Hi Dan
could you get the genes into the TreeFam project also? Will the
ensembl genomes project be 'doing' the trees?
Mark
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
> |USDA-ARS
> |
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