Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds

Molecular analysis of collagen sequences from an 80 million year old hadrosaur B. canadensis and a 68 million year old dinosaur T. rex suggest that the two dinosaurs belong to a clade to the exclusion of birds [1,2,3].  However, well-established morphological analyses of fossils show that T. rex is more closely related to birds than it is to the ornithischian hadrosaur B. canadensis [4].  The molecular analyses were based on the molecular clock paradigm, which is known to be contradicted by fossil sequences [5,6].  It is therefore necessary to reevaluate the molecular data independent of the molecular clock paradigm. 

Here, I analyzed all the collagen sequences reported for B. canadensis and T. rex.  There are a total of four peptides whose sequences are known in the two dinosaurs and extant chicken.  But, only one of these is informative as the other three are identical among the three species.  For this single informative 18 amino acid peptide (GLPGESGAVGPAGPPGSR), I compared its sequence from all extant species including birds, reptiles, amphibians, fishes, and mammals where the sequence information is available (Table 1).  The data show that T. rex is identical to G. gallus whereas B. canadensis differs from T. rex and G. gallus at residue position 15.  An Ile residue at this position is completely conserved in all extant species of mammals, birds, and reptiles.  And yet, B. canadensis has a Pro at this position.  From the Dayhoff’s PAM (accepted point mutation) matrix [7], a change from Ile to Pro or vice versa is highly uncommon.  Furthermore, not a single extant species from mammals, birds, reptiles, amphibians, and fishes (19 species analyzed) has a Pro at this position.

These molecular data therefore suggest strongly that B. canadensis is an outgroup to a clade containing T. rex and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils [4].  The unusual change from a conserved Ile to a Pro also show that B. canadensis is genetically more distant to the outgroup fish than extant birds and reptiles, confirming the previous observation that ancient fossil specimens of extinct species are more distant to a simpler outgroup than extant sister species [5,6].  Thus, fossil sequences consistently contradict the molecular clock paradigm and would inevitably lead to absurd conclusions if analyzed under the assumptions of that paradigm.  

Reference:

1. Schweitzer MH, Zheng W, Organ CL, Avci R, Suo Z, et al. (2009) Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324: 626-631.

2. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316: 280-285.

3. Asara JM, Schweitzer MH (2008) Response to Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 319: 33.

4. Pisani D, Yates AM, Langer MC, Benton MJ (2002) A genus-level supertree of the Dinosauria. Proc Biol Sci 269: 915-921.

5. Huang S (2008) Ancient fossil specimens are genetically more distant to an outgroup than extant sister species are. Riv Biol 101: 93-108.

6. Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416-426.

7. Dayhoff MO (1978) Atlas of protein sequence and structure. Washington, D.C.: National Biomedical Research Foundation.

Table 1. Sequence alignment of a peptide from collagen alpha 2 type 1.

 

B. Canadensis         GLPGESGAVGPAGPPGSR

 

T. rex                ..............I...

G. gallus             ..............I...

T. guttata            .P............I...

S. camelus            .P............I...

 

A. mississippiensis   ...........V..I...

A. carolinensis       .A.........S..I...

 

H. sapiens            .P......A..T..I...

M. mulluta            .P......A..T..I...

B. taurus             .P......A..T..I...

M. americanum         .P..Q...A..T..I...

L. afiricana          .P..Q...A..T..I...

M. musculus           .T......A..S..I...

R. norvegicus         .P......A..S..I...

E. telfairi           .P..Q...A..T.SI...

 

M. domestica          .P.........T.SI...

 

X. levis              .T......A..F..L.P.

X. tropicalis         .A......A..L.AL.P.

R. catesbeiana        .A.....GA..H.PS...

 

D. rerio              .N..PA..A.AQ..I.A.

O. mykiss             .NS.PA.SA.SQ.AI.A.

P. olivaceus          .IN.VA..S.VQ.AV.A.