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. 2016 Dec 14:6:38935.
doi: 10.1038/srep38935.

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

Amparo Martínez  1 , Arianna Manunza  2 , Juan Vicente Delgado  1 , Vincenzo Landi  1 , Ayotunde Adebambo  3 , Muritala Ismaila  3 , Juan Capote  4 , Mabrouk El Ouni  5 , Ahmed Elbeltagy  6 , Asmaa M Abushady  7 , Salah Galal  8 , Ainhoa Ferrando  9 , Mariano Gómez  10 , Agueda Pons  11 , Bouabid Badaoui  12 , Jordi Jordana  9 , Oriol Vidal  13 , Marcel Amills  2   9
Affiliations

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

Amparo Martínez et al. Sci Rep. .

Abstract

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

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Figures

Figure 1
Figure 1. Principal coordinates analysis of 32 goat populations based on a pairwise FST matrix.
Populations under analysis are: Southern Spain: Blanca Andaluza (BLAN), Blanca Celtibérica (CELT), Malagueña (MALA), Murciano-Granadina (MURC), Florida (FLOR), Payoya (PAYO), Negra Serrana (SERR), Retinta (RETI); Northern Spain: Azpi-Gorri (AZPI), Blanca de Rasquera (RASQ); Balearic Islands: Eivissenca (EIVI), Mallorquina (MALL); Canary Islands: Ajuy (AJUY), Majorera (MAJO), Palmera (PALM), Tinerfeña del Norte (TINN), Tinerfeña del Sur (TINS); Cape Verde (CVER); Central West Europe: Saanen (SAAN), Alpine (ALPI); Northwest Africa: Moroccan (MORO), TUNE (Tunisian), Algerian (ALGE); Egypt: Barki (BARK), Baladi (BALA), Saidi (SAID); Nigeria: Maradi (MARA), West African Dwarf (WEAF), Sahel (SAHE); South Africa: Boer (BOER), Kalahari Red (KALA). The Anglo-Nubian breed (mixed British, African and Indian origins) is indicated as NUBI.
Figure 2
Figure 2. Structure analysis of 32 goat populations on the basis of the most significant K-value (K = 4), as inferred with the method reported by Evanno.
The complete analysis (K = 2–6) can be found in Supplementary Fig. S1. Southern Spain: Blanca Andaluza (BLAN), Blanca Celtibérica (CELT), Malagueña (MALA), Murciano-Granadina (MURC), Florida (FLOR), Payoya (PAYO), Negra Serrana (SERR), Retinta (RETI); Northern Spain: Azpi-Gorri (AZPI), Blanca de Rasquera (RASQ); Balearic Islands: Eivissenca (EIVI), Mallorquina (MALL); Canary Islands: Ajuy (AJUY), Majorera (MAJO), Palmera (PALM), Tinerfeña del Norte (TINN), Tinerfeña del Sur (TINS); Cape Verde (CVER); Central West Europe: Saanen (SAAN), Alpine (ALPI); Northwest Africa: Moroccan (MORO), TUNE (Tunisian), Algerian (ALGE); Egypt: Barki (BARK), Baladi (BALA), Saidi (SAID); Nigeria: Maradi (MARA), West African Dwarf (WEAF), Sahel (SAHE); South Africa: Boer (BOER), Kalahari Red (KALA). The Anglo-Nubian breed (mixed British, African and Indian origins) is indicated as NUBI.
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