[HELICONIUS] Heliconius genomics and flycatcher genomics

[James Mallet]

I thought i ought to share with you correspondence I have had with 
Hans Ellegren on Heliconius genomics.

I met him in Sweden at one of the endless Darwin 200 conferences this 
year. His group at Uppsala are doing a similar kind of non-model 
organism genomics project, on the pied flycatcher. Like us, they have 
other species which are the models (we have Bombyx, they have 
chicken, and maybe zebra finch), and also like Lepidoptera, they have 
very low rates of chromosome evolution. He makes some interesting 
suggestions below for why birds hybridize more readily at greater 
genetic distances than other organisms. Can it really be as simple as 
low rates of chromosomal evolution? Actually, I kind of doubt that 
mammals are that far behind in hybridization rates (in my 2005 TREE 
paper I estimate that 6% of European mammal species, vs. 12% of 
European butterflies, are known to hybridize in nature, which doesn't 
seen that different).

Jim
____________________________________________________________________
From: Hans Ellegren <hans.ellegren at ebc.uu.se>
To: James Mallet <james.mallet at wiko-berlin.de>
Subject: late response


Dear Jim,


I had a look at the Heliconius genome web site and found the
initiative well-thought and well described. I'm not sure you would
have some use for our 'pipeline' (given the careful and well-organized
plan you already have there) but to the extent we can be of some help
I would be just happy to assist. For example, we've just got funding
for buying a 454 instrument and perhaps we can do some runs here in
the future to assist your project. It is attractive that these
organisms have such (relatively) small genome size, likely
facilitating the assembly process. Moreover, I guess at least part of
this small size is due to a relatively low number of repeat elements,
which should be a further benefit in assembly.


Thanks for the references about hybridization rates. What I
understand, birds have low speciation rates. We are currently doing
some work on quantifying the rate of chromosomal rearrangement in
birds, which appear unusually low (you may remember a slide I showed,
which demonstrated that there had been very few interchromosomal
rearrangements between chicken and zebra finch). My thinking is that
the low rate of chromosomal changes means that speciation is slow
(while hybridization can be high).


All the best,


Hans

_________________________________________________________________
Dear Hans,


I really enjoyed talking with you at length, and would like to direct
you to
http://heliconius.zoo.cam.ac.uk/heliconius/2009/heliconius-genome-consortium-meeting-summary/
for our genome sequencing consortium. In my own recently funded
project, we will design around 60,000 mapped SNPs for within and
between species of the Heliconius melpomene group, which contains
around 15 closely related species all of which can be hybridized and
backcrossed (and which do so naturally) in spite of some Haldane's
Rule infertility in females.


We ought to combine forces, since your flycatcher pipelines (as I have
learned to call them) will help ours, and maybe vice versa when we get
cranking. We've already got lots of genomics data, and now we want to
go for the complete thing. It will  be excellent for studying comparative
genomics and should open up whole new research avenues in Heliconius.


The hybrid bird data I referred to is on "www.bird-hybrids.com". My
paper on hybridization rates is in TREE in 2005
(http://www.ucl.ac.uk/taxome/jim/pap/mallethyb05.pdf). You will find
an errata in my Table 1 in this version concerning the old world
warblers. My source was a different one, a guide book of warblers. My
information for the Paridae hybrids was from: Harrap, S. and Quinn, D.
(1996) Tits, Nuthatches and Treecreepers, Christopher Helm. I
justified some of the hybrid bird and other data in Table 1 in an
online appendix, Appendix 1:
http://www.ucl.ac.uk/taxome/jim/pap/mallethyb05ap1.pdf



________________________________

James Mallet
UCL
www.ucl.ac.uk/taxome/jim
2008-2009 Fellow, Wissenschaftskolleg zu Berlin
Wallotstrasse 19
14193 BERLIN
Germany

tel: +49 (0) 30 89 00 1-264
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