Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code. 1. Introduction The biophysical properties of amino acids determine their use in proteins. Amino acid polarity and molecular volume are especially important for protein stability and function in hyper thermophilic and barophilic conditions. These two properties have been associated to the origins of the genetic code [1]. Thus, tracing amino acids with common physicochemical properties may help derive the conditions in which the genetic code originated. A method was developed previously to assign temperature and pressure asymmetry indices to amino acids [2]. These indices are based on patterns of amino acid substitution within homologous sequences of phylogenetically related organisms living in two different environmental conditions, including barophilic versus nonbarophilic and thermophilic versus nonthermophilic conditions. The temperature asymmetry index (TAI) reflects the extent to which an amino acid is preferred by hyper thermophiles and was studied in Deinococcus radiodurans, Thermus thermophilus [3], Methanococci, and Bacilli [2]. The hydrostatic pressure asymmetry index (PAI) reflects the extent to which an amino acid is preferred by barophiles; it was studied in Pyrococcus
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