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      Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient

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          Abstract

          We studied hybrid interactions of Lilium meleagrinum, Lilium gongshanense, and Lilium saluenense using an integrative approach combining population genetics, fieldwork, and phenological research. These three species occur along an elevational gradient, with L. meleagrinum occurring at lower elevations, L. saluenense at higher elevations, and L. gongshanense between them. The species show strong morphological differentiation despite there being no clear environmental barriers to gene flow among them. Lilium gongshanense is likely to have a hybrid origin based on our prior work, but its progenitors remain uncertain. We sought to determine whether gene flow occurs among these three parapatric species, and, if so, whether L. gongshanense is a hybrid of L. meleagrinum and/or L. saluenense. We analyzed data from multiple chloroplast genes and spacers, nuclear internal transcribed spacer (ITS), and 18 nuclear Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) microsatellites for accessions of the three species representing dense population-level sampling. We also inferred phenology by examining species in the field and using herbarium specimens. We found that there are only two types of chloroplast genomes shared among the three species and that L. gongshanense forms two distinct groups with closest links to other species of Lilium based on ITS. Taken together, L. gongshanense is unlikely to be a hybrid species resulting from a cross between L. meleagrinum and L. saluenense, but gene flow is occurring among the three species. The gene flow is likely to be rare according to evidence from all molecular datasets, and this is corroborated by detection of only one putative hybrid individual in the field and asynchronous phenology. We suspect that the rarity of hybridization events among the species facilitates their continued genetic separation.

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          Detecting the number of clusters of individuals using the software structure: a simulation study

          The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
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            Very high resolution interpolated climate surfaces for global land areas

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              DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.

              DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser. Freely available to academic users from: (http://www.ub.edu/dnasp).
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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
                07 December 2020
                2020
                : 11
                : 576407
                Affiliations
                [1] 1CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu, China
                [2] 2Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China
                [3] 3Institut für Biologie, Freie Universität Berlin , Berlin, Germany
                Author notes

                Edited by: Nina Rønsted, National Tropical Botanical Garden, United States

                Reviewed by: Adrian Christopher Brennan, Durham University, United Kingdom; Jianquan Liu, Lanzhou University, China

                *Correspondence: Yundong Gao, gaoyd@ 123456cib.ac.cn

                These authors have contributed equally to this work

                This article was submitted to Plant Systematics and Evolution, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2020.576407
                7750405
                dc419957-dfb0-4015-9599-9e89a26abe17
                Copyright © 2020 Gao, Harris, Li and Gao.

                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
                : 26 June 2020
                : 02 November 2020
                Page count
                Figures: 5, Tables: 2, Equations: 0, References: 94, Pages: 16, Words: 0
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                divergence with gene flow,introgression,species boundary,lilium,hengduan mountains,southwestern china,nomocharis,hybridzation

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