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Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

Nature Genetics volume 47, pages 1141–1148 (2015)Cite this article

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Abstract

Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

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Figure 1: Schematics of the models tested in this study.
Figure 2: Ancestry of wild boars and domestic pigs in Europe and Asia.
Figure 3: Model-based ancestry analysis.
Figure 4: Posterior density distributions of demographic parameters.
Figure 5: Example of a parallel sweep in ASD and EUD.

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Acknowledgements

We thank B. Peter for his help and guidance during the model-fitting step of the analysis as well as for kindly sharing his code. We are also indebted to D. Wegmann for providing us with the latest version of ABCtoolbox. We also thank K. Lohse for his insights during the conception of the project and D. Caspani for his help with the figures. We thank B. Dibbits for his help during the laboratory work. This project is financially supported by the European Research Council under the European Community's 256 Seventh Framework Programme (FP7/2007–2013)/ERC (SelSweep), grant agreements 249894 and ERC-2013-StG 337574-UNDEAD. J.G.S. was supported by US National Institutes of Health grant R01-GM40282 and National Science Foundation postdoctoral fellowship DBI-1402120.

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Authors and Affiliations

  1. Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands

    Laurent A F Frantz, Ole Madsen, Hendrik-Jan Megens, Mirte Bosse, Yogesh Paudel, Richard P M A Crooijmans & Martien A M Groenen

  2. Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK

    Laurent A F Frantz & Greger Larson

  3. Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA

    Joshua G Schraiber

  4. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    Joshua G Schraiber

  5. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    Alex Cagan

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  1. Laurent A F Frantz
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Contributions

M.A.M.G., L.A.F.F. and G.L. designed the study. R.P.M.A.C. provided the samples. L.A.F.F., H.-J.M., O.M., M.B. and Y.P. aligned and filtered the data. L.A.F.F. and J.G.S. performed the modeling. L.A.F.F., J.G.S. and A.C. performed the selection scan. L.A.F.F., J.G.S., G.L. and M.A.M.G. wrote the manuscript with input from all authors.

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Correspondence to Laurent A F Frantz.

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Integrated supplementary information

Supplementary Figure 1 Nucleotide distance to the outgroup (S. verrucosus).

Each circle represents the mean distance computed in 10-kb windows across the genome. The dashed lines correspond to ±1 s.d. of the mean distance computed across all individuals.

Supplementary Figure 2 All models investigated in this study.

Schematic of all models tested in this study. The upper six models were first compared together. In this comparison, the full model (outlined with a gray square) was the best-fitting model. When all seven models were tested together, the ghost model had the best fit (outlined with a black square). All priors and support values are reported in Supplementary Table 5.

Supplementary Figure 3 Distribution of raw summary statistics under the full and null models.

The dashed red line represents the value of the observed summary statistic. S_mean, mean number of segregating sites; n1, number of singletons; thetaPi, θπ; tajd, Tajima’s D.

Supplementary Figure 4 Result of the TreeMix analysis for the 602 pigs genotyped on the porcine 60SNP array data set.

Supplementary Figure 5 Posterior distribution of all parameters in the full model.

Population sizes are the relative population size (the ratio of the current population size over the population size at t0; Fig. 1). Dashed lines represent the prior distributions. The full model is as in Supplementary Figure 1.

Supplementary Figure 6 Result of PCA (PC1-PC2) based on 602 genotyped pigs.

Supplementary Figure 7 Result of PCA (PC3-PC4) based on 602 genotyped pigs.

Supplementary Figure 8 Example of genealogy at a sweep region that could be explained by admixture ASD ↔ EUD.

Supplementary Figure 9 Diverse sweep statistics computed in the PLAG1 region.

Dashed blue and red lines represent thresholds of P = 0.05 and P = 0.01, respectively. (a) CLR. (b) DAF. (c) Tajima’s D. (d) H12 statistic.

Supplementary Figure 10 Nucleotide divergence relative to the outgroup in the swept region.

Each box plot, for the samples shown along the y axis represents the distribution of raw nucleotide divergence relative to the outgroup in 1,000 randomly selected 10-kb bins across the genome. Red dots represent the mean nucleotide divergence relative to the outgroup in the sweep region in Figure 4.

Supplementary Figure 11 PLS distribution of 10,000 (out of 2,000,000) retained simulations and observed data under the full model.

Simulations are shown in black, and observed data are shown in red.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11, Supplementary Tables 4–6 and Supplementary Note. (PDF 2662 kb)

Supplementary Table 1

List of samples used in this study. (XLSX 34 kb)

Supplementary Table 2

Support for each model in Supplementary Figure 3. (XLSX 36 kb)

Supplementary Table 3

Prior and posterior distributions for the full model. All population size (N) and migration rate (m) parameters are in log scale. All other models (Supplementary Fig. 3) use the same prior bound. RMSE is the root mean square error. P_value_KS corresponds to the P value of the Kolomogorov-Smirnov test of uniformity of the posterior quantiles (see “Validation of ABC procedure” in the Supplementary Note). (XLSX 9 kb)

Supplementary Table 7

List of genes with GO term enrichment (P < 0.01) in sweep regions in EUD. (XLSX 6 kb)

Supplementary Table 8

List of genes with GO term enrichment (P < 0.01) in sweep regions in ASD. (XLSX 5 kb)

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Frantz, L., Schraiber, J., Madsen, O. et al. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Nat Genet 47, 1141–1148 (2015). https://doi.org/10.1038/ng.3394

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