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

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          Abstract

          Common walnut ( Juglans regia L) is an economically important species cultivated worldwide for its high-quality wood and nuts. It is generally accepted that after the last glaciation J. regia 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.

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          Detection of reduction in population size using data from microsatellite loci.

          We demonstrate that the mean ratio of the number of alleles to the range in allele size, which we term M, calculated from a population sample of microsatellite loci, can be used to detect reductions in population size. Using simulations, we show that, for a general class of mutation models, the value of M decreases when a population is reduced in size. The magnitude of the decrease is positively correlated with the severity and duration of the reduction in size. We also find that the rate of recovery of M following a reduction in size is positively correlated with post-reduction population size, but that recovery occurs in both small and large populations. This indicates that M can distinguish between populations that have been recently reduced in size and those which have been small for a long time. We employ M to develop a statistical test for recent reductions in population size that can detect such changes for more than 100 generations with the post-reduction demographic scenarios we examine. We also compute M for a variety of populations and species using microsatellite data collected from the literature. We find that the value of M consistently predicts the reported demographic history for these populations. This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery.
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            Phylogeographic insights into cryptic glacial refugia.

            The glacial episodes of the Quaternary (2.6 million years ago-present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.
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              POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.

              Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version (POPTREE) was a command-line program that runs on the Command Prompt of Windows and Unix. In POPTREE2 genetic distances (measures of the extent of genetic differentiation between populations) for constructing phylogenetic trees, average heterozygosities (H) (a measure of genetic variation within populations) and G(ST) (a measure of genetic differentiation of subdivided populations) are computed through a simple and intuitive Windows interface. It will facilitate statistical analyses of polymorphism data for researchers in many different fields. POPTREE2 is available at http://www.med.kagawa-u.ac.jp/ approximately genomelb/takezaki/poptree2/index.html.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 March 2017
                2017
                : 12
                : 3
                : e0172541
                Affiliations
                [1 ]Institute of Agro-environmental and Forest Biology, National Research Council, Porano, Terni, Italy
                [2 ]U.S.D.A. Forest Service, Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
                [3 ]The Institute of Archaeological and Monumental Heritage, National Research Council, Tito Scalo, Potenza, Italy
                [4 ]Earth Trust, Little Wittenham, Abingdon, Oxfordshire, United Kingdom
                [5 ]Sylva Foundation, Little Wittenham, Oxfordshire, United Kingdom
                [6 ]Institute of Agricultural Biology and Biotechnology, National Research Council, Milan, Italy
                National Cheng Kung University, TAIWAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: PP KW MEM.

                • Data curation: PP FC MC.

                • Formal analysis: PP FC MC SDL.

                • Funding acquisition: PP KW MEM.

                • Investigation: PP FC IO VT JC GEH SM.

                • Methodology: PP FC MC.

                • Project administration: KW MEM.

                • Resources: KW JC GEH SM MEM.

                • Software: PP FC MC.

                • Supervision: KW MEM.

                • Validation: PP.

                • Visualization: PP FC MC.

                • Writing – original draft: PP KW FC SDL MEM.

                • Writing – review & editing: PP KW FC SDL JC MEM.

                [¤]

                Current address: Genomics, Genetics and Biology Innovation Pole, Perugia, Italy

                Article
                PONE-D-16-38047
                10.1371/journal.pone.0172541
                5336217
                28257470
                7552b61b-b237-4a98-a60f-7b437d539827
                © 2017 Pollegioni et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 22 September 2016
                : 5 February 2017
                Page count
                Figures: 5, Tables: 2, Pages: 24
                Funding
                Funded by: European Community in the framework of the Seventh Framework Programme under the Marie Curie Actions COFUND project “I-MOVE” (N. 267232)
                Award ID: 206405
                Award Recipient :
                This study was supported by the European Community in the framework of the Seventh Framework Programme under the Marie Curie Actions COFUND project “I-MOVE” (N. 267232) Grant number 206405.
                Categories
                Research Article
                People and Places
                Geographical Locations
                Europe
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
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                Population Biology
                Population Genetics
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                Evolutionary Biology
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                Gene Pool
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                Genetics
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                Gene Pool
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                Population Biology
                Population Genetics
                Gene Pool
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                Paleontology
                Paleogenetics
                Earth Sciences
                Paleontology
                Paleogenetics
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
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                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                People and Places
                Geographical Locations
                Asia
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Pollen
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Custom metadata
                The data set for this study is available from the figshare repository ( https://doi.org/10.6084/m9.figshare.4665235.v1). The data set includes geographic sites and SSR genetic data for 91 walnut populations sampled in Eurasia.

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