-termination and 454 approaches, cloning,
454 transcriptomics, AFLPs, microsatellite and SNP development and
multiplex screening, and in-depth skills in analysing population genetic and
molecular phylogeographic and phylogenetic data. Bioinformatic facilities are
enhanced by a dedicated Biowulf cluster and server, with a new
bioinformatics suite located adjacent to the molecular laboratories.
The Molecular Ecology and Fisheries Genetics Laboratory (MEFGL)
The new appointee will become a member of The Molecular Ecology
and Fisheries Genetics Laboratory (MEFGL), a leading research division
within the School of Biological Sciences' (SBS) Molecular Ecology and
Evolution Group, one of the largest research areas within the University. The
MEFGL represents one of Europe’s largest centres focusing on population
and species diversity of aquatic animals, with additional activities on terrestrial
invertebrates. The current membership of 30 includes 3 Chairs, 1 Lecturer, 6
Postdoctoral Research Officers/Fellows, 10 PhD students, 4 MSc students, 2
Research Technicians/Research Support Staff, 3 Honorary Fellows/Research
Associates, and one Visiting Scientist. A central part of our work is the
application of molecular markers such as microsatellites, AFLPs, single
nucleotide polymorphisms (SNPs) and sequence data (454 and Sanger) to
fundamental evolutionary and ecological questions relating to the origins,
levels, distribution and ecological significance of genetic variation in wild
populations. In addition to the focus on neutral markers, facilities and
expertise are expanding on the functional analysis of genomes, including
application of transcriptomics and Real-Time PCR. The MEFGL complements
molecular genetic data with detailed ecological, behavioural and physiological
information to facilitate examination of the underlying causes of individual,
population or species diversity in time and space.
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Our research interests include:
The analysis of population genetic structure
Phylogeography and phylogenetics
Evolution of adaptive traits and functional analysis of genomes
Molecular evolution of genes and genomes
Ecological genetics of clonal animals
Ancient/recovered DNA in molecular ecology
Mechanisms of speciation, especially in tropical freshwater fishes
Conservation genetics
Genetic management of commercially exploited species
DNA barcoding and environmental metagenetics
Wildlife forensics
Traceability of fish and fish products
Pattern, implications and functions of social structure in animal
populations
Additionally, the MEFGL generates long-term population genetic data
sets through the exploitation of natural (e.g. resting eggs, skeletal materials)
and archived (e.g. fish scales and otoliths) biological repositories using
ancient DNA technology. The MEFGL, originally based at the University of
Hull, is a recognised International Centre of Excellence in the molecular
ecology of aquatic animals, as indicated by its past record: (1) an external
research income exceeding £3,000,000 since 1998; (2) considerable support
from a major UK Research Council (Natural Environment Research Council,
NERC: approx. £1,400,000 since 1998); (3) organisation of a NATO
Advanced Study Institute (ASI) in 1998 on Advances in Molecular Ecology
(ASI Director: G.R. Carvalho); (4) publication in leading international journals
including Nature, Science, Proc. Nat. Acad. Sci. USA, Genetics, Evolution,
Trends Ecol. Evol., Proc. Roy. Soc. Lond. The MEFGL is a member of the
Marine Genomics Europe Network of Excellence and the MARBEF Genetic
Biodiversity Key Area, both of which has training and gender issues as active
priorities. Strong international links have been established with the Fisheries
Centre (Vancouver), Max-Planck Institute for Limnology (Germany), the
Bergen Marine Laboratory (Norway), the Danish Institute for Fisheries
Research (Copenhagen),The Royal Belgian Institute for Natural Sciences
(Brussels), the Institute for Biology at Leiden University (Netherlands), the
University of Lisbon, the University of Aveiro and Minho in Portugal, the Royal
Museum of Central Africa (Tervuren, Belgium), Boston University, The Marine
Biological Laboratory (Woods Hole, USA), University of California at Long
Beach, the Falkland Islands Fisheries Department, Liverpool’s Advanced
Genome Facility and the Natural History Museum. Since 1998, Carvalho and
his previous group has attracted 45 international visiting scientists for stays of
between 3 months and 2 years (e.g. Fellowships from NATO, UNESCO,
NSERC, EU-TMR, National Governments of Argentina, Brazil, China, India,
Malaysia, Mexico, Portugal, Spain, Turkey),and has conducted research and
training with numerous international colleagues and species groups,
representing links to Europe, Africa, Australia, New Zealand, South Africa,
Canada, USA, Russia and Antarctica.. The laboratory regularly acts as host to
visiting scientists for training and the development of molecular genetic
markers, especially the isolation of species-specific microsatellites, and
molecular genetic data analysis.
Recent group developments
The MEFGL, together with other members of the Molecular Ecology &
Evolution Group, has recently moved into to the purpose-built research suite
embedded within the Environment Centre Wales (ECW). The new facility
provides open-plan office space for up to 28 postgraduate and postdoctoral
researchers, alongside dedicated PCR, sequencing, bioinformatic, and main
laboratory facilities. The recent appointment of a new Chair in Environmental
Genomics, Professor Peter Golyshin, to the School of Biological Sciences at
Bangor, provides a valuable extension of expertise in technologies, as well as
new opportunities for collaborations. Opportunities and activities in
behavioural ecology, speciation and the analysis of social structure, especially
in tropical freshwater fishes, has received a significant boost with the recent
arrival of Professor George Turner and his Group from Hull University.
Furthermore, additional interactions with members of the Universities of
Bangor and Aberystwyth’s Centre for Catchment and Coastal Research
(CCR) partnership (http://www.aberbangorpartnership.ac.uk/en/catchmentcoastal.php) further enable an integrative ecosystem approach to
understanding biodiversity.
Management and infrastructure
Management of research and training in the MEFGL is coordinated by
Professor Carvalho, in conjunction with other staff. Fortnightly meetings of all
Group members take place, at which individuals present recent project
progress for general discussion/trouble-shooting. A monthly Molecular
Ecology and Evolution Journal club, coordinated by postgraduate students,
provides a forum for discussion of recent topical and controversial
publications. Formal regular individual meetings are held between Principal
Investigators and research staff, together with appropriate collaborators.
Extensive training is available to all new Group members, both in molecular
and statistical techniques by specialist technicians, as well as more broadly
from the University in research skills, time management and preparation of
grant applications. Financial support is available to promote Fellow’s activities
at international conferences, and Group members are encouraged to invite
speakers to an occasional MEFGL seminar programme.
Key staff associated with the available position:
Simon Creer (PI) has developed wide-ranging expertise in the application of
molecular ecological markers to a diverse array of ecological and evolutionary
scenarios. Simon’s PhD and subsequent postdoctoral research has
contributed to the understanding of phylogeographical mechanisms,
calibration of molecular clocks, molecular systematics and the identification of
evolutionary significant units and cryptic genetic diversity. Further research
regarding the utility of nuclear (intron) sequence data in molecular
phylogenetics has led to further publications (including award winning) in high
impact factor journals focusing on the analysis of interspecific nuclear
sequence datasets. Simon now holds a Senior Research Fellowship in
Molecular Ecology with Prof. Gary Carvalho within the Molecular Ecology and
Fisheries
Genetics
Laboratory
(MEFGL
http://biology.bangor.ac.uk/research/mefgl/) in Bangor. During this time, he
has developed the application of new technologies to facilitate the
characterization of population and species biodiversity in marine meiofaunal
populations. Importantly, Creer is currently performing massively parallel
sequencing analyses of littoral meiofaunal communities across larger spatial
scales to address key questions concerning species biodiversity, supported
by a NERC New Investigator grant. He is also in the process of developing
microarray-based meiofaunal identification tools (NERC MGF grant),
performing 454 mitogenomics (Co-Syst/BBSRC grant), digital transcriptomics
and collaborating on a range of speciation, phylogenetic, environmental
genomic, population genetic and evolutionary biology-based projects within
the MEFGL.
Further details of MEFGL activities and staff membership can be found at:
http://biology.bangor.ac.uk/research/mefgl/.