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      A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae)

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          Abstract

          The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east–west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east–west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet.

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          Statistical confidence for likelihood-based paternity inference in natural populations.

          Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.
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            DNASTAR's Lasergene sequence analysis software.

            Lasergene's eight modules provide tools that enable users to accomplish each step of sequence analysis, from trimming and assembly of sequence data, to gene discovery, annotation, gene product analysis, sequence similarity searches, sequence alignment, phylogenetic analysis, oligonucleotide primer design, cloning strategies, and publication of the results. The Lasergene software suite provides the functions and customization tools needed so that users can perform analyses the software writers never imagined.
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              Measuring and testing genetic differentiation with ordered versus unordered alleles.

              Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                05 March 2019
                2019
                : 10
                : 149
                Affiliations
                Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu, China
                Author notes

                Edited by: Genlou Sun, Saint Mary’s University, Canada

                Reviewed by: Yessica Rico, Instituto de Ecología (INECOL), Mexico; Ferhat Celep, Kırıkkale University, Turkey

                *Correspondence: XingJin He, xjhe@ 123456scu.edu.cn

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2019.00149
                6412145
                30891047
                eda75248-8334-4132-b0be-afcbc10787fd
                Copyright © 2019 Li, Xie, Xie, Deng, Zhong, Yu and He.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 24 July 2018
                : 28 January 2019
                Page count
                Figures: 7, Tables: 3, Equations: 0, References: 59, Pages: 18, Words: 0
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                allium,phytogeographic divide,genetic breaks,pleistocene,qinghai-tibet plateau

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