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Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia
Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected fr...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Japan Poultry Science Association
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9596289/ https://www.ncbi.nlm.nih.gov/pubmed/36382062 http://dx.doi.org/10.2141/jpsa.0210140 |
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author | Compendio, Jade Dhapnee Z. Mantana, Jam Marrie Nanche P. Nishibori, Masahide |
author_facet | Compendio, Jade Dhapnee Z. Mantana, Jam Marrie Nanche P. Nishibori, Masahide |
author_sort | Compendio, Jade Dhapnee Z. |
collection | PubMed |
description | Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800–3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines. |
format | Online Article Text |
id | pubmed-9596289 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Japan Poultry Science Association |
record_format | MEDLINE/PubMed |
spelling | pubmed-95962892022-11-14 Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia Compendio, Jade Dhapnee Z. Mantana, Jam Marrie Nanche P. Nishibori, Masahide J Poult Sci Full Papers Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800–3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines. Japan Poultry Science Association 2022-10-25 /pmc/articles/PMC9596289/ /pubmed/36382062 http://dx.doi.org/10.2141/jpsa.0210140 Text en 2022, Japan Poultry Science Association. https://creativecommons.org/licenses/by-nc-sa/4.0/The Journal of Poultry Science is an Open Access journal distributed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view the details of this license, please visit (https://creativecommons.org/licenses/by-nc-sa/4.0/). |
spellingShingle | Full Papers Compendio, Jade Dhapnee Z. Mantana, Jam Marrie Nanche P. Nishibori, Masahide Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title | Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title_full | Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title_fullStr | Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title_full_unstemmed | Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title_short | Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia |
title_sort | analysis of the mtdna d-loop region casts new light on philippine red junglefowl phylogeny and relationships to other junglefowl species in asia |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9596289/ https://www.ncbi.nlm.nih.gov/pubmed/36382062 http://dx.doi.org/10.2141/jpsa.0210140 |
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