.2021 Dec 13;11(24):18562-18574.

doi: 10.1002/ece3.8458. eCollection 2021 Dec.

Demographic history and genetic diversity of wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya

Stephen Ogada¹, Newton O Otecko^{2 3}, Grace Moraa Kennedy¹, John Musina⁴, Bernard Agwanda⁴, Vincent Obanda⁵, Jacqueline Lichoti⁶, Min-Sheng Peng^{2 3}, Sheila Ommeh^{1 4}

Affiliations

¹ Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya.
² State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming China.
³ Sino-Africa Joint Research Center Chinese Academy of Sciences Nairobi Kenya.
⁴ Department of Zoology National Museums of Kenya Nairobi Kenya.
⁵ Department of Veterinary Services Kenya Wildlife Service Nairobi Kenya.
⁶ Central Veterinary Laboratories Kabete State Department of Livestock Ministry of Agriculture, Livestock and Fisheries Nairobi Kenya.

PMID:35003693
PMCID: PMC8717324
DOI: 10.1002/ece3.8458

Demographic history and genetic diversity of wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya

Stephen Ogada et al. Ecol Evol.2021.

.2021 Dec 13;11(24):18562-18574.

doi: 10.1002/ece3.8458. eCollection 2021 Dec.

Authors

Stephen Ogada¹, Newton O Otecko^{2 3}, Grace Moraa Kennedy¹, John Musina⁴, Bernard Agwanda⁴, Vincent Obanda⁵, Jacqueline Lichoti⁶, Min-Sheng Peng^{2 3}, Sheila Ommeh^{1 4}

Affiliations

¹ Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya.
² State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming China.
³ Sino-Africa Joint Research Center Chinese Academy of Sciences Nairobi Kenya.
⁴ Department of Zoology National Museums of Kenya Nairobi Kenya.
⁵ Department of Veterinary Services Kenya Wildlife Service Nairobi Kenya.
⁶ Central Veterinary Laboratories Kabete State Department of Livestock Ministry of Agriculture, Livestock and Fisheries Nairobi Kenya.

PMID:35003693
PMCID: PMC8717324
DOI: 10.1002/ece3.8458

Abstract

Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mitochondrial DNA (mtDNA) control region fragment and 119,339 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS) data. Genetic diversity analyses revealed that the genetic variation in wild African harlequin quails was predominantly among individuals than populations. Demographic analyses indicated a signal of rapid demographic expansion, and the estimated time since population expansion was found to be 150,000-350,000 years ago, corresponding to around the Pliocene-Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. These results provide the first account of the genetic diversity of wild African harlequin quails of Siaya, thereby creating a helpful foundation in their biodiversity conservation.

Keywords: admixture; demographic inference; genetic differentiation; genotyping‐by‐sequencing; mtDNA.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

**FIGURE 1**
Sampling locations in Kenya

**FIGURE 2**
Wild African harlequin quail capture using traditional methods. (a) Wild African harlequin quail sample photograph. (b) Long poles containing bait quails. (c) Man‐made thicket with traps. (d) Captured wild African harlequin quails in woven baskets

**FIGURE 3**
A maximum‐likelihood tree showing the phylogenetic relationships between wild African harlequin quails (haplo 1 wild – haplo 32 wild) and otherCoturnix species

**FIGURE 4**
Median‐joining phylogenetic network constructed for quail mtDNA haplotypes. Circled areas show the haplotype frequencies

**FIGURE 5**
Principal component analysis of wild African harlequin quail populations (Siaya_North, Siaya_Central, and Siaya_South) and domestic Japanese quail (Kajiado)

**FIGURE 6**
Admixture plot showing the relationship between wild African harlequin (Siaya) and domestic Japanese quails (Kajiado) at ancestry number (K) = 2–3

**FIGURE 7**
Stairway plot showing historical changes in effective population size of Siaya wild African harlequin quails

See this image and copyright information in PMC

Cited by

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail.
Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Sermyagin AA, Anshakov DV, Fisinin VI, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA.Volkova NA, et al.Genes (Basel). 2024 Feb 25;15(3):294. doi: 10.3390/genes15030294.Genes (Basel). 2024.PMID:38540354Free PMC article.
Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds.
Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA.Volkova NA, et al.Animals (Basel). 2023 Nov 7;13(22):3439. doi: 10.3390/ani13223439.Animals (Basel). 2023.PMID:38003057Free PMC article.

References

1. Alexander, D. H. , & Lange, K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics, 12, 1–6. 10.1186/1471-2105-12-246 - DOI - PMC - PubMed
1. Amaral, A. J. , Silva, A. B. , Grosso, A. R. , Chikhi, L. , Bastos‐Silveira, C. , & Dias, D. (2007). Detection of hybridization and species identification in domesticated and wild quails using genetic markers. Folia Zoologica‐Praha‐, 56, 285.
1. Aoki, D. , Kinoshita, G. , Kryukov, A. P. , Nishiumi, I. , Lee, S.‐I. , & Suzuki, H. (2018). Quaternary‐related genetic differentiation and parallel population dynamics of the Eurasian Jay (Garrulus glandarius) in the circum‐Japan Sea region. Journal of Ornithology, 159, 1087–1097. 10.1007/s10336-018-1573-9 - DOI
1. Bandelt, H. J. , Forster, P. , & Röhl, A. (1999). Median‐joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48. 10.1093/oxfordjournals.molbev.a026036 - DOI - PubMed
1. Barilani, M. , Deregnaucourt, S. , Gallego, S. , Galli, L. , Mucci, N. , Piombo, R. , Puigcerver, M. , Rimondi, S. , Rodríguez‐Teijeiro, J. D. , Spanò, S. , & Randi, E. (2005). Detecting hybridization in wild (Coturnix c. coturnix) and domesticated (Coturnix c. japonica) quail populations. Biological Conservation, 126, 445–455. 10.1016/j.biocon.2005.06.027 - DOI

Related information

MedGen

LinkOut - more resources

Full Text Sources

Movatterモバイル変換

Account

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Full text links

Actions

Share

Demographic history and genetic diversity of wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya

Affiliations

Demographic history and genetic diversity of wild African harlequin quail (Coturnix delegorguei delegorguei) populations of Kenya

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Similar articles

Cited by

References

Related information

LinkOut - more resources

Full Text Sources