Rethinking the history of common walnut (<i>Juglans regia</i> L.) in Europe: Its origins and human interactions

<div><p>Common walnut (<i>Juglans regia</i> L) is an economically important species cultivated worldwide for its high-quality wood and nuts. It is generally accepted that after the last glaciation <i>J</i>. <i>regia</i> survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new habitats via trade and cultural expansion. The history of walnut in Europe is a matter of debate, however. In this study, we estimated the genetic diversity and structure of 91 Eurasian walnut populations using 14 neutral microsatellites. By integrating fossil pollen, cultural, and historical data with population genetics, and approximate Bayesian analysis, we reconstructed the demographic history of walnut and its routes of dispersal across Europe. The genetic data confirmed the presence of walnut in glacial refugia in the Balkans and western Europe. We conclude that human-mediated admixture between Anatolian and Balkan walnut germplasm started in the Early Bronze Age, and between western Europe and the Balkans in eastern Europe during the Roman Empire. A population size expansion and subsequent decline in northeastern and western Europe was detected in the last five centuries. The actual distribution of walnut in Europe resulted from the combined effects of expansion/contraction from multiple refugia after the Last Glacial Maximum and its human exploitation over the last 5,000 years.</p></div

Genetic diversity of 91 walnut populations in Eurasia.

<p>Inverse Distance Weighted (IDW) interpolation of the allelic richness values (<i>Rs</i>) (a) and unbiased heterozygosity <i>UH</i>_E (b) calculated for 91 walnut populations (black dots) in Eurasia using 14 SSR markers (abbreviations CN = China, UZ = Uzbekistan, KG = Kyrgyzstan, TJ = Tajikistan, PK = Pakistan, IR = Iran, GE = Georgia, TR = Turkey, MD = Moldova, RO = Romania, HU = Hungary, SK = Slovakia, GR = Greece, IT = Italy, FR = France, ES = Spain).</p

Parameters estimates of the most likely scenarios of walnut expansion.

<p>Parameters estimates of the most likely scenarios (scenarios 6b) inferred by the Approximate Bayesian DIYABC Computation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172541#pone.0172541.ref045" target="_blank">45</a>] in the stage 2. Estimation of parameters is based on 1% of the closest data sets and subsequent logit transformation.</p

Spatial genetic sub-structure of the inferred clusters 1, 2 and 4 of walnut populations.

<p>Synthetic maps of Inverse Distance Weighted (IDW) interpolations of the estimated mean population membership values (<i>Q</i>_<i>i</i>) and bar plot for (a) K’, the most probable number of sub-clusters, based on microsatellite analysis of 217 walnut samples of cluster 1, (b) for K”, the most probable number of sub-clusters, based on microsatellite analysis of 280 walnut samples of cluster 2 and (c) for K”‘ the most probable number of sub-clusters, based on microsatellite analysis of 929 walnut samples of cluster 4.</p

Neighbor Joining cluster analysis of 91 walnut populations based on unbiased Nei’s genetic distance.

<p>Neighbor Joining-based circular tree for 91 walnut populations from the species’ Eurasian range based on unbiased Nei’s genetic distance [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172541#pone.0172541.ref043" target="_blank">43</a>]. The assignment of walnut populations to four clusters and eight sub-clusters inferred by STRUCTURE is shown.</p

Spatial genetic structure of 91 walnut populations in Eurasia.

<p>Population structure inference for 91 walnut populations by Bayesian assignment using STRUCTURE for K = 4. Synthetic map of Inverse Distance Weighted (IDW) interpolations of the estimated mean population membership values (<i>Q</i>_<i>i</i>) (a) and bar plot showing assignment probabilities of individuals to K clusters (b). Abbreviations: CN = China, UZ = Uzbekistan, KG = Kyrgyzstan, TJ = Tajikistan, PK = Pakistan, IR = Iran, GE = Georgia, TR = Turkey, MD = Moldova, RO = Romania, HU = Hungary, SK = Slovakia, GR = Greece, IT = Italy, FR = France, ES = Spain.</p

Most likely demographic scenario for European walnut by the DIYABC approach.

<p>Posterior probability (<i>P</i>) and 95% confidence interval of <i>P</i> (in brackets) computed using a direct (<i>P</i>_<i>1</i>) and logistic regression (<i>P</i>_<i>2</i>) approach are provided for each scenario tested by the DIYABC approach. The most likely scenario for each stage is reported in grey. Confidence in scenarios was evaluated using type <i>I</i> error (False negative) and type <i>II</i> error (False positive) rates for logistic regression.</p