Tyrannosaurus rex Osborn 1905
Creators: name: Michael Buckley
name: Stacey Warwood
name: Bart van Dongen
name: Andrew C. Kitchener
name: Phillip L. Manning
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Reptilia
Dinosauria
Tyrannosauridae
Tyrannosaurus
Tyrannosaurus rex

description: (a) Tyrannosaurus rex collagen sequences   
 In the case of the T. rex specimen (MOR 1125)̗ these initial studies were supported by two main lines of supporting molecular evidence: immunological data and sequence information [1]. This first choice of support is no longer widely accepted as ideal for such claims̗ given that immunological techniques have been shown to yield false-positive results [8]. The authenticity of any findings based on this approach rests solely on sequence interpretation. In its first release̗ this was fraught with multiple incorrect post-translational modification (PTM) assignments in the form of hydroxylated glycine residues [5]; a clear indication of the potential problems is the reliance on probability-based matching algorithms of current proteomics-based techniques. In direct response to this first report̗ several criticisms arose related to potential forms of contamination [6 ̗ 9 ̗ 10] or statistical artefact relating to such a proteomics approach [11].   
 On the grounds that mineralized and non-mineralized coatings have been found extensively in the porous trabecular bone of a variety of vertebrate fossils across time̗ including dinosaurs̗ Kaye et al. [10] proposed that the T. rex specimen was likely similarly contaminated with bacterial biofilm̗ thus explaining the morphological similarity to the blood vessels and osteocytes that they attack. In addition̗ the blood-celllike iron–oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Interestingly̗ similar thin linings on Haversian canals within apatite were identified by infrared and electron microprobe analysis of ossified tendon by Manning et al. [7] and clearly showed preserved mineral zonation̗ with silica and trapped carbon dioxide. FTIR analysis of the tendon showed clear structural control of organic compounds within the Haversian canals̗ suggesting that organic material may have persisted. However̗ this study concluded that the organic signal may have been associated with breakdown products of the original biomaterial deposited within the tendon̗ consistent with the presence of the endogenous breakdown products of organic material identified from other regions of the specimen but not able to yield any such sequence information [7].   
 Bern et al. [9] reanalysed the original T. rex sequence data to infer that the sample was predominantly laboratory contaminants̗ soil bacteria and bird-like haemoglobin and collagen. They suggested that of the six peptides that Asara et al. [5] deposited in GenBank (GATGAPGIAGAPGFPGARGA- PGPQGPSGAPGPK̗ GSAGPPGATGFPGAAGR̗ GVQG- PPGPQGPR̗ and GVVGLPGQR from collagen alpha-I type I̗ GLVGAPGLRGLPGK from collagen alpha-1 type II and GLPGESGAVGPAGPIGSR from collagen alpha-2 type I)̗ only the first three of these could be considered statistically significant̗ calling for the latter to be dropped from GenBank. However̗ despite the unexpected presence of haemoglobin̗ a protein only typically seen in relatively recent samples [12̗ 13]̗ the presence of the remaining collagen peptides was not accepted as being contamination for reasons that remain unclear.
description: Published as part of Michael Buckley, Stacey Warwood, Bart van Dongen, Andrew C. Kitchener & Phillip L. Manning, 2017, A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination, pp. 544 in Proceedings of the Royal Society, Series B 284 on page 544, DOI: 10.1098/rspb.2017.0544, http://zenodo.org/record/3748698