Phylogenetics and Mitochondrial Genomics of Turtles

Turtles represent one of the most ancient and morphologically diverse lineages of reptiles, with extant species spanning marine, freshwater and terrestrial habitats. Phylogenetic studies have long relied on mitochondrial DNA (mtDNA) to resolve relationships among major chelonian clades, owing to its high mutation rate, maternal inheritance and conserved gene complement. Complete mitogenomes now allow researchers to compare gene order, nucleotide composition and selection regimes across species, yielding robust phylogenies and divergence-time estimates. These data illuminate deep splits—such as the Testudinoidea, Chelonioidea and Trionychia—and clarify the placement of enigmatic lineages. Mitogenomic evidence also reveals instances of ancient introgression and gene rearrangement, informing taxonomy and conservation. In parallel, advances in high-throughput sequencing and analytical frameworks (for example, Bayesian relaxed clocks and codon-based selection tests) have refined our understanding of adaptive evolution in mitochondrial protein-coding genes. Together, phylogenetics and mitogenomics underpin efforts to delineate species boundaries, reconstruct biogeographical histories and guide conservation management for threatened turtles worldwide.

Research from Nature Portfolio

Recent studies have assembled and annotated complete mitogenomes of two soft-shelled turtles, revealing that inclusion of all 37 mitochondrial genes greatly improves phylogenetic resolution within Trionychia. Comparative analyses detected strong purifying selection across most protein-coding genes alongside a site under positive selection in the cytb gene, indicating both conservation and lineage-specific adaptation. Bayesian relaxed-clock dating placed the crown group of extant soft-shelled turtles in the mid-Cretaceous, with speciation pulses linked to Eocene–Oligocene palaeoclimatic shifts. In another landmark effort, mitogenomes were recovered from historical type specimens of Australasian side-necked turtles using high-throughput sequencing of degraded DNA. These reconstructions resolved long-standing taxonomic ambiguities, uncovered deep mitochondrial introgressions and reconciled morphological and molecular phylogenies, thereby setting a new standard for the integration of museum collections into systematic research.

Phylogenetics and Mitochondrial Genomics of Turtles publication trend

The graph below shows the total number of articles in phylogenetics and mitochondrial genomics of turtles across all publications each year (not limited to Nature Index journals).

Technical terms

Mitogenome: The complete mitochondrial DNA sequence, typically ~16–18 kb in vertebrates, encoding 13 protein-coding genes, 22 tRNAs, two rRNAs and a non-coding control region.

Phylogenetics: The study of evolutionary relationships among organisms, often depicted as a branching tree or cladogram based on genetic or morphological data.

Monophyly: A group of organisms that includes an ancestor and all its descendants, forming a single “clade” in a phylogenetic tree.

Control region: A non-coding segment of the mitogenome involved in replication and transcription initiation; also known as the D-loop.

Purifying selection: The evolutionary process by which deleterious mutations are removed from a population, resulting in a low nonsynonymous/synonymous substitution ratio.

Bayesian relaxed clock: A statistical model that allows substitution rates to vary among branches when estimating divergence times in a phylogeny.

References

1. Comparative analysis of the mitochondrial genomes of the soft-shelled turtles Palea steindachneri and Pelodiscus axenaria and phylogenetic implications for Trionychia. Scientific Reports (2025).
2. Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression. Scientific Reports (2019).
3. Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species. Biology (2023).
4. The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny. PLOS ONE (2020).