Molecular Phylogenetics of Octocorallia

Molecular phylogenetics has transformed our understanding of Octocorallia by employing high‐throughput sequencing of mitochondrial and nuclear markers to resolve evolutionary relationships among soft corals and sea fans. Early studies relied heavily on mitochondrial genes such as mtMutS and cox1, revealing deep lineage divergences but often yielding poorly supported deeper nodes due to low substitution rates. Recent phylogenomic approaches use target‐capture enrichment of ultraconserved elements and exon loci, providing robust, fully resolved phylogenies that have exposed polyphyly in traditional orders and families. Analyses of mitochondrial genomes have uncovered unique gene rearrangements and horizontal gene transfer events, while comparisons of mitochondrial and nuclear datasets have highlighted widespread mito‐nuclear discordance driven by introgressive hybridisation and strong purifying selection. Integrating these genomic data has led to a comprehensive revision of octocoral classification, clarified species boundaries in cryptic complexes, and shed light on the adaptive evolution of deep‐sea lineages. This enriched phylogenetic framework underpins global assessments of octocoral diversity, informs conservation priorities in vulnerable marine habitats, and serves as a model for evolutionary biology across Cnidaria.

Research from Nature Portfolio

Whole mitochondrial genomes and hundreds of nuclear loci from diverse Anthozoan samples have been assembled using target‐capture enrichment sequencing, revealing rampant discordance between mitochondrial and nuclear phylogenies in octocorals. This discordance, observed at every taxonomic level, is attributed to widespread introgressive hybridisation and the slow, purifying‐selection‐driven evolution of mitochondrial genomes. Analyses uncovered genome rearrangements and intron presence in key genes, cautioning against sole reliance on mitochondrial markers for neutral phylogenetic inference and highlighting the need for integrated nuclear datasets in reconstructing evolutionary histories.

Molecular Phylogenetics of Octocorallia publication trend

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

Technical terms

mtMutS: A mitochondrial gene coding for a mismatch repair protein unique to Octocorallia.

Target‐capture enrichment: A sequencing method that isolates selected genomic regions for high‐coverage analysis.

Ultraconserved elements (UCEs): Genomic regions highly conserved across taxa, used as anchors for phylogenomic studies.

Purifying selection: Evolutionary pressure that removes deleterious mutations, leading to low rates of change in essential genes.

Introgressive hybridisation: The incorporation of genetic material from one species into another through backcrossing.

References

1. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Scientific Reports (2023).
2. Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments. 动物学研究 (2024).
3. Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics. Bulletin of the Society of Systematic Biologists (2022).
4. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Ecology and Evolution (2019).
5. A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function. BMC Ecology and Evolution (2011).
6. Octocoral Mitochondrial Genomes Provide Insights into the Phylogenetic History of Gene Order Rearrangements, Order Reversals, and Cnidarian Phylogenetics. Genome Biology and Evolution (2014).