One Species, Many Names: Mitochondrial Evidence Unites Humans, Neanderthals, Denisovans, and Heidelbergensis

One barcode. Four “species.” One story.
Using the first 650 bp of the mitochondrial COI-5P gene, this study pulls public BOLD data for Homo sapiens, Neanderthals, Denisovans, and H. heidelbergensis and asks a deceptively simple question: Do these lineages form distinct barcode clusters—or a single maternal line? The answer is striking: all sequences fall into a single BOLD BIN, with >96% identity, no indels, and only minor SNP differences (≈7 for Neanderthals; ≈18–20 for Denisovans/Heidelbergensis). Reverting lineage-specific SNPs yields a consensus sequence identical to modern H. sapiens, consistent with a recent shared maternal ancestor after a severe bottleneck.
Beyond the clustering result, we outline why barcode-level homogeneity challenges “splitter” taxonomies, summarize interbreeding evidence, and review population-size modeling that explains rapid loss/stabilization of archaic segments. Bottom line: within COI-5P, these hominins look like one interbreeding human family, not four barcode-separable species.

What you’ll see inside

Data: COI-5P (650 bp) from BOLD for H. sapiens, H. neanderthalensis, H. denisova, H. heidelbergensis

Methods: MUSCLE alignment, BIN clustering (RESL), pairwise divergence, consensus reconstruction

Key results: Single BIN; ≤3% divergence; SNP-only differences; modern-human consensus after reverting lineage SNPs

Implications: Supports a shared recent maternal lineage and a lumper view of human variation; aligns with a post-bottleneck history and rapid stabilization of archaic DNA after limited admixture

Why it matters

Clarifies what COI-5P can—and can’t—resolve inside Homo

Provides a clean, visual framework (BIN + consensus) for discussing “ancestral” labels vs. actual barcode evidence

Offers testable predictions for other taxa and barcodes in post-bottleneck scenarios

How to cite (APA)
Nailor, M. (2025). One Species, Many Names: Mitochondrial COI-5P Barcode Unites Sapiens, Neanderthals, Denisovans, and Heidelbergensis. https://doi.org/10.5281/zenodo.17039432