Understanding the detailed phylogenetic divergence of animals is a key challenge in evolutionary biology. Among the most persistent debates is the classification of the Lophophorata. This animal group possesses the lophophore, a ciliated feeding organ, and includes the phyla Brachiopoda, Phoronida, and Bryozoa. However, whether these three animal phyla share a common ancestor as a monophyletic group or evolved independently has been discussed for over a century.
An international joint research group led by Assistant Research Fellow Yi-Jyun Luo from the Biodiversity Research Center, Academia Sinica (Taiwan); Professor Mayuko Hamada from the Graduate School of Environmental, Life, Natural Science and Technology (Science) / Ushimado Marine Institute, Okayama University; and Professor Kazuyoshi Endo from the Graduate School of Science, the University of Tokyo decoded the phoronid genome at the chromosome level for the first time and revealed the monophyly of the Lophophorata through comparative genomic analysis. This has settled this phylogenetic debate, which lasted more than 100 years. Their findings were published in Current Biology.
For the first time at the chromosome level, this international joint research team decoded the genome of the phoronid Phoronis australis, collected in Ushimado Town, Okayama Prefecture. By comparing this with the genomes of brachiopods and bryozoans, the team revealed the monophyly of the Lophophorata.
The study identified seven chromosomal fusions shared between phoronids and bryozoans, with one of these also shared with brachiopods. These chromosomal fusions are not found in other lophotrochozoans such as mollusks and annelids. This demonstrates the three animal phyla (Brachiopoda, Phoronida, and Bryozoa) form a monophyletic group derived from a common ancestor.
Furthermore, the team collected the brachiopod Lingula anatina from Kasari Bay, Amami Oshima Island, Kagoshima Prefecture, and the bryozoan Flustrellidra hispida (a species of moss animal) from Plymouth Bay in the United Kingdom. Through transcriptome analysis, they revealed gene expression in the lophophore. The results showed that all three animal phyla share a common gene set, and that genes involved in head development in vertebrates are utilized for lophophore formation. This indicates the lophophores of these three phyla are homologous organs with a common evolutionary origin, rather than merely similar structures resulting from convergent evolution as an adaptation for filter feeding.
This research has revealed the monophyly of the Lophophorata through comparative analysis of lophophorate genomic structure as well as transcriptome analysis of the lophophore, a characteristic feeding organ, thus settling a major long-standing question in the field of evolutionary biology. The results demonstrate that comparison of genomic structure is an important and powerful approach for elucidating animal phylogenetic evolution. Through applying this approach to various animal groups, greater details of the evolutionary lineage of animals are anticipated.
Hamada commented: "When we were collecting phoronids in Ushimado, the waves were strong, and I thought we might not succeed that day. However, we were able to collect them thanks to the remarkable eye of Technical Expert Staff Member Kazuhiro Saito from the Division of Technical Support for Education (Ushimado Marine Institute), Department of Comprehensive Technical Solutions, Okayama University. That was the starting point of this research. Additionally, Dr. Tosuke Sakagami, who has been sent to Academia Sinica in Taiwan on a JSPS Overseas Research Fellowship, is a graduate of our university and has served as a bridge for this collaborative research. I hope to continue deepening our international collaboration with these wonderful team members."
Journal Information
Publication: Current Biology
Title: Phoronid genome supports a monophyletic Lophophorata
DOI: 10.1016/j.cub.2025.10.020
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