IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

[Arthropod] Re: Daphnia has the most ancestral genes

Mark Blaxter via arthropod%40net.bio.net (by mark.blaxter from ed.ac.uk)
Tue Feb 2 02:52:32 EST 2010

Hi Dan
could you get the genes into the TreeFam project also? Will the  
ensembl genomes project be 'doing' the trees?

On 1 Feb 2010, at 22:28, Daniel Lawson wrote:

> HI
> Well this is one of the aims for the Ensembl Genomes project (excuse  
> the blatant advertising). All of Don's model organism genomes are  
> represented and from an arthropod point of view we are missing  
> Daphnia, Tribolium, Nasonia, Aphid, Apis and Bombyx (so 6 out of 14  
> species). Some of these will be incorporated during the spring so we  
> could consider such an analysis in the summer.
> regards
> Dan
> -- 
> Ensembl Genomes | VectorBase
> On 1 February 2010 20:59, Mark Blaxter <mark.blaxter from ed.ac.uk> wrote:
> 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.
> Mark
> 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
> |
> _______________________________________________
> Arthropod mailing list
> Arthropod from net.bio.net
> http://www.bio.net/biomail/listinfo/arthropod
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> _______________________________________________
> Arthropod mailing list
> Arthropod from net.bio.net
> http://www.bio.net/biomail/listinfo/arthropod
> -- 
> Ensembl Genomes | VectorBase

-------------- next part --------------
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

More information about the Arthropod mailing list

Send comments to us at archive@iubioarchive.bio.net