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      Possible Source Populations of the White-backed Planthopper in the Greater Mekong Subregion Revealed by Mitochondrial DNA Analysis

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          Abstract

          The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), is a serious pest of rice in Asia. However, little is known regarding the migration of this pest insect from the Greater Mekong Subregion (GMS) including Cambodia, Laos, Myanmar (Burma), Thailand, and Vietnam, into China’s Yunnan Province. To determine the migration patterns of S. furcifera in the GMS and putative secondary immigration inside China’s Yunnan Province, we investigated the population genetic diversity, genetic structure, and gene flow of 42 S. furcifera populations across the six countries in the GMS by intensive sampling using mitochondrial genes. Our study revealed the potential emigration of S. furcifera from the GMS consists primarily of three major sources: 1) the S. furcifera from Laos and Vietnam migrate into south and southeast Yunnan, where they proceed to further migrate into northeast and central Yunnan; 2) the S. furcifera from Myanmar migrate into west Yunnan, and/or central Yunnan, and/or northeast Yunnan; 3) the S. furcifera from Cambodia migrate into southwest Yunnan, where the populations can migrate further into central Yunnan. The new data will not only be helpful in predicting population dynamics of the planthopper, but will also aid in regional control programs for this economically important pest insect.

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          DnaSP, DNA polymorphism analyses by the coalescent and other methods.

          DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
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            Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.

            A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-population n-island model and a source-sink population model. Our estimation method as coded in migrate is tested against genetree; both programs deliver a very similar likelihood surface. The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.
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              Isolation by distance, web service

              Background The population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly. Results We have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, population geneticists can perform a variety of powerful statistical tests including Mantel tests, Reduced Major Axis (RMA) regression analysis, as well as calculate F ST between all pairs of populations and perform basic summary statistics (e.g., heterozygosity). All statistical results, including publication-quality scatter plots in Postscript format, are returned rapidly to the user and can be easily downloaded. Conclusion IBDWS population genetics analysis software is hosted at and documentation is available at . The source code has been made available on Source Forge at .
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                19 December 2016
                2016
                : 6
                : 39167
                Affiliations
                [1 ]Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming 650205, China
                [2 ]Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University , Qingdao 266109, China
                [3 ]Plant Protection Office, Cambodian Agricultural Research and Development Institute , Phnom Penh 01, Cambodia
                [4 ]Horticulture Research Center, National Agriculture and Forestry Research Institute , Vientiane 7170, Lao PDR
                [5 ]Department of Agricultural Research, Ministry of Agriculture and Irrigation , Nay Pyi Taw, Myanmar
                [6 ]Plant Protection Research and Development Office, Department of Agriculture , Bangkok 10170, Thailand
                [7 ]Plant Protection Research Institute, Vietnam Academy of Agricultural Sciences , Hanoi, Vietnam
                Author notes
                [*]

                These authors contributed equally to this work.

                Article
                srep39167
                10.1038/srep39167
                5171772
                27991532
                8fb1ab80-9fcf-4ef7-aa41-75682e7b3ecc
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 04 August 2016
                : 18 November 2016
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