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[Arthropod] Re: Daphnia has the most ancestral genes

Daniel Lawson via arthropod%40net.bio.net (by lawson from ebi.ac.uk)
Mon Feb 1 17:28:58 EST 2010


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.


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
>> |
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