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Written in stone: fossils, genes and evo–devo

Nature Reviews Genetics volume 8, pages 911–920 (2007)Cite this article

Key Points

  • Evo–devo is tied to geological time through the necessity of placing developmental evolution in its context within geological history. This involves finding when and how rapidly developmental features evolved, and the integration of developmental evolution into major transitions in body plans.

  • The inclusion of fossils into phylogenetic trees yields other kinds of information that are crucial to evo–devo, the direction of change in evolving homologous features in a lineage and the identification of convergent evolution of features that appear to be homologous but have evolved independently on separate branches of a phylogenetic tree.

  • It is crucial for developmental evolution to know the time of divergence of taxa, the time of appearance of evolving features within taxa and their rates of evolutionary change. This information is obtained from geochronology combined with the fossil record of living taxa. These data underlie the calibration of 'molecular clocks'.

  • Fossils are crucial for constraining hypotheses derived from evo–devo, such as the case of the homology of digits in the bird wing, the origins of paired appendages and the gene regulation of appendage development, as well as the evolution of the mammalian middle ear.

  • Fossils in some cases allow evo–devo studies on now extinct organisms.

  • There is an important complementarity between the search for the earliest animals in the fossil record and the identification of the genetic toolkit of the most ancient animal groups.

  • Occasionally, unexpected fossils that exceed the expected limits of fossilization give data on the evo–devo of soft parts, such as feathers on dinosaurs or the well-preserved embryos and larvae from the late Precambrian and Cambrian.

Abstract

Fossils give evo–devo a past. They inform phylogenetic trees to show the direction of evolution of developmental features, and they can reveal ancient body plans. Fossils also provide the primary data that are used to date past events, including divergence times needed to estimate molecular clocks, which provide rates of developmental evolution. Fossils can set boundaries for hypotheses that are generated from living developmental systems, and for predictions of ancestral development and morphologies. Finally, although fossils rarely yield data on developmental processes directly, informative examples occur of extraordinary preservation of soft body parts, embryos and genomic information.

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Figure 1: Example of a metazoan stem taxon.
Figure 2: Fossils can reveal evolutionary pathways in the evolution of body features.
Figure 3: Finding pattern and time estimates from a phylogenetic tree.
Figure 4: Relationships between different levels of investigation.
Figure 5: Phylogeny of the forelimb in lobe-finned vertebrates.

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Article Open access 13 June 2023

Alexandra A. de Sousa, Amélie Beaudet, … Yongbin Wei

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Acknowledgements

I thank M. Friedman and M. I. Coates for the figure used in Figure 5, S. Conway Morris and J. B. Caron for providing Figure 1, A. Moczek and P. C. J. Donoghue for helpful advice and M. I. Coates, E. C. Raff, J. W. Valentine and two anonymous reviewers for their critical reading and suggestions.

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  1. Department of Biology, Indiana University, Bloomington, 47401, Indiana, USA

    Rudolf A. Raff

  2. School of Biological Sciences, University of Sydney, Sydney, 2006, New South Wales, Australia

    Rudolf A. Raff

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Glossary

Protostome

(First mouth). The animal superphylum that contains annelids, molluscs, arthropods and several other phyla that are linked by a pattern of development and body organization that is distinct from deuterostomes, especially in development of the larval mouth.

Deuterostome

(Second mouth). The animal superphylum containing chordates, hemichordates and echinoderms. These are linked by their pattern of development, notably of the larval mouth.

Bilaterians

Animals with a bilaterally symmetrical body plan.

Tetrapod

Vertebrates ancestrally having four legs.

Taxon

Named groups of organisms that are arranged in the hierarchical taxonomic order: species, genus, family, order, class and phylum (plural taxa).

Clade

A group of species in a phylogenetic tree that share a single ancestral species.

Radula

A rasping organ in the mouth of molluscs that is equipped with chitinous teeth.

Setae

Spine-like projections found in annelid worms and brachiopods.

Chordates

Deuterostomes that possess a notochord. Vertebrates belong to the chordates.

Hemichordates

Worm-like deuterostomes that are related to echinoderms.

Crown groups

Crown groups represent the most derived living taxa in a clade.

Pentameral

A fivefold radial body plan.

Stem groups

Stem groups represent the less derived extinct branches of the phylogenetic tree.

Stereom

The porous calcitic endoskeleton that is characteristic of echinoderms.

Phylogeny

Evolutionary relationships among organisms shown in the diagrammatical form of phylogenetic trees.

Sarcopterygians

A group that includes the lobe-fin fish, a once diverse fish group, and their tetrapod descendants.

Homology

Similarity in structural features such as genes or morphology that are derived from a shared ancestor by common descent.

Lophotrochozoans

A major division of protostome animals, including such phyla as brachiopods and other lophophore-bearing animals, plus molluscs, annelids and other phyla that develop via a trochophore larva.

Metazoan

A multicellular animal.

Homoplasy

False homology. Similar features that have evolved independently, as identified by their position in phylogenetic trees, are homoplastic.

Orthologue

Refers to a member of a gene families. The orthologue is the same member of a family across species.

Cnidarians

Jellyfish and their kin, which have a two-cell layer (diploblastic) organization that is simpler than that of bilaterians.

Bayesian inference of phylogeny

A method for inference of phylogenetic trees from data that gives the probability that a tree and model is correct given the data, using Bayes theorem to find posterior probability.

Geminate species

Species that were recently derived from a common ancestor.

Meckel's cartilage

The ancestral jaw of vertebrates, which evolved from an ancestral gill arch. Its derivatives include the bones of the lower jaw that are now parts of the mammalian middle ear.

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Raff, R. Written in stone: fossils, genes and evo–devo. Nat Rev Genet 8, 911–920 (2007). https://doi.org/10.1038/nrg2225

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