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RE: South American unuglate origin mystery solved

The concerns are unwarranted.  

The article quotes O'Leary as saying "Before creating their tree, ... the team 
should have combined their data with published information on other molecules 
and physical features."  But this would only be useful if the collagen tree 
were different than the tree found when using total evidence analyses, which it 
apparently isn't.  It's as if you have a tooth-based taxon, and running it in 
an analysis of only tooth characters leads to a certain tree.  If this tree is 
the same as the tree you get when also using skull, limb and vertebral 
characters all together, adding all those characters in isn't going to affect 
the position of the tooth-only taxon.  Its relationships are already determined 
purely due to the arrangement of tooth characters in the other taxa.  As they 
have the same arrangement in both tooth-only and total-evidence trees, the 
tooth-only taxon is going to have the same placement in both.

Similarly, the article quotes Cooper as saying "ancient proteins have their 
problems. Collagen does such an important job that it doesn't change very 
easily; when it does, it is severely constrained in how it can change. As such, 
similarities between two collagen sequences might imply that their owners are 
genuinely related, or that they were independently forced down the same 
convergent routes."  But since the rest of the collagen tree is apparently 
about the same as the standard phylogeny we get from other sources of data, it 
seems convergence wasn't a notable factor in this case.  If collagen 
convergence didn't affect other mammals, there's no reason to suppose it 
affected notungulates.

Mickey Mortimer

> Date: Wed, 18 Mar 2015 22:34:50 +0000
> From: ron.orenstein@rogers.com
> To: bcreisler@gmail.com; dinosaur@usc.edu
> Subject: Re: South American unuglate origin mystery solved
> Some concerns have already been raised about the methodology:  see 
> http://phenomena.nationalgeographic.com/2015/03/18/darwins-strangest-beast-finds-place-on-tree/.
>  Ronald Orenstein
> 1825 Shady Creek Court
> Mississauga, ON L5L 3W2
> Canada
> ronorenstein.blogspot.com
> ronorensteinwriter.blogspot.com
> From: Ben Creisler <bcreisler@gmail.com>
> To: dinosaur@usc.edu; VRTPALEO@usc.edu
> Sent: Wednesday, March 18, 2015 2:54 PM
> Subject: South American unuglate origin mystery solved
> Ben Creisler
> bcreisler@gmail.com
> A new non-dinosaur article that may be of interest:
> Frido Welker, Matthew J. Collins, Jessica A. Thomas, Marc Wadsley,
> Selina Brace, Enrico Cappellini, Samuel T. Turvey, Marcelo Reguero,
> Javier N. Gelfo, Alejandro Kramarz, Joachim Burger, Jane Thomas-Oates,
> David A. Ashford, Peter D. Ashton, Keri Rowsell, Duncan M. Porter,
> Benedikt Kessler, Roman Fischer, Carsten Baessmann, Stephanie Kaspar,
> Jesper V. Olsen, Patrick Kiley, James A. Elliott, Christian D.
> Kelstrup, Victoria Mullin, Michael Hofreiter, Eske Willerslev,
> Jean-Jacques Hublin, Ludovic Orlando, Ian Barnes & Ross D. E. MacPhee
> (2015)
> Ancient proteins resolve the evolutionary history of Darwin's South
> American ungulates.
> Nature (advance online publication)
> doi:10.1038/nature14249
> http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14249.html
> No large group of recently extinct placental mammals remains as
> evolutionarily cryptic as the approximately 280 genera grouped as
> 'South American native ungulates'. To Charles Darwin,  who first
> collected their remains, they included perhaps the 'strangest
> animal[s] ever discovered'. Today, much like 180 years ago, it is no
> clearer whether they had one origin or several, arose before or after
> the Cretaceous/Palaeogene transition 66.2 million years ago, or are
> more likely to belong with the elephants and sirenians of superorder
> Afrotheria than with the euungulates (cattle, horses, and allies) of
> superorder Laurasiatheria. Morphology-based analyses have proved
> unconvincing because convergences are pervasive among unrelated
> ungulate-like placentals. Approaches using ancient DNA have also been
> unsuccessful, probably because of rapid DNA degradation in
> semitropical and temperate deposits. Here we apply proteomic analysis
> to screen bone samples of the Late Quaternary South American native
> ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for
> phylogenetically informative protein sequences. For each ungulate, we
> obtain approximately 90% direct sequence coverage of type I collagen
> α1- and α2-chains, representing approximately 900 of 1,140 amino-acid
> residues for each subunit. A phylogeny is estimated from an alignment
> of these fossil sequences with collagen (I) gene transcripts from
> available mammalian genomes or mass spectrometrically derived sequence
> data obtained for this study. The resulting consensus tree agrees well
> with recent higher-level mammalian phylogenies. Toxodon and
> Macrauchenia form a monophyletic group whose sister taxon is not
> Afrotheria or any of its constituent clades as recently claimed, but
> instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These
> results are consistent with the origin of at least some South American
> native ungulates from 'condylarths', a paraphyletic assembly of
> archaic placentals. With ongoing improvements in instrumentation and
> analytical procedures, proteomics may produce a revolution in
> systematics such as that achieved by genomics, but with the
> possibility of reaching much further back in time.
> ==
> News:
> http://phys.org/news/2015-03-protein-sequencing-darwinian-mystery-strange.html
> http://www.mpg.de/9040884/toxodon-macrauchenia-protein-evolution?filter_order=L&research_topic=
> http://phenomena.nationalgeographic.com/2015/03/18/darwins-strangest-beast-finds-place-on-tree/