Deep Dive Into the Living Fossil Family Tree

Jenn Hoskins
9th June, 2025

Deep Dive Into the Living Fossil Family Tree

The skull roof of Rieppelia heinzfurreri reveals a sutured, non-functional intracranial joint, evidenced by overlap zones on the postparietal bone (a–c), representing a significant morphological deviation used to refine the coelacanth phylogeny.

Image adapted from: Ferrante et al. / CC BY (Source)

Key Findings

  • We revised the scoring of 112 morphological characters in 46 coelacanth genera, yielding a phylogeny that remains stable over 420 million years
  • Our analysis groups Paleozoic coelacanths into a distinct clade (Diplocercidae) while all Mesozoic forms—including extant Latimeria—belong to Coelacanthiformes that originated in the Permian
  • Within Coelacanthiformes, most Mesozoic taxa form the Latimerioidei, which are split into two families (Latimeriidae and Mawsoniidae) with each family further divided into two subfamilies
In 1938 the discovery of a living coelacanth sparked decades of research into these ancient fishes, prompting scientists to reassess their evolutionary history and relationships. A recent study by researchers at the Natural History Museum of Geneva[1] builds on this long tradition by updating the phylogeny for coelacanths—with a particular focus on a group known as Actinistia. This work refines our understanding of coelacanth relationships by using a considerably updated data matrix and proposes a new classification that brings together both long-studied and newly recognized genera. The study began with a critical reexamination of previously used character matrices, which once served as the backbone for coelacanth phylogenetic analyses over the past several decades. By eliminating 16 ambiguous characters, revising definitions for another 16, and adding 18 new characters, the researchers expanded the dataset to 112 characters. They also corrected numerous miscoding errors for 37 taxa. This comprehensive revision resulted in a phylogenetic tree that organizes 46 coelacanth genera into nine families and four sub-families. This reorganization clarifies the boundaries between various clades that earlier studies had only loosely defined or entirely overlooked. One significant outcome of the study is the identification of a clade comprising several Paleozoic coelacanth genera, now referred to as the Diplocercidae. In previous work, coelacanths were celebrated for their evolutionary conservatism—for example, the observation that their body plan had not changed dramatically since the Devonian[2]. However, studies such as those examining Holopterygius and related taxa have complicated this view by revealing episodes of rapid morphological adaptations[3]. By grouping Paleaozoic genera into the Diplocercidae, the new phylogeny supports the idea that these early coelacanths have a clearer evolutionary relationship than previously thought. Further on, the study confirms that all Mesozoic coelacanths—including the extant Latimeria—belong to the order Coelacanthiformes, which the analysis indicates first emerged in the Permian period. Within Coelacanthiformes, the divergence of Coelacanthus stands at the base, followed by a broader grouping of Mesozoic forms organized as the Latimerioidei. This group is split into two main families: the Latimeriidae, which includes the modern coelacanth, and the Mawsoniidae. Both families are further subdivided into two subfamilies each, providing a novel framework that captures subtle differences in morphology across millions of years. This refined arrangement aligns with some earlier suggestions of morphological stability that have characterized coelacanth evolution[4], yet it also reveals nuances in the historical pattern of divergence that previous matrices did not fully capture. A compelling aspect of the new analysis is how it addresses the long-standing contradiction between the perception of coelacanths as “living fossils” and the evidence for divergent morphologies early in their history. Several recent studies, including an examination of molecular versus morphological evolution, have shown that low rates of molecular evolution and apparent morphological conservatism may not always be directly linked[4]. Moreover, discoveries such as the diversified body shapes in Holopterygius challenge the notion of uniform conservatism[3]. The revised phylogenetic framework incorporates these earlier insights and demonstrates that while many aspects of the coelacanth anatomy have remained stable, there were key periods of morphological experimentation as new adaptive solutions emerged in response to changing environmental pressures. To achieve these findings, the research team adopted an updated and rigorous approach to character selection. By scrutinizing character definitions, removing ambiguous data, and incorporating new features, they ensured that the phylogeny was built on a more reliable set of information. The revised matrix included both traditional characters and new criteria that had not been previously used, allowing for a more precise delimitation of clades. This methodological update is essential when dealing with a lineage that shows both long-term conservatism and pockets of rapid evolutionary change, echoing similar updates seen in studies of other ancient groups, such as those investigating bursts of disparity following mass extinctions[5]. The increased resolution of the coelacanth family tree offers several benefits. It provides a clearer reference point for comparing present-day species with their fossil counterparts, elucidating how certain anatomical features have been retained or modified over geological time. In doing so, the study helps resolve earlier controversies about the rates of morphological change in coelacanths. The discovery of distinctive clusters like the Diplocercidae strengthens the case that morphological divergence in coelacanths was more dynamic than the traditional “living fossil” narrative suggests. The new classification may also help future researchers by offering a more stable baseline for analyzing both fossil remains and genetic data. It reflects a synthesis of decades of paleontological and molecular research on this unique clade. The revised phylogeny recognizes the contributions of earlier studies while also overturning or refining some of their assumptions. In particular, while earlier molecular investigations linked low intraspecific mutation rates directly to morphological stasis[4], this study’s comprehensive taxon sampling and more diverse character set illustrate that even a lineage known for its slow molecular evolution can exhibit complex patterns of morphological diversification. By tying together these strands—early diversification evident from fossil records, the challenges of interpreting “living fossil” status, and the ongoing refinement of phylogenies—the study represents a significant step forward in our understanding of coelacanth evolution. It not only consolidates previous findings but also provides a more nuanced picture of the evolutionary forces at play. As researchers continue to mine the fossil record and refine genetic analyses, the updated schema offered by the Natural History Museum of Geneva is likely to serve as a crucial tool in unravelling the intricate history of these enigmatic fishes.

Marine BiologyEvolution

References

Main Study

1) A deep dive into the coelacanth phylogeny

Published 6th June, 2025

https://doi.org/10.1371/journal.pone.0320214

Related Studies

2) Earliest known coelacanth skull extends the range of anatomically modern coelacanths to the Early Devonian.

https://doi.org/10.1038/ncomms1764

3) A newly recognized fossil coelacanth highlights the early morphological diversification of the clade.

Journal: Proceedings. Biological sciences, Issue: Vol 273, Issue 1583, Jan 2006

4) Why coelacanths are not 'living fossils': a review of molecular and morphological data.

https://doi.org/10.1002/bies.201200145

5) Early Mesozoic burst of morphological disparity in the slow-evolving coelacanth fish lineage.

https://doi.org/10.1038/s41598-023-37849-9


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