Macrauchenia_Museo Olavarria (MO)

Proteomics MGF file

Example tandem MS spectra of three homologous peptides.

<p>The spectra are from peptide COL1A2_495–509 (peak ‘α’ in Fig. 2) with precursor (MH+) ions at (from top to bottom) <i>m/z</i> 1453 (elephants, pangolin anteater and tamandua), 1463 (hyrax and aardvark) and 1477 (armadillos and all afrosoricids including the extinct <i>Plesiorycteropus</i>). Labeling of fragment ions (inset) follows <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059614#pone.0059614-Roepstorff1" target="_blank">[37]</a>, underline represents hydroxylation site, red text highlights amino acids that differ from the inset (elephant, anteater & pangolin) sequence. Isobaric amino acids (I/L) were estimated based on conserved DNA sequence data where possible; for sites that have more than one isobaric amino acid present, the most abundant was used (see Supplementary Information).</p

Cropped ML tree

Maximum Likelihood tree from sequences when cropped to match only sequences present in specimens analysed

Toxodon_MLP 86-III-25-15

Toxodon_MLP 86-III-25-1

Toxodon_MLP 81-II-5-7

Proteomics MGF file

PMF tree

Maximum Likelihood tree from sequences observed in PM

Maximum Likelihood tree

Maximum Likelihood tree from sequences found in both specimens for each taxa above highest false positive match

Parsimony tree created in Phylip

Parsimony tree created in Phylip from sequences found in both specimens for each taxa

Phylogenetic analyses of <i>Plesiorycteropus</i> collagen (I) sequences obtained by LC-MS in comparison to previously postulated closest relatives.

<p>The results are from A) Maximum Likelihood (rooted to <i>Gallus</i>; only bootstrap support >50 is shown) and B) Neighbor-Net analysis in SplitzTree4. <i>Plesiorycteropus</i> consistently forms a monophyletic group with the tenrecs within the order Tenrecoidea, forming a sister group to the aardvark (tubulidentates), rock hyrax, and the proboscideans. Silhouette denotes sequences obtained from LC-MS data; scale shows average amino acid substitutions per site.</p

MALDI-ToF-MS spectra of collagen digests from the sub-fossil ‘malagasy aardvark’ <i>Plesiorycteropus</i> and modern specimens.

<p>The peptide mass fingerprints (PMFs) show that the quality of the collagen extracted from the fossil is as good as from modern specimens (from top to bottom; aardvark (<i>Orycteropus afer</i>), <i>Plesiorycteropus sp.,</i> rock hyrax (<i>Procavia capensis</i>) and greater hedgehog tenrec (<i>Setifer setosus</i>)). Peaks marked α and β represent some of the most variable homologous peptides manually sequenced (Fig. 3 & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059614#pone.0059614.s002" target="_blank">Fig. S2</a>). A greater similarity between peptide <i>m/z</i> values can be seen between <i>Plesiorycteropus</i> and tenrec than any other species sampled.</p