^ Yes all very good points and interesting about the coyote/wolf.
The issue that comes out of doing molecular level genomics rather than some sort of DNA fingerprinting etc is that there is more to genomic comparison than 'XX %' as I'm sure you're aware.
So it is becoming apparent that the thing to do is look for the occurances of protein families. Within a protein family one might still have large variations but yet the genes are still recognizable as being part of the same family - and doing the analogous thing in that organism. Such variations within a protein familiy can be considered to be allelic. So the idea would be to carefully look, in the genomes we have, for what blocks of genes seem to travel together and what sort of genomic differences you get within the currently defined species, genera, families and higher taxa. Some of this has undoubtedly been done but there is still a long way to go and there may not even be that many people talking quite as you and I are.
So one would see if there are some sort of clear patterns and then see if redefinitions of species/genera/families etc allow the patterns to improve. What sort of patterns? OK - one might find that at some level animals are related purely allelically - ie they have the 'same' genes (in terms of function) but diffent alleles. At the next level one might see novel 'luxury' genes: non-essential genes that distinguish a horse from a zebra for example but do not disallow hybridization. Then at higher levels one would look for essential sets of genes that appear as blocks. One would try and see what type of changes one gets comparing acroos classes or orders. I'm thinking aloud here but basically although a lot of this would be partailly known 'anecdotally' it has probably not been done systematically due to the newness of the genome sequence determinations.
At some point one will have to think about loss vs gain and try and use pseudo-genes to distinguish between these two. I think it would undoubtedly be a good post-grad project/collaboraiton between a genomicist and a taxonomist.
On the other hand you have to take this with a few grains of salt. My genomics work so far concerns (i) protein folding mechanisms (not very genomic really) and 3D structure prediction and (ii) the use of protein folds across pathways. I really know almost nothing about taxonomy - it is only what I have picked up subliminally. And yet I am convinced this is a good project and would be confident of supervising it. I am a fan of multidisciplinary science.
Here's a question for you. How exactly do modern taxonomists define new genera or families for example? How clear cut is it? What makes the wolf and dog part of the same genus
Canus and not just in the same family? It intuitively makes sense but what are the objective criteria?
[This message has been edited by Tranquility Base, 09-12-2002]
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