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Genetic diversity and population structure analysis of Philippine native pigs highlights four priority populations for conservation
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  • Joy Banayo,
  • Kathlyn Louise Manese,
  • Kaito Furusho,
  • Agapita Salces,
  • Takahiro Yamagata
Joy Banayo
University of the Philippines Los Banos

Corresponding Author:[email protected]

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Kathlyn Louise Manese
University of the Philippines Los Banos
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Kaito Furusho
University of the Philippines Los Banos
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Agapita Salces
University of the Philippines Los Banos
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Takahiro Yamagata
Nagoya University
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The Philippine native pig (PhNP) is a unique genetic resource with complex genetics due to multiple ancestries and hybridizations with wild pigs. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed 157 native pigs representing 7 populations (Benguet (B), Kalinga (K), Nueva Vizcaya, Isabela (I), Quezon (Q), Marinduque (M), and Samar (S)) and 39 pigs of transboundary distribution (Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 21 ISAG–FAO recommended microsatellite markers. We tested for population structure at the island, administrative region and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by analysis of molecular variance (Frt: 0.08; F’st: 0.288-0.728), Bayesian clustering (k = 2) and Nei’s DA genetic distance (98% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.72), a high allele count (Na: 9.24) and a low inbreeding coefficient (Fis: -0.022 to 0.150). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), administrative region (k = 4) and population (k= 9) levels. The pairwise F’st between PhNP populations ranged from 0.130 (Q and M) to 0.427 (Q and K), confirming that PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that the seven previously assigned PhNP populations, roughly delimited by provincial origin, are unique genetic units for conservation. Furthermore, the small effective population sizes of B, Q, I, and S (Ne: 5, 17, 24, and 26, respectively) necessitate immediate conservation actions, such as incentivizing the farming of PhNP.
18 Nov 2022Submitted to Ecology and Evolution
19 Nov 2022Submission Checks Completed
19 Nov 2022Assigned to Editor
21 Nov 2022Reviewer(s) Assigned
19 Jan 2023Review(s) Completed, Editorial Evaluation Pending
21 Feb 2023Editorial Decision: Revise Minor
28 Apr 20231st Revision Received
28 Apr 2023Assigned to Editor
28 Apr 2023Submission Checks Completed
28 Apr 2023Review(s) Completed, Editorial Evaluation Pending
17 May 2023Editorial Decision: Revise Minor
31 Aug 20232nd Revision Received
01 Sep 2023Submission Checks Completed
01 Sep 2023Assigned to Editor
01 Sep 2023Review(s) Completed, Editorial Evaluation Pending
04 Oct 2023Editorial Decision: Accept