Experiment context

Reader notes supplied by the result owner to help interpret this Covary run.

Experiment or dataset title

Human mitochondrial gene coalescence with bacterial homologs associated with mitochondrial ancestry

Objectives

This run evaluates whether human mitochondrial protein-coding gene signatures reconstruct closer coalescence with bacterial representatives associated with mitochondrial ancestry than with broader alphaproteobacterial context/outgroup taxa. The goal is to test whether Covary Coalescence Analysis can recover an expected endosymbiotic-origin signal using marker-level sequence similarity patterns across shared mitochondrial genes and bacterial homologs.

Background / experimental context

Mitochondria are widely understood to have originated from an ancestral bacterial endosymbiont related to Alphaproteobacteria. This analysis uses human mitochondrial genes and homologous bacterial gene sequences to explore whether alignment-free, translation-aware Covary embeddings can reconstruct sample-level closeness between human mtDNA and representative bacterial lineages. The analysis is intended as an exploratory computational test of mitochondrial ancestry signal, not as a definitive phylogenetic placement or taxonomic proof.

Samples / sequences

The dataset includes human mitochondrial gene sequences from the human mtDNA reference and bacterial homologs selected from representative taxa including Rickettsiales/SAR11-associated bacteria and broader alphaproteobacterial comparators. Human mitochondrial markers include protein-coding mtDNA genes such as MT-ND, MT-CO, MT-ATP, and MT-CYB genes where suitable homologs were identified. Sample labels were structured as marker_species/sample combinations so that Coalescence Analysis could aggregate marker-level distances into sample-level relatedness.

Interpretation notes

Readers should focus on whether HumanMt clusters closer to mitochondria-associated bacterial representatives than to broader alphaproteobacterial context taxa. A biologically expected pattern would place HumanMt nearer to Rickettsiales/SAR11-side representatives and away from broader comparators such as Rhodobacter, Rhodospirillum, Caulobacter, or Brucella. The desired result was achieved by the fitting model to the following parameters: Projection: PCA Distance aggregation: Median distance Linkage: Complete