SlonikOlla/Hominids-CpG-nucleotide-mutations: Ancestral sequence context predicts cytosine substitution patterns in hominids

Abstract

Phase 1 — Genome-wide ancestral sequence-context analysis across hominids This initial release provides the computational code and reproducibility documentation for a comparative evolutionary-genomics study of ancestral cytosine substitution patterns across hominid lineages. The study uses seven-primate whole-genome alignments to reconstruct ancestral nucleotide states and examine cytosine substitution frequencies across the 22 human autosomes. Four terminal lineages—human, chimpanzee, bonobo and gorilla—are analyzed, with particular attention to CG, CHG and CHH contexts and the influence of neighboring nucleotides. Included in this release Python and shell scripts for genome alignment processing, ancestral-state reconstruction and substitution analysis. Ancestral 5-mer reconstruction and strand-canonicalized cytosine substitution classification. Chromosome-level validation and reproducibility checks. Statistical analyses of sequence-context enrichment, motif conservation and lineage-specific differences. Chromosome-bootstrap uncertainty estimation and multiple-testing-adjusted motif comparisons. Leave-one-autosome-out comparison of 3-mer and 5-mer predictive performance. Scripts for generating publication figures. README, workflow documentation and dependency information. Principal scientific objectives Characterize ancestral sequence-context-associated cytosine substitutions across hominid lineages. Determine whether fine-scale substitution patterns are evolutionarily conserved or exhibit lineage-specific divergence. Evaluate whether ancestral 5-mer context improves substitution prediction beyond trinucleotide context. Establish a computational foundation for future studies of CpG turnover, DNA methylation and regulatory evolution. Data and reproducibility This is a code-only release. Raw genomic alignments, intermediate files, numerical results, figures and manuscript files are intentionally excluded. The workflow was developed for the Nibi high-performance computing environment. Reproduction requires obtaining the relevant UCSC multiz alignments, configuring the reference files and phylogenetic tree, and installing the documented software dependencies. The release preserves the original computational scripts, including historical pilot scripts, which are distinguished from the final production workflow. Scope Phase 1 examines ancestral sequence context and accumulated substitution frequencies. It does not directly measure ancestral DNA methylation, net CpG depletion, gene-expression divergence or the causal contribution of these processes to speciation. Future phases will address CpG gain and loss, comparative primate methylomes and potential regulatory consequences.