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Personnel and
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| I develop Bayesian
methods to draw inferences from genetic data about the action of
selection and population history and gene flow in shaping the
distribution of genetic variants. In particular I am investigating methods to take into account the patterns of spatial autocorrelation in allele frequencies, and in using systems-biology networks to construct prior probability distributions on genetic co-variances. Approximate Bayesian computation (ABC) is proving very effective in many areas of genetics in dealing with the wide variety of parameters that affect genetic variation. However, I am also interested in the merits an alternative approach: of making explicit simplifying assumptions, which are computationally convenient, but (arguably) no less realistic than those implicit in alternative methods. |
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I work on a joint
project with Bill
Sherwin at UNSW Sydney, Clare
Holleley & Gianluca Maio on a project on the effcts of gene
flow in lab Drosophila
populations. The results suggest that genetic divergence throughout the
genome is constrained, to an unanticipated degree, by the action of
selection a adjacent loci. James Cotton and I are working with PhD student Vernonica Comper on phylogeographic inference and problems of calibrating the molecular clock, particularly the long times to common ancestry between two lineages in common ancestor of two species (E.g. the figure illustrates the way that gene trees in Human Chimp Gorilla ancestry may not reflect the species tree). A further PhD student, Bob Verity, is working on Bayesian methods for characterising the isolation-by-distance in the distribution of genetic variation in natural populations. |
The methods we have used to study gene flow between populations can also be used to investigate the movement of DNA sequences from one part of the genome to another, to study the propagation of viruses within the human body, their spread from one individual to another, and even the transmission of viruses from species to species. |
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I collaborate with Judy Breuer at UCL on the evolution of varicella zoster virus, including the evolution of the live vaccine within the body of vacinees. Our latest project uses a Bayesian analysis of the DNA sequence obtained from virus in different patients to work out transmission routes (who infected whom). The figure shows an abrupt decline in infection rate coinciding with the date of the school holidays. |
| These theoretical
approaches enable the use of genetic data
to guide the management
of
wild
populations. I am working on two main areas: the role of introduced disease in European frog populations and the conservation of endangered species on Mauritius. In both cases I am lucky to be able to collaborate with, and be guided by, experts working directly on the biology of the species in question. |
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Trent Garner
at
the
Institute
of
Zoology
is
interested
in
genetic
diversity
and
its
importance
for
a
species' response to pathogens. We have two
PhD students Stephen
Price and Amanda
Duffus working on the decline in frog
populations. We are using historical records and genetic data to characterize the spatial pattern of genetic diversity in a virus affecting frogs (Figure) that recently invated the UK and to infer the dynamics of transmission between populations. |
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Carl Jones (pictured) of the Mauritian Wildlife Foundation has been instrumental in several successful conservation projects on the island. We have had PhD students working on the works on the origins and hybridization of different petrel taxa on one of the outlying islands. She is a CASE student with the Institute of Zoology. |
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| The hybrid zone
in
the alpine grasshopper Podisma
pedestris has intrigued me since it was the focus of my
PhD with Godfrey Hewitt at UEA Norwich. Two taxa (sub-species)
apear to have met and interbreed where they met after climbing the Alps
from
different directions at the end of the last ice age (although ex PhD
student Paris disagrees, see here).
Despite
successful
hybridization
since
then,
they
remain
genetically
distinct.
The
evidence
of
genetic
incompatibility
is
strong
but
confusing: e.g. direct estimates suggest selection is strong, yet the
width of the mixing between the two taxa is wide. Recent
discoveries may at last be getting to the heart of the matter |
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Paris
Veltsos obtained extraordinary data showing that the
populations in
and around the zone show dramatic differences in the number and
location of rDNA tandem arrays. More at his site. Andrew Leitch and his team work on plant polyploidy at QMUL. We share insights from our studies of different types of hybrization. In particular the hybridization that initiates allopolyploidy and that occurring in the hybrid zone. One common theme is the highly unusual evolution of rDNA in both cases. Ex posdocs Ioana Marquier and Irene Keller continue to collaborate on the project. Irene has discovered ancient rDNA pseudogenes, dated by Ioana at several million years old. Irene has also shown that the sequence composition of the rDNA appears just as dynamic as the variation in location found by Paris, but with no obvious correlation between the two. |
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Genetic evidence and demography. Our analysis colonization patterns in seals (Gaggiotti et al.), exemplifies a major theme of my research. We developed a Bayesian analysis of genetic data to draw inferences about the demography of natural populations. The method allowed us to characterize the origin of colonists from genetic data, even though there was minimal genetic differentiation between the potential source populations. This was achieved by combining the small amounts of information from each pup, over a large number of pups. |
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Genetic Evidence in Forensic Science. A controversial line of research was a project to quantify the differentiation between human populations at the genetic markers used in forensic science. These values are required to evaluate forensic evidence in court. David Balding and I developed the method currently used to deal with population differentiation in UK courts, and this has led to extensive consulting work. |
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Range expansion and inbreeding. The forensic strand of research has developed into diverse projects. They include the analysis of the human genetic patterns generated by the colonization of Europe and by the movements triggered by the development of agriculture (in a project with Mark Beaumont, Lounès Chikhi et al.). More recent human history and current practice have been studied in a project with Andy Overall on the effects of inbreeding in the UK Asian population (Overall et al.). |
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Phylogeography.
The analysis of geographic patterns is, in fact, a long-standing
interest dating back to my PhD work with Godfrey Hewitt. A series
of publications on Iberian lizards with Octavio Paulo (Paulo et al)
have a wider relevance, because
they reveal major features of Iberian biogeography. The
theoretical tools for this sort of work is
being extended by a current project. |
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| Lab member |
Institute |
|
Ferrara |
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|
Reading |
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Edinburgh |
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| Cardiff | |
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Sabatier, Toulouse |
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| Pete Clarke |
Nottingham |
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Conservation research |
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| Karen Freeman |
Conservation
manager |
| Oscar Gaggiotti |
Grenoble |
|
Jim Groombridge |
DICE Canterbury |
| Kamal Ibrahim |
Southern Illinois |
| Irene Keller |
Eawag, Switzerland |
| Ioana Marquier |
Grenoble |
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Andy Overall |
Brighton |
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Octavio Paulo |
Lisbon |
| Ilik Saccheri |
Liverpool |
| Amber
Teacher |
RHBNC London |
| Paris Veltsos |
St Andrews |
| Mike Weale |
UCL London |
| Helen Wilcock |
(Deceased) |
| Ian Wilson | Newcastle |