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Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex

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Abstract

Hybridization is common for many forest trees, where weak barriers to reproduction obscure species boundaries. We characterized the genomic structure of Picea populations comprising three species spanning two well-known contact zones, the Picea sitchensis × Picea glauca and the P. engelmannii × P. glauca hybrid zones, using a set of 71 candidate-gene single nucleotide polymorphisms. The genetic structure of populations suggests a complex genomic architecture shaped by interspecific gene flow and strong environmental selection, with increased genetic diversity in hybrids. The presence of admixture among all three species suggests that three-way hybrids with mixed ancestry occur where species ranges overlap in transitional environments. Significant clinal variation and associations with climatic variables (including continentality, temperature, and precipitation) differ between hybrid zones, indicating that individual species and their hybrids are adapted to distinct environmental niches. Allele–environmental association analysis revealed that most of the candidate genes with evidence of selection were unique to either the Sitka × white or the Engelmann × white hybrid zones, with few shared between these zones. Management of these widespread and diverse gene pools will be best served through development of climate-based seed transfer, with recommended seed sources informed by a combination of genetic and climatic information for future climates.

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Acknowledgments

We thank John King and Barry Jaquish from the British Columbia Ministry of Forests, Lands and Natural Resource Operations for establishing the common garden trials and providing material, and Christine Chourmouzis, Lisa Erdle, Nina Lobo, Jon Sweetman, Pia Smets, and Jordan Bemmels for field assistance. We also thank Eric Frichot and Graham Coop for valuable suggestions on the environmental association analyses. Particular thanks to Santiago Gonzalez-Martinez and anonymous referees for thoughtful suggestions that have greatly improved the manuscript. This work was supported by Genome British Columbia, Genome Canada, the Province of British Columbia and the British Columbia Forest Genetics Council (grant to S.N.A.), the Natural Science and Engineering Research Council of Canada (NSERC Discovery grant to S.N.A.), an NSERC Canada Graduate Scholarship to J.H., and UBC Fellowships to J.H and A.R.T.

Data archiving statement

SNP data for the Picea glauca × P. engelmannii hybrid zone is available at Dryad doi:10.5061/dryad.7h65f. Population origin and SNP genotypes for the Picea sitchensis × P. glauca are available at Dryad doi: 10.5061/dryad.s11b6.

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Correspondence to Jill A. Hamilton.

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Communicated by S.C. González-Martínez

J. A. Hamilton and A. R. De la Torre contributed equally to this work.

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Table S1

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Table S3

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Table S4

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Fig. S1

Population genetic structure analyses based on ten replicate Structure runs for Sitka, white, Engelmann, and admixed spruce. Mean ln P[D] (dotted line) and K genetic clusters (solid line) for K = 1–10. (PDF 106 kb)

Fig. S2

Loading plot of SNP contributions to the first discriminant principle component function (a) and second discriminant principle component function (b) based on 71 SNPs across the Sitka, white, Engelmann, and admixed populations. The gray line indicates the 95% quantile. (GIF 54 kb)

High Resolution Image (TIFF 8154 kb)

Fig. S3

(GIF 607 kb)

High Resolution Image (TIFF 6641 kb)

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Hamilton, J.A., De la Torre, A.R. & Aitken, S.N. Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex. Tree Genetics & Genomes 11, 817 (2015). https://doi.org/10.1007/s11295-014-0817-y

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