[Arthropod] Re: Daphnia has the most ancestral genes

Don Gilbert via arthropod%40net.bio.net (by gilbertd from cricket.bio.indiana.edu)
Mon Feb 1 12:40:47 EST 2010


Scott,

Yes, to be sure, I qualified it 'the most ancestral arthropod gene set (of
	those available)'..

It may be a slog thru many arthropod genomes to find "the ancestral" model;
from insect genomes, it is clear even the phylogenetically basal ones are 
more derived than ixodes or daphnia, and that agrees with known phylogeny (?).  Part
of Ixodes lower score is its highly repetitive genome, subsequent poor assembly, and
artifactually poorer gene models (missing in all or parts).  But the distinction
in Ixodes better score to mammal genes vs plant/worm suggests a real difference
from Daphnia.

Another thing I noticed in these stats of non-arthropod homology, I can't put too much
weight on its biological accuracy but someone could investigate further:
  pediculus (mammal parasite) and aphid (plant parasite) are two relatively close insects,
and should by phylogeny have about same gene distance from non-arthropods.  Not quite:  
pediculus favors mammal genes over aphid by 2%, and aphid favors plant genes over 
pediculus by 1%, the only case I looked at where aphid exceeds louse.  More details are here:
http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt

- Don

|Subject: Re: Daphnia has the most ancestral genes
|
|Hi Don,
|
|I thought that was an interesting comparison you posted on Arthropod
|Digest, but I wonder if there will be a non-parasitic arthropod genome
|coming out that would be a better indicator of ancestral genes (eg a
|spider?). Mites and ticks have a long history of parasitism and that
|has been shown to be associated with gene loss, I believe.
|
|Scott Cornman
|Beltsville Bee Research Lab
|USDA-ARS
|



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