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[Arthropod] Re: Daphnia has the most ancestral genes

Mark Blaxter via arthropod%40net.bio.net (by mark.blaxter from ed.ac.uk)
Mon Feb 1 15:59:49 EST 2010

Hi folks
I'm always worried when BLAST is used as a phylogenetic tool...  
basically the 'scores' returned are contingent on the underlying  
model, which in BLAST is evolutionary/biological of course, but is  
generalised across all proteins. Statements of 'basal' imply a tree,  
and a tree implies a model driven reconstruction, and, well, BLAST  
doesnt reconstruct trees.

A top blast match (or reciprocal best blast) algorithm is severely  
biased by
- the relative rates of substitution in each genome
	all extant genomes are equally 'evolved'; the differences are in  
rates and patterns of rates of evolution across genes
	two genomes with relatively low substitution rates will appear more  
similar than expected when compared to their sister taxa, when sister  
taxa have elevated rates
- the patterns of substitution that are driven by other forces, such  
as base composition
	its well known in mitochondrial genomes that protein substitution  
patterns are driven by genome AT content, resulting in significant and  
completely confounding homoplastic convergence at the amino acid level
	thus global comparisons using BLAST, using a single substitution  
matrix (that implicitly assumes equivalence of amino acid composition  
bias) will mislead

It would be good to derive trees for all of the protein sets Don has  
generated and ask what their topologies are. Are these genes not in  
TreeFam, where there are trees derived that can be mined for data  
affirming this finding.


On 1 Feb 2010, at 17:40, Don Gilbert wrote:

> 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
> |
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