Abstract
Background
The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea.
Objectives
Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples.
Results
The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased.
Conclusion
The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5–1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Baptista LF, Trail PW, Horbit HM, Kirwan GM (2020) Hill pigeon (Columba rupestris), version 1.0. In: del Hoyo J, Elliott A, Sargatal J, Christies DA, de Juana E (eds) Birds of the world. Cornell Laboratory of Ornithology, Ithaca. https://doi.org/10.2173/bow.hilpig1.01
Blechman A (2007) Pigeons-the fascinating saga of the world’s most revered and reviled bird. University of Queensland Press, St Lucia, Queensland (ISBN 978-0-7022-3641-9)
Dunn JC, Hamer KC, Morris AJ, Grice PV, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J et al (2021) The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758 [version 1; peer review: awaiting peer review]. Wellcome Open Res 6:191. https://doi.org/10.12688/wellcomeopenres.17060.1
Esmailizadeh A, Kharrati-Koopaee H, Assdoullahpour H (2021) Whole genome resequencing data for rock pigeon (Columba livia). BMC Res Notes. https://doi.org/10.1186/s13104-021-05718-1
Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, Domyan ET, Suh A, Warren WC, Yandell M et al (2018) Improved genome assembly and annotation for the rock pigeon (Columba livia). G3 8:1391. https://doi.org/10.1534/g3.117.300443
Kim HJ, Park JY, Kang SG, Kim DW, Oh MR, Lee KS, Yeo YG, Lee JW (2016) Conservation and restoration of the endangered hill pigeon Columba rupestris (III). National Institute of Biological Resources of Korea. (https://www.nibr.go.kr/aiibook/ecatalog5.jsp?Dir=446&catimage=&callmode=admin)
Kim JY, Eo SH, Kang SG, Hwang JE, Yeo YG, Yoon JM (2022) population genetic structure and conservation management of hill pigeons (Columba rupestris) recently endangered in South Korea. Genes Genom. https://doi.org/10.1007/s13258-021-01212-x
Li H, Durbin R (2011) Inference of human population history from individual whole genome sequence. Nature 475:493–496
Li S, Li B, Cheng C, Xiong Z, Liu Q, Lai J, Carey HV, Zhang Q, Zheng H, Wei S, Zhang H et al (2014) Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. Genome Biol 15:557
McVean GAT, Cardin NJ (2005) Approximating the coalescent with recombination. Phil Trans R Soc B 360:1387–1393. https://doi.org/10.1098/rstb.2005.1673
Mei C, Wang H, Zhu W, Wang H, Cheng G, Qu K, Guang X, Li A, Zhao C, Yang W et al (2016) Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features. Sci Rep 6:19787. https://doi.org/10.1038/srep19787
Muir WM, Wong GK, Zhang Y, Wang J, Groenen MAM, Grooijmans R, Megens HJ, Zhang H, Okimoto R, Vereijken A et al (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA 105:17312–17317. https://doi.org/10.1073/pnas.0806569105
Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H (2016) PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatcher. Mol Ecol 25:1058–1072. https://doi.org/10.1111/moc.13540
Nagai K, Takahashi Y, Tokita KI, Anzai T, Uchida K (2020) Genetic diversity in Japanese populations of the Eurasian collared dove. Avian Res 11:21. https://doi.org/10.1186/s40657-020-00207-8
Pereira SL, Johnson KP, Clayton DL, Baker AJ (2007) Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene. Syst Biol 56:656–672. https://doi.org/10.1080/10635150701549672
Shao Y, Tian HY, Zhang JJ, Kharrati-Koopaee H, Guo X, Zhung XL, Li ML, Nanai HA, Tafti ED, Shojaei B et al (2020) Genomic and phenotypic analyses reveal mechanisms underlying homing ability in pigeon. Mol Biol Evol 37:134–148. https://doi.org/10.1093/molbev/msz208
Shapiro MD, Domyan ET (2013) Domestic pigeons. Curr Biol 23(8):R302-303
Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Binida-Edonds ORP, Lee LM, Cooper A (2002) Flight of the dodo. Science 295:1683. https://doi.org/10.1126/science.295.5560.1683
Shapiro M, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI et al (2013) Genomic diversity and evolution of the head crest in the rock pigeon. Science 339:1063–1067. https://doi.org/10.1126/science.1230422
Sims KB (2012) Norrie Disease. National Organization for rare Disorder (NORD) 2012: http://raredisease.org/rare-diseases/norrie-disease/
Sweet AD, Maddox JD, Johnson KP (2017) A complete molecular phylogeny of Claravis confirms its paraphyly within small New World ground-doves (Aves: Peristerinae) and implies multiple plumage state transitions. J Avian Biol 48(3):459–464. https://doi.org/10.1111/jav.01077
Vickrey A, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary E, Maynez R, Osborne E, Johnson K, Huff CD et al (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 7:e34803. https://doi.org/10.7554/eLife.334803
Zhang G (2015) Bird sequencing project takes off. Nature 522:34. https://doi.org/10.1038/522034d
Zhang G, Li C, Li Q, Larkin DM, Lee C, Storz F, Antunes A, Greenwold MJ, Meredith RW, Odeen A et al (2015) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320. https://doi.org/10.1126/science.1251385
Zheng BX, Xu QQ, Shen YP (2002) The relationship between climate change and Quaternary glacial cycle on the Qinhai-Tonbetan Plateau: review and speculation. Quat Int 97–98:93–101. https://doi.org/10.1016/s1040-6182(02)00054-x
Acknowledgements
This work was supported by a grant (NIBR201803101) from the National Institute of Biological Resources (NIBR) funded by the Ministry of Environment (MOE), Republic of Korea.
Author information
Authors and Affiliations
Contributions
I-YC and JAK conceived and designed the project and edited the manuscript. JAK and B-SC analyzed the data. N-SK wrote the draft manuscript. S-GK, Y-GY, J-HB and J-HL prepared the sample materials and performed the bio experiment. J-YP and TU edited and completed the manuscript. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Conflicts of interest
All authors have read the manuscript and have no conflicts of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Kim, J.A., Choi, BS., Kim, NS. et al. Whole-genome sequencing revealed different demographic histories among the Korean endemic hill pigeon (Columba rupestris), rock pigeon (Columba livia var. domestica) and oriental turtle dove (Streptopelia orientalis). Genes Genom 44, 1231–1242 (2022). https://doi.org/10.1007/s13258-022-01288-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-022-01288-z