Deep Homology and the Origins of Evolutionary Novelty

Overview

Journal Nature

Specialty Science

Date 2009 Feb 13

PMID 19212399

Citations 280

Authors

Neil Shubin

Cliff Tabin

Sean Carroll

Affiliations

Soon will be listed here.

Abstract

Do new anatomical structures arise de novo, or do they evolve from pre-existing structures? Advances in developmental genetics, palaeontology and evolutionary developmental biology have recently shed light on the origins of some of the structures that most intrigued Charles Darwin, including animal eyes, tetrapod limbs and giant beetle horns. In each case, structures arose by the modification of pre-existing genetic regulatory circuits established in early metazoans. The deep homology of generative processes and cell-type specification mechanisms in animal development has provided the foundation for the independent evolution of a great variety of structures.

Citing Articles

A new analogous organ in bony fishes and amphibians: an anatomical structure related with the cerebrospinal fluid circulation.

Chen C, Yang H, Song Y, Dong Y, Zhang J, Shah M Sci Rep. 2025; 15(1):5646.

PMID: 39955354 PMC: 11829981. DOI: 10.1038/s41598-025-89599-5.

On the prospects of basal cognition research becoming fully evolutionary: promising avenues and cautionary notes.

Fabregas-Tejeda A, Sims M Hist Philos Life Sci. 2025; 47(1):10.

PMID: 39913055 PMC: 11802611. DOI: 10.1007/s40656-025-00660-y.

Multiplexed transcriptomic analyzes of the plant embryonic hourglass.

Wu H, Zhang R, Niklas K, Scanlon M Nat Commun. 2025; 16(1):802.

PMID: 39824817 PMC: 11742662. DOI: 10.1038/s41467-024-55803-9.

Transcriptomic Data Reveal Divergent Paths of Chitinase Evolution Underlying Dietary Convergence in Anteaters and Pangolins.

Allio R, Teullet S, Lutgen D, Magdeleine A, Koual R, Tilak M Genome Biol Evol. 2025; 17(2).

PMID: 39780438 PMC: 11789784. DOI: 10.1093/gbe/evaf002.

Novelty versus innovation of gene regulatory elements in human evolution and disease.

Katikaneni A, Lowe C Curr Opin Genet Dev. 2024; 90:102279.

PMID: 39591813 PMC: 11769741. DOI: 10.1016/j.gde.2024.102279.

References

Moczek A, Rose D, Sewell W, Kesselring B . Conservation, innovation, and the evolution of horned beetle diversity. Dev Genes Evol. 2006; 216(11):655-65. DOI: 10.1007/s00427-006-0087-2. View

Panganiban G, Irvine S, Lowe C, Roehl H, Corley L, Sherbon B . The origin and evolution of animal appendages. Proc Natl Acad Sci U S A. 1997; 94(10):5162-6. PMC: 24649. DOI: 10.1073/pnas.94.10.5162. View

Gehring W . New perspectives on eye development and the evolution of eyes and photoreceptors. J Hered. 2005; 96(3):171-84. DOI: 10.1093/jhered/esi027. View

Erclik T, Hartenstein V, Lipshitz H, McInnes R . Conserved role of the Vsx genes supports a monophyletic origin for bilaterian visual systems. Curr Biol. 2008; 18(17):1278-87. DOI: 10.1016/j.cub.2008.07.076. View

Pueyo J, Lanfear R, Couso J . Ancestral Notch-mediated segmentation revealed in the cockroach Periplaneta americana. Proc Natl Acad Sci U S A. 2008; 105(43):16614-9. PMC: 2568983. DOI: 10.1073/pnas.0804093105. View

Moczek A, Nagy L . Diverse developmental mechanisms contribute to different levels of diversity in horned beetles. Evol Dev. 2005; 7(3):175-85. DOI: 10.1111/j.1525-142X.2005.05020.x. View

Capdevila J, Tsukui T, Rodriquez Esteban C, Zappavigna V, Izpisua Belmonte J . Control of vertebrate limb outgrowth by the proximal factor Meis2 and distal antagonism of BMPs by Gremlin. Mol Cell. 2000; 4(5):839-49. DOI: 10.1016/s1097-2765(00)80393-7. View

Emlen D, Lavine L, Ewen-Campen B . On the origin and evolutionary diversification of beetle horns. Proc Natl Acad Sci U S A. 2007; 104 Suppl 1:8661-8. PMC: 1876444. DOI: 10.1073/pnas.0701209104. View

Moczek A . Integrating micro- and macroevolution of development through the study of horned beetles. Heredity (Edinb). 2006; 97(3):168-78. DOI: 10.1038/sj.hdy.6800871. View

10.

Suga H, Schmid V, Gehring W . Evolution and functional diversity of jellyfish opsins. Curr Biol. 2007; 18(1):51-5. DOI: 10.1016/j.cub.2007.11.059. View

11.

Hunt J, Simmons L . Status-dependent selection in the dimorphic beetle Onthophagus taurus. Proc Biol Sci. 2001; 268(1484):2409-14. PMC: 1088894. DOI: 10.1098/rspb.2001.1758. View

12.

Arendt D, Tessmar-Raible K, Snyman H, Dorresteijn A, Wittbrodt J . Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science. 2004; 306(5697):869-71. DOI: 10.1126/science.1099955. View

13.

Halder G, Callaerts P, Gehring W . Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science. 1995; 267(5205):1788-92. DOI: 10.1126/science.7892602. View

14.

MERCADER N, Leonardo E, Azpiazu N, Serrano A, Morata G, Martinez C . Conserved regulation of proximodistal limb axis development by Meis1/Hth. Nature. 1999; 402(6760):425-9. DOI: 10.1038/46580. View

15.

Denes A, Jekely G, Steinmetz P, Raible F, Snyman H, Prudhomme B . Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell. 2007; 129(2):277-88. DOI: 10.1016/j.cell.2007.02.040. View

16.

Pearse J, Pearse V . Vision of cubomedusan jellyfishes. Science. 1978; 199(4327):458. DOI: 10.1126/science.22934. View

17.

Sordino P, Duboule D . A molecular approach to the evolution of vertebrate paired appendages. Trends Ecol Evol. 2011; 11(3):114-9. DOI: 10.1016/0169-5347(96)81089-5. View

18.

Zakany J, Warot X, Duboule D . Regulation of number and size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary implications. Proc Natl Acad Sci U S A. 1998; 94(25):13695-700. PMC: 28368. DOI: 10.1073/pnas.94.25.13695. View

19.

Shubin N, Tabin C, Carroll S . Fossils, genes and the evolution of animal limbs. Nature. 1997; 388(6643):639-48. DOI: 10.1038/41710. View

20.

Coates M, Jeffery J, Rut M . Fins to limbs: what the fossils say. Evol Dev. 2002; 4(5):390-401. DOI: 10.1046/j.1525-142x.2002.02026.x. View