OMIA:002617-8868 : Feather colour, black in Cygnus atratus (black swan)

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 227240 (trait) , 606574 (trait) , 606202 (gene)

Mendelian trait/disorder: unknown

Considered a defect: no

History: As noted by Karawita et al. (2023), "The distinctive black plumage of the native Australian black swan (Cygnus atratus) is in stark contrast to the white swans that are native to Europe and North America. This unique feature has resulted in the black swan playing an important role in Australian heraldry and culture." Haworth (2021) expands on the importance of the black swan: "The black swan is an Australian icon. The official emblem of Western Australia, depicted in the state flag and coat-of-arms, it decorates several public buildings. The bird is also the namesake for Perth’s Swan River, where the British established the Swan River Colony in 1829. The swan’s likeness has featured on stamps, sporting team uniforms, and in the logo for Swan Brewery, built on the sacred Noongar site of Goonininup on the banks of the Swan. But this post-colonial history hides a much older and broader story. Not only is the black swan important for many Aboriginal people, it was also a potent symbol within the European imagination — 1500 years before Europeans even knew it existed."

Molecular basis: Pointer and Mundy (2008) reported polymorphisms in the MC1R gene but could not discern a clear association between these polymorphisms and feather colour (including black versus white) in swans. By comparing feather-colour candidate genes in genome assemblies of the black swan (Cygnus atratus) and the (white) mute swan (Cygnus olor), Karawite et al. (2023) "observed that SLC45A2 in the mute swan had a nucleotide deletion in the open reading frame instigating a frame-shift mutation and an in-frame early stop codon . . . [which] . . . "suggest that this deletion in SLC45A2 is a candidate genetic change that could be responsible for the white plumage in white swans in the genus Cygnus". While this evidence is not sufficient to conclude that the deletion is a likely causal variant, it did enable the authors to draw the intriguing conclusion that "should a mutation of SLC45A2 have resulted in the differential plumage of the black and mute swan, it would suggest that the last common ancestor of these birds was, in fact, black. This is direct contrast to the metaphor of “black swan events” that are so defined because of their unprecedented and unexpected nature. Instead, it would appear that at one point in history black plumage for the swan was the norm rather than the exception." Chong et al. (2023) also "present two high-quality genomes for C. olor and C. atratus ... . A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, [the authors] also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, [the authors] demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production."

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SLC45A2 Cygnus atratus Z NC_066396.1 (11871603..11854510) SLC45A2 Homologene, Ensembl , NCBI gene

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:002617-8868: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2023 Chong, Y., Tu, X., Lu, Y., Gao, Z., He, X., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :
Two high-quality Cygnus genome assemblies reveal genomic variations associated with plumage color. Int J Mol Sci 24:16953, 2023. Pubmed reference: 38069278. DOI: 10.3390/ijms242316953.
Karawita, A.C., Cheng, Y., Chew, K.Y., Challagulla, A., Kraus, R., Mueller, R.C., Tong, M.Z.W., Hulme, K.D., Bielefeldt-Ohmann, H., Steele, L.E., Wu, M., Sng, J., Noye, E., Bruxner, T.J., Au, G.G., Lowther, S., Blommaert, J., Suh, A., McCauley, A.J., Kaur, P., Dudchenko, O., Aiden, E., Fedrigo, O., Formenti, G., Mountcastle, J., Chow, W., Martin, F.J., Ogeh, D.N., Thiaud-Nissen, F., Howe, K., Tracey, A., Smith, J., Kuo, R.I., Renfree, M.B., Kimura, T., Sakoda, Y., McDougall, M., Spencer, H.G., Pyne, M., Tolf, C., Waldenström, J., Jarvis, E.D., Baker, M.L., Burt, D.W., Short, K.R. :
The swan genome and transcriptome, it is not all black and white. Genome Biol 24:13, 2023. Pubmed reference: 36683094. DOI: 10.1186/s13059-022-02838-0.
2021 Haworth, D. :
A rare bird — how Europeans got the black swan so wrong , 2021.
2008 Pointer, MA., Mundy, NI. :
Testing whether macroevolution follows microevolution: are colour differences among swans (Cygnus) attributable to variation at the MCIR locus? BMC Evol Biol 8:249, 2008. Pubmed reference: 18789136. DOI: 10.1186/1471-2148-8-249.

Edit History

  • Created by Frank Nicholas on 25 Jan 2023
  • Changed by Frank Nicholas on 25 Jan 2023
  • Changed by Frank Nicholas on 27 Jan 2023
  • Changed by Imke Tammen2 on 08 Jan 2024