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Bristol, UK: PhD, phylogenomics PDF Tisk Email
Measuring and interpreting convergence in molecular data
Supervisors: Davide Pisani (University of Bristol), Matthew Wills
(University of Bath), and Mark Wilkinson (The Natural History Museum,
Deadline for application: 31st March.
Informal inquiries: 
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Please Apply Online:
In biology, convergent similarity is a form of correspondence
(e.g. between morphological features or of molecular sequences/structures
from different species) not caused by common ancestry.  Two species that
display a convergent feature therefore acquired it starting from distinct
ancestral features.  At the least at the morphological level convergence
is generally considered a consequence of evolutionary adaptation, and
is generally achieved in species that adapted to a common lifestyle. An
example is the evolution of fins in dolphins (mammals) and ichthyosaurs
(reptiles).  Convergence happens also at the molecular level and
stricking examples have been discovered in the prestin gene in bats and
dolphins. Prestin plays a key role in echolocation and convergence of
this molecule was achieved in these two echolocating lineages.  However,
the extent to which convergence affect molecular data is not clear, and
the forces underpinning molecular convergence are often equally unclear.
Further on, how we should measure molecular convergence is not fully
clear.  Sequence similarity should obviously be included in the equation,
but whether this similarity should be weighted, for example based on
the phylogenetic distance between the considered species, is not known.
Yet this can significantly impact our perception of the pervasiveness
of convergence in genomic evolution.
Generally, evolutionary convergence is assumed to be more common and
more detailed in more closely related species, simply because closely
related species tend to be more similar and tend to have more similar
evolutionary constraints and potentialities. Further to that, it is often
argued that molecular (i.e. genetic) data tend to be less affected by
homoplasy than morphological data. We would argue that these expectations
or believes are the closest thing we currently have to any 'Law of
Convergence' and that a sensible and promising way of investigating
the importance of convergence and its broader significance is by testing
these expectations.  If patterns of convergence are not so constrained
and data-dependent, this would provide a powerful novel insight into
the nature of evolutionary change.
This PhD project is part of a larger Templeton Foundation founded
research programme, the aim of which is investigating the pervasiveness
of convergence in biology and its role in the process of adaptation. In
specific, the student working on this project will investigate how to
measure convergence in molecular data sets, and investigate how common
is molecular convergence.
In particular the student will: (1) develop measures to quantify
convergence and address the following questions. (2) How common is
convergence in molecular datasets? (2) Is molecular convergence more
common within specific lineages (e.g. mammals versus birds)? (3)
Are specific parts of the genome more prone to convergent evolution
(e.g. protein coding genes versus regulatory non-coding sequences like
microRNA)?  (4) Are alternative forms of the same data (e.g. amino acid
versus nucleotide sequences) differently prone to undergo convergent
processes? (4) To what extent is adaptive evolution underpinning the
origin of molecular convergences?
The project is entirely computational and will fit a
mathematically-inclined student with some experience in computer
programming (or the will to learn about computational methods and
programming).  You will be based at the University of Bristol, in
the newly built 'Life Sciences Building', where you will join the
Palaeobiology and Biodiversity Research Group. However, more broadly, you
will be the member of a diverse, Templeton funded, research group spread
between the University of Bristol, Bath, and the Natural History Museum
of London, and interactions and visits to Bath and London will be common.
Dr Davide Pisani
Reader in Phylogenomics
School of Biological Sciences and School of Earth Sciences
University of Bristol
Life Sciences Building
24 Tyndall Avenue
Bristol, BS8 1TG
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Phone: +44 (0) 117 39 41196
Davide Pisani <
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