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Molecular taxonomy for dummies?

In the course of following (at some considerable distance) the discussion on 
Passeriformes, I am increasingly realizing that I need a basic, simple guide to 
the subject of molecular taxonomy. I mean something directed at a poor ignorant 
fellow like myself who hasn't the faintest idea what a retroposon is, or who 
thinks that long branch attraction has something to do with romance. Does such 
a thing exist?

Ronald Orenstein 
1825 Shady Creek Court
Mississauga, ON
Canada L5L 3W2

On 2011-09-25, at 4:19 PM, evelyn sobielski <koreke77@yahoo.de> wrote:

>>> Although the taxon sampling is a bit patchy (e.g., no
>> representatives of
>>> Acciptriformes and Strigiformes)
> You need at least 2 of _Sagittarius_, _Pandion_ and elanids plus 2 of 
> eagle/hawk/buteo. One of _Sagittarius_/_Pandion_ will usually go rogue.
>> Isn't that rather strange if one is interested in the
>> position of falcons?
> Coliiformes and _Aegotheles_ (haven't seen _Steatornis_) give the strongest 
> bogus signal. Coliiformes are hopeless via DNA. But the framework now exists 
> for morph. _Aegotheles_ is... funny. I wouldn't be surprised if _Steatornis_ 
> was no better. Something the entire base of the cypselomorphs has a high 
> probability to be rogue (Apodiforms are the only thing I could get to clade 
> dependably)
> Seriemas pose much the same problem as mousebirds. Their relationship based 
> on DNA is simply not to be taken seriously. They were one of the *major* Pg 
> radiations, so this needs to be reanalyzed. You could leave out fossils *if* 
> they behaved predictably on DNA, but they don't. (Any more seriema DNA is 
> gladly appreciated though) They are not major upsetters though.
> Psittaciforms, accipitrids, falconids and passerines are in the same major 
> clade it looks. Strigiforms probably too. Other than these, "picocoracines". 
> It looks like 2 subsequent radiations, one is the basal split of Neoavesa 
> into - basically - Aequornithes and "higher landbirds" and *perhaps* 2-3 more 
> distinct lineages surviving from that time.  Some taxa are "weird" though - 
> all "Metaves", essentially, though *most* do in fact reliably go in one clade 
> or the other for *most* loci. The second radiation is very explosive and 
> somewhat obfuscated (but not usually destabilized) in Aequornithes by 
> ciconiids etc, in the other clade by upupiforms. 
> As I said, mousebirds and _Aegotheles_ usually manage to completely upset at 
> least one of the 2 major clades by their sheer presence.
> I woudn't trust anything that doesn't compare the tree with and without them.
> Falconids tend to turn up close to passerines, and perhaps reliably so. 
> Psittaciforms are perhaps more often among Aequornithes than close to 
> falconids, and if not rogue they are usually closer to accipitrids.
> NWvultures clade irregularly, with about even likelihood for them to turn up 
> next to falconids, accipitrids or within Aequornithes. Removing them, 
> however, usually has little effect on the tree.
> Both radiations must have occurred in the late K. We have some fossils which 
> very much look as if they'd turn out on one "side" of charadriiforms, 
> Aequornithes etc. or the "opposite" one, so the basal radiation of these was 
> very likely already ongoing. 
> There are regions all over the genome where oligo-indels "happen", i.e. they 
> are not repaired (conspicuous in an alignment because there are many 
> oligo-gaps and consensus is low).
> There are other regions where there is a higher probability of long indels 
> (usually ins rather than dels). They are rarely phylogenetically informative 
> per se. A certain insert (and perhaps deletion) may consist of several 
> independent elements; I found one of the retroposons apparently a fusion of 4 
> elements, 2 of which were ubiquitious in Neornithes, 1 has human(?) and 1 was 
> likely protist.
> In strigiforms, it *may* be necessary to always sample _Phodilus_.
> I have not found a viable solution for cypselomorphs yet. This and the low 
> taxon sampling among "picocoracines" is the present obstacle on resolving the 
> "higher landbirds". And of course, either the tree with a mousebird or 
> without one (two doesn't help either, not even when both genera are sampled) 
> or neither may be true. We cannot tell.
> The two most common taxa to stand basal in Neoaves (mis-rooting to 
> Galloanseres/paleognaths) are passeriforms and columbiforms. I haven't really 
> checked what the latter are closest to when you unroot Neoaves (passeriforms 
> are usually close to something "higher landbird", not rarely to falcons), but 
> IIRC they *might* be Aequornithes. (Need to add charadriiiforms and some more 
> Aequornithes to the sample now.
> 1. Has anyone ever tested the population genetics of 
> retroelements/transposons? (Should be possible in chicken)
> 2. What were the BLAST settings used in Suh et al for checking the retroposon 
> sequences against nr/nt?
> 3. What specimens were used from _Falco_? Wild or captive? If captive, how 
> many generations from the wild? (the human-like piece is... odd)
> 4. What does a cladistic analysis of the more widespread transposons' 
> sequence say? (Some of the more ubiquitious long transposons seem to carry 
> significant phylogenetic signal)
> There is something odd in the pattern of rogue taxa. Can't lay my finger on 
> it, but in some cases I could fix it by sampling a close relative instead. In 
> these cases there were often massive indels in the rogue taxa (in one 
> trochiline genus there was 1 rogue and 1 unrogue sp.). Not finding them in 
> close relatives would mean that such indels, which are assumed to persist in 
> situ through evolutionary time with high probability, don't. 
> -----
> PNAS has a new paper about avian extinction at the K-Pg boundary. Looks 
> interesting in the news, anyone seen it yet?
> Regards,
> Eike