[Taxacom] DNA only descriptions

Fri Aug 20 23:39:45 CDT 2010

Sorry, if that was your impression, than I did a bad job explaining.

Kim

On 8/20/2010 7:55 PM, Stephen Thorpe wrote:
> Yes, that is fine, but Kim seemed to be claiming that if you knew the genome,
> then the morphology would not be worth bothering with ...
>
>
>
>
> ________________________________
> From: Robin Leech<releech at telusplanet.net>
> To: Stephen Thorpe<stephen_thorpe at yahoo.co.nz>; Kim van der Linde
> <kim at kimvdlinde.com>; Kenneth Kinman<kennethkinman at webtv.net>
> Cc: taxacom at mailman.nhm.ku.edu
> Sent: Sat, 21 August, 2010 11:42:57 AM
> Subject: Re: [Taxacom] DNA only descriptions
>
> If one does it right, one can describe the genome as part of the normal
> morphological,
> descriptive taxonomy.
> Robin
>
> ----- Original Message ----- From: "Stephen Thorpe"<stephen_thorpe at yahoo.co.nz>
> To: "Kim van der Linde"<kim at kimvdlinde.com>; "Kenneth Kinman"
> <kennethkinman at webtv.net>
> Cc:<taxacom at mailman.nhm.ku.edu>
> Sent: Friday, August 20, 2010 5:35 PM
> Subject: Re: [Taxacom] DNA only descriptions
>
>
>> In my opinion, the crucial aspect we should not forget is that we use
>> morphology
>> as a proxy for genetic differences
>
> IT DEPENDS WHAT ONE IS DOING! Descriptive taxonomy, or "systematics"?
> Descriptive taxonomists would still describe morphology even if systematists
> knew EVERYTHING about the genetics ...
>
>
>
> ________________________________
> From: Kim van der Linde<kim at kimvdlinde.com>
> To: Kenneth Kinman<kennethkinman at webtv.net>
> Cc: taxacom at mailman.nhm.ku.edu
> Sent: Sat, 21 August, 2010 3:16:00 AM
> Subject: Re: [Taxacom] DNA only descriptions
>
> Hi Ken,
>
> I agree with most what you said. There is one item I would like to
> elaborate on.
>
> On 8/18/2010 11:55 PM, Kenneth Kinman wrote:
>> For many taxa, an appropriate weighing "from all possible sources" is
>> still a work in progress, and molecular data is perhaps still often
>> given too much weight when such data is still far from complete.
>> What you regard as "far more [molecular] data" may not impress
>> morphologists of some taxa. As you said, it has to be weighed on a
>> case to case basis, and therefore it is unwise to make any
>> generalizations one way or another without reference to the
>> particular taxa being discussed.
>
> I think the worst 'solutions' are the cases in which molecular and
> morphological data are lumped in a single analysis. Those generally tend
> to be dominated by the molecular data as it is often numerically
> outweighing the morphological data.
>
> In the drosophilid taxonomy, we have two competing morphological studies
> resulting in substantially different trees. The first phylogeny
> (Throckmorton) is primarily based on internal morphological
> characteristics, while the second (Grimaldi) scored a huge number of
> external traits. Now, 20+ molecular studies and 12 genomes later, we
> know rather precise the phylogeny of the genus and 12+ included genera.
> The Throckmorton phylogeny was rather close to the molecular tree,
> while the Grimaldi phylogeny was substantially further off. So, there is
> an obvious conflict between the Grimaldi tree at one hand, and the
> molecular and Throckmorton's trees at the other hand. So, what to do
> with the Grimaldi tree? Generally, it is given limited weight,
> especially after it became clear that the cladistic analysis was only
> partial and reanalysis of the data in a more thorough way did not result
> in the same answer.
>
> It is really easy to sit down with a bunch of people, find the worst
> offending molecular articles and use that to dismiss everything. It is
> easy to do the opposite as well.
>
> In my opinion, the crucial aspect we should not forget is that we use
> morphology as a proxy for genetic differences. Species delineation is
> one thing, but taxonomists also group species in genera, tribes,
> families etc. to roughly reflect genetic relatedness (yes, I know,
> paraphyletic taxa, but let's keep the discussion focused). And because
> of that, if there is a conflict between morphology and DNA, the only
> sensible question to ask is what causes this difference. The more we
> study the evolution of traits at the molecular level, the more examples
> we get where large morphological differences are determined by minimal
> genetic differences, like a single point mutation in a regulatory
> element. Do I have to give such a morphological characteristic a lot of
> weight? Of course not.
>
> Similar issues arise with molecular data. We routinely use genes for
> phylogenetic reconstructions, but once those genes are subject to
> directional selection, you can fall in the same pitfalls as with
> morphological traits.
>
> Really, the whole morphology vs molecular discussion is so passe. Sure,
> individuals can keep sitting on their little islands, but reality is
> that the world moves forward. Just producing a molecular phylogeny
> becomes less and less important; many of them are produced in studies
> examining the (molecular) evolution of morphological traits. In most of
> those studies, there is no dispute about what to use as a basis, the
> molecular tree is used to map the morphological traits over, not the
> other way around (sure, I suspect there will be some exceptions, I just
> haven't seen them).
>
> Knowing all this, I do not have a problem with DNA-only descriptions.
> Just as we have to determine the variability in morphological traits
> before we can determine the boundaries between species, we have to do
> the same with DNA circumscriptions.
>
> But I think the most important aspect is that we forget that we make
> *proposals* when we publish either species or a phylogeny. Only when it
> is accepted by our peers, and used accordingly, we know that out
> *proposal* has merits as long as nothing better comes along. Many are
> far too obsessed with wanting to have the final answer, but reality is,
> we are always limited in what we actually know and hence, even the best
> supported hypothesis could one day be superseded by a better one. So,
> instead of fighting about morphology vs molecular, let's all do our job
> with the tools we have at hand and let's keep an open mind to what other
> have to offer as well, even if that means that you might be wrong. In an
> upcoming era in which a genome can be sequenced in one day for less than
> $100, you bet that it is going to dominate the field of systematics. The
> question we should ask ourselves is how do we integrate that the best way.
>
> Kim
>
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