Genetic and ecological insights into glacial refugia of walnut (<i>Juglans regia</i> L.)

<div><p>The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21–18 kyr BP) and LIG (130–116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.</p></div

Population structure inferred from a model based Bayesian cluster analysis.

<p>(A) Posterior probabilities (Ln Pr <i>X</i>|<i>K</i>) averaged over 20 replicate runs, (B) The <i>ad hoc</i> statistic delta <i>K</i> related to the second order rate of change of log probability of data between successive values of <i>K</i> with a distinct peak at <i>K</i> = 5 with some minor peaks at <i>K</i> = 9, 13, and 16, and (C) Bayesian Inferred population structure of walnut for <i>K</i> = 5 groups.</p

Genetic relationships among walnut genotypes.

<p>(A) Neighbor-joining cluster analysis using pair-wise Nei and Li distance matrix. (B) Principal components analysis using multilocus microsatellite genotype data.</p

Model settings (evaluation metrics) for AIC_<i>c</i>-selected MaxEnt model predictions.

<p>Model settings (evaluation metrics) for AIC_<i>c</i>-selected MaxEnt model predictions.</p

Locus-wise genetic variability in walnut germplasm.

<p>Locus-wise genetic variability in walnut germplasm.</p

Ecological niche modeling of walnut distributions.

<p>AIC_c-selected model prediction of occurrence of walnut for current, last glacial maximum (LGM; 21–18 kyr BP), and last interglacial (LIG; 130–107 kyr BP) climatic conditions for the data set filtered at 10 km with 137 occurrence points (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185974#pone.0185974.t006" target="_blank">Table 6</a> for feature class and regularization multiplier settings).</p

Inverse distance weighted (IDW) interpolation of allelic diversity estimates in walnut.

<p>(A) allelic richness, (B) private allelic richness, and (C) expected levels of heterozygosity among walnut geographic groups.</p

Genetic differentiation among geographic groups in walnut.

<p>Genetic differentiation among geographic groups in walnut.</p

Pair-wise <i>F</i>_<i>ST</i> values showing genetic differentiation among geographic groups in walnut.

<p>Pair-wise <i>F</i>_<i>ST</i> values showing genetic differentiation among geographic groups in walnut.</p

Within-group genetic variability in walnut.

<p>Within-group genetic variability in walnut.</p