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Turtles (and Afrotheria) (long)

Original message forwarded on request. Answers included.

----- Original Message -----
From: "ekaterina A" <a_ekaterina@yahoo.com>
To: <david.marjanovic@gmx.at>
Sent: Saturday, October 05, 2002 6:59 AM
Subject: Re: Chelonians and Small et al's Archosauromorph

> --- David Marjanovic <david.marjanovic@gmx.at> wrote:
> > Sometimes they do find them within lepidosaurs,
> > though. :-)
> Which work are you talking about here?


BTW, the search engine in the archives doesn't work at the moment.
Fortunately I have that post in my inbox and found it with the search engine
in Outlook Express.

> > sistergroup of crocs, and this divergence was dated
> > to the end of the
> > Triassic when both crocodylomorphs and turtles
> > already existed! Means, their
> > sequences are too similar for them to be close
> > relatives. :-P But see below.
> The failure of correct molecular extrapolation of a
> branch point does not mean that the tree topology is
> wrong.

It does not automatically mean that the topology is wrong, as opposed to the
presumed molecular clock rates. But it strongly suggests so IMHO.

> > Never seen that. Weird.
> PLease see these papers if you did not do so before:
> Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa
> M.
> Phylogenetic position of turtles among amniotes:
> evidence from mitochondrial and
> nuclear genes.
> Gene. 2000 Dec 23;259(1-2):139-48.
> Hedges SB, Poling LL.
> A molecular phylogeny of reptiles.
> Science. 1999 Feb 12;283(5404):998-1001.

Thanks a lot, haven't found the former (I hope Gene is in the biosciences
library...) The latter is outdated.

> > today it still is. There are extremely few turtle
> > sequences. The only 18S
> > rDNA sequence from a turtle (*Trachemys scripta*) is
> > short and full of
> > mistakes, or so I've heard.
> See the above papers: there is considerable amount of
> sequence data.

Still only one for 18S rDNA, no?

> There are many more site available for
> phylogenetic inference


> than any of the morphological
> studies can hope to have.

Hm. Substitutions of single bases happen a lot more often than morphological
changes... so I wouldn't equate them 1 : 1. In any case I'd use several
genes at once. There is a great eukaryote phylogeny right behind the
description of *Eudibamus* (Science, November 1999) that was made with four
genes at once instead of just one as usual. It eliminates a lot of
long-branch attraction & stuff.

> > If the alignment was correct... and if there are
> > enough taxa in the matrix... now a basal
> > pareiasaur genome would be nice...
> The genes used here are obvious orthologs so these
> alignments are trivial to make.

Because of insertions, deletions, domain shuffling and what more jokes there
are, alignment is hardly ever trivial, at least in such distant taxa.

> People well versed in
> these issues tell me that these alignments are good
> enough not to skew the trees. You can look up these
> alignments yourself if you are not conserved.
> David also look a these papers:
> Kumazawa Y, Nishida M. Complete mitochondrial DNA
> sequences of the green turtle and blue-tailed mole
> skink: statistical evidence for archosaurian affinity
> of turtles. Mol Biol Evol. 1999 Jun;16(6):784-92.
> Here they use quite large alignments and obtain strong
> statistical support for the archosauromorph affinities
> of turtles.
> Now se this paper:
> Zardoya R, Meyer A.
> Complete mitochondrial genome suggests diapsid
> affinities of turtles. Proc Natl Acad Sci U S A. 1998
> Nov 24;95(24):14226-31.
> Here the whole genome of the miotchondrial genome of
> the turtles was determined.

Of one turtle, or of three, as in their 2001 paper? :-)

> Again the data set is
> large and gives a reliable turtle-archosaur grouping.

Reliable is a relative term.

> Paleontologists doubted Afrotheria too! Not intutive
> but likely.

Afrotheria is indeed likely. And slowly, very slowly, morphologists are
moving towards it, even the similarities between hyrax and *Hyracotherium*
are diminishing:

Rodolphe Tabuce, Brigitte Coiffait, Philippe-Émmanuel Coiffait, Mohamed
Mahboubi & Jean-Jacques Jaeger: A new genus of Macroscelidea (Mammalia) from
the Eocene of Algeria: A possible origin for elephant-shrews, JVP 21(3),
535 -- 546 (September 2001)

>From the abstract: "The phylogenetic analysis suggests also that the
Macroscelidea-*Microhyus* clade is closely related to the Proboscidea. Like
molecular phylogenies, especially thise concerning the African molecular
clade ( = Afrotheria), our results, [sic] provide evidence for a
macroscelid-tethytherian relationship." *Microhyus* is a European
"condylarth" from the start of the Eocene. Everything based on teeth as if
it were Mesozoic.

>From the text... "This [disjunct distribution] suggests that the characters
shared by Glires and some macroscelidids could be the result of
convergences. Indeed the character of the prismatic jugal teeth seems to
have been acquired very late (during the Miocene?) in elephant-shrews: the
Miocene primitive Rhynchocyoninae (*Miorhynchocyon*) and Macroscelidinae
(*Pronasilio*) have no prismatic jugal teeth".

The cladogram is quite interesting... *Aspanlestes*, *Eoungulatum* and the
plesiadapiform *Palaechthon* were used for rooting. The former two form a
trichotomy with everything else, including *Palaechthon*, thereby setting
themselves outside crown-group Boreo(eu)theria! This is evidence against
"Ungulatomorpha". *Bunohyrax* comes out as sister to either *Hyracotherium*
or (less often) *Numidotherium* (a basal proboscidean). The latter is sister
to (Macroscelidea + *Microhyus*). Next to the last two sentences are
*Phenacodus* and *Ectocion*, traditionally near Perissodactyla, then
*Mioclaenus* + (*Periptychus* + *Hyopsodus*) (3 more NA "condylarths"), then
*Eoconodon* (traditionally in or near Mesonychia), then a bunch of
"Hyopsodontidae", one of which has been considered a hedgehog (untested
because no eulipotyphlan is in the matrix) and some of which have been
considered close to Macroscelidea, then *Diacodexis* (basalmost
Artiodactyla) and another "hyopsodontid", then the arctocyonid *Loxolophus*,
then *Protungulatum*, and then *Palaechthon*. Only 44 characters were used.

"The lack of homologous dental characters between ungulates and
tenrecids-chrysochlorids does not allow us to include these insectivores in
our analysis. Moreover, early tenrecids and chrysochlorids are unknown
before the Miocene."

Donald D. de Blieux & Elwyn L. Simons: Cranial and dental anatomy of
*Antilohyrax pectidens*: a late Eocene hyracoid (Mammalia) from the Fayum,
Egypt, JVP 22(1), 122 -- 136 (March 2002)

"_Paenungulate Phylogenetics_ -- [...] Studies of the higher level phylogeny
of mammalian orders have foud relationships within the ungulates [and the
monophyly of Ungulata!] to be a difficult problem. The position of the
Hyracoidea has been one of the few fairly confident links at the
superordinal level. Most workers support the concept of Paenungulata that
allies the hyracoids with Proboscidea and Sirenia, as well as the extinct
Desmostylia [damn far from Africa...] and Embrithopoda [...]. A few workers
supported the concept of Pantomesaxonia that links the hyracoids with
Perissodactyla [...]. Molecular studies have provided additional evidence
for Paenungulata [...]. Most recently [...] Afrotheria, that groups
Paenungulata with Macroscelidea, Tubulidentata, and Afrosoricida (tenrecs
and golden moles [...].
    Cranial characters of extant hyracoids have been used by proponents of
both the Paenungulata and the Pantomesaxonia. Fossils are important to this
question because they show that modern hyracoids have many derived features
that are not representative of primitive hyracoids [...].
    The contact of the frontal and the maxilla in *Antilohyrax* [...] broad
region of contact between these two elements. The anterior shift of the
orbits in extant hyraxes has resulted in either a loss of contact (with the
lacrimal contacting the nasal as in perissodactyls) or a very narrow contact
[...] (as in proboscideans and sirenians). Our observations of additional
early hyracoid genera reveal that a broad region of contact is typical.

And then there's the case of whales. Morphology makes Whippomorpha rather
improbable, though it now corrobates Cetartiodactyla as a whole. Maybe it's
now time for the molecular biologists to move a little? ;-) (Remember the
discussions... www.cmnh.org/dinoarch/2001Sep/msg00555.html,