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South American unuglate origin mystery solved

Ben Creisler

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
Ancient proteins resolve the evolutionary history of Darwin’s South
American ungulates.
Nature (advance online publication)

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.