1. 1) Frozen-accident – once the complete code was formed this defined the universal common ancestor from which all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid. Possible explanations for the unity of the genetic code entertained by Crick

2. 1) Frozen-accident – once the complete code evolved this defined the universal common ancestor from which to all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid. 3)Genetic code is unified because of natural selection for unity per se – i.e. horizontal gene transfer is essential to evolution itself. Possible explanations for the unity of the genetic code entertained by Crick But there was a third possible explanation

3. 0.1 Metcoc ja Aquifex Thermot ma CAUCR Ecoli Chlamy tr Chloro te B.subtilus Synecococ Strep coe Haloba ma Metsar ma Thermo ac Archae fu Metpyr ka Metthe th Pyroco-ab Pyrobac ae Aeropyrum Sulfolobus Plasmodium Yeast Neurospora C.elegans Human Catfish Rice Ribosomal protein tree

4. eukaryote archaea gram (-) gram (+) eukaryotearchaea gram (-) gram (+) eukaryote archaea gram (-) gram (+) Tree 1 Tree 3 Tree 2 Quartet partitions

5. What was found was support for NONE of the three trees, instead: eukaryote archaea gram (-) gram (+) Star phylogeny

6. 18 of the 26 homologue submitted to the quartet analysis displayed the star phylogeny. They include: argDornithine carbamoyl transferase argTarginine tRNA synthetase argHarginine biosynthesis trpAtryptophan synthetase α trpBtryptophan synthetase β mutS,Hmismatched DNA repair purApurine biosynthesis purB“ pur5“ pur6“

7. 0.1 Metcoc ja Aquifex Thermot ma CAUCR Ecoli Chlamy tr Chloro te B.subtilus Synecococ Strep coe Haloba ma Metsar ma Thermo ac Archae fu Metpyr ka Metthe th Pyroco-ab Pyrobac ae Aeropyrum Sulfolobus Plasmodium Yeast Neurospora C.elegans Human Catfish Rice Ribosomal protein tree

8. 0.1 Neurospora C.elegans sch pombe Yeast Drosophila Human Zebrafish themoc ac metcoc ja synecoc metsar ma pyrococ ab CAUCR thermo ma E.coli Streptomyc aeropyrum pyrobac B.subtilis metthe th aquifex metpyr ka halobacter chlorobium rice Arabidopsi Ornithine carbamoyl transferase Bifurcated tree

9. 0.1 Neurospora C.elegans sch pombe Yeast Drosophila Human Zebrafish themoc ac metcoc ja synecoc metsar ma pyrococ ab CAUCR thermo ma E.coli Streptomyc aeropyrum pyrobac B.subtilis metthe th aquifex metpyr ka halobacter chlorobium rice Arabidopsi Ornithine carbamoyl transferase Colapse unsupported bifurcations

10. 0.1 Archaeog haloferax Methanolob Methanosar thet thermus legionel zymonas Caucre Rhodomic Pseudomo bacillis E.coli buchnera Acantham Guillard trametes coprinus neucra nodulisp candida spathosp Halobacte Clostrid Nostoc arabidopsi oryza Trptophan synthase (α and β) Bifurcated tree

11. 0.1 Archaeog haloferax Methanolob Methanosar thet thermus legionel zymonas Caucre Rhodomic Pseudomo bacillis E.coli buchnera Acantham Guillard trametes coprinus neucra nodulisp candida spathosp Halobacte Clostrid Nostoc arabidopsi oryza Trptophan synthase (α and β) Collapse bifurcations

12. 0.1 HumanMt Neurospora Yeast Sch.pombe E.coli CAUCR Strep coe Orzya Synecococ Chlamy tr Plasmodium D.melanoga C.elegans Zebra fish Human Pyroco-ab Pyrobac ae Aeropyrum sulfolobus Archae fu Thermo ac Chlorobium Thermot ma B.subtilis Aguifex Haloba ma Metpyr ka Metcoc ja Metthe th Metsar ma Arginine-tRNA ligase

13. Tryptophan-tRNA Ligase 0.1 Yeast strmy co E.col B.subtilis C.elegans synecoc CAUCR chlamy tr Chlorobium Aquifex thermot ma metcoc ja metpyr ka thermo ac methe th Aeropyrum archae fu haloba su2 metsar ma pyrobac ae pyroco ab sulfolobus Plasmodium haloba su1 schizop Neurospora Rice Human

14. 0.1 ecoli metbar thermmar halmar natrpha clotet strpne bacanth caucre dictyoste celegans plafal saccer drosophila ciona seaurchin gallus schpom arabidopsi neucra zfish mouse human oryza MutS protein family

15. Distance ACTase Distance OCTase 1 E.coli/Salmonella; Pea/arabidopsis 2 E.coli/Haemophilis; Yeast/neurospora 3 Plants/metazoa; plants/ fungi Whole matrix rate test comparing Ornithine carbamoyl and Aspartate carbamoyl Transferases

16. Whole matrix rate test comparing Tryptophan synthetase and Aspartate carbamoylTransferases Distance trpA Distance ACTase

17. I have shown that the evolution for multiple genes in the tryptophan and arginine biosynthetic pathways, as well as their tRNA ligases show unusual phylogenies. If we discard functional constraint arguments (i.e. that some kind of peculiar protein chemistry is driving their evolution) then we can offer the following interpretation: These genes “found in the three kingdoms that are not just unusually highly conserved but whose topologies, when deduced from their sequences, strongly suggest that they evolved after Archaea, Bacteria and Eukaryotes had already diversified. In other words, these universal genes appear to be younger than the taxonomic groups in which they are found today “ That is to say, there was a time when Archaea, Bacteria and Eukaryotes existed but that they lacked the amino acids arginine and tryptophan. If so, then LUCA, if it ever existed, could not have had those two amino acids. Thus the current universal distribution of arginine and tryptophan is not explained by LUCA. Once we start down this road of reasoning there is no reason why we cannot imagine the the entire genetic code evolved within multiple demes that are linked together by Horizontal gene transfer.

18. Possible outline for the emergence of tryptophan (W) tRNA ligase by duplication and horizontal spread of tyrosine (Y) tRNA ligase Archaea Ytl Eukarya Ytl Bacteria Ytl Ytl + Wtl Ytl Ytl + Wtl ??

19. Xianchi Dong, Minyun Zhou, Chen Zhong1, Bei Yang, Ning Shen and Jianping Ding (2010) “Crystal structure of Pyrococcus horikoshiitryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase” Nucleic Acids Research Volume 38,. 1401-1412 “Our results raise the possibility that present day tyrosyl- and tryptophanyl-tRNA synthetases appeared after the separation of nucleated cells from eubacteria.”

20. Darwin’s notion of the Tree of Life

21. “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” ― Charles Darwin, The Origin of SpeciesCharles DarwinThe Origin of Species