{'fraction_non_alphanumeric': 0.031318923687692984, 'fraction_numerical': 0.016321129245699163, 'mean_word_length': 4.425837320574162, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Codon usage and the origin of P elements.

Codon usage in Drosophila is highly variable both from gene to gene within a species as well as within a gene between species (Shields et al. 1988; Starmer and Sullivan 1989; Sharp and Lloyd 1993). An extreme shift in codon usage for the same gene among species was documented for Alcohol dehydrogenase (Adh) between Drosophila melanogaster and Drosophila willistoni (Anderson, Carew, and Powell 1993). The major shift occurred for codons that are twofold redundant and can use C or U (T) in the third position. In D. melanogaster Adh, as well as generally in this species, the C-ending codons predominate, whereas in D. willistoni Adh, all such codon families shift to using predominantly U. Two more genes have now been sequenced in D. willistoni and at least based on these three genes, this shift seems to be characteristic of the species (table 1). While the transposable P element was first discovered in D. melanogaster, it has been strongly suggested that it may have originated in D. willistoni and have been acquired by D. melunogaster by horizontal transfer (Daniels et al. 1990; Kidwell 1993; Clark, Maddison, and Kidwell 1994). Here we ask the question as to whether the codon usage pattern of the one protein-coding gene in P elements (the transposase) is more similar to that characteristic of D. melanogaster or D. willistoni. Table 1 summarizes the patterns. The P element has a codon usage pattern more similar to D. willistoni than to D. melanogaster. It is important to point out that the data for the P element shown in this table is for a copy isolated from D. meZunogaster; P element sequences in D. willistoni are greater than 99% identical at the nucleotide level (Clark, Maddison, and Kidwell 1994), so codon usage for copies from this latter species is virtually identical. For the six amino acids with two codons that differ by ending in C or U the sample sizes are sufficient to perform statistical tests (G-tests) to determine if the genes differ significantly in codon usage. (Amino acids with more than two codons often have cells with zeros and it is not clear how to combine cells, so we have not performed similar tests for these cases.) Table 2 shows the results. P element codon usage is