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      Genetic diversity of the submerged macrophyte Ceratophyllum demersum depends on habitat hydrology and habitat fragmentation

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          Abstract

          The adaptability of plant populations to a changing environment depends on their genetic diversity, which in turn is influenced by the degree of sexual reproduction and gene flow from distant areas. Aquatic macrophytes can reproduce both sexually and asexually, and their reproductive fragments are spread in various ways (e.g. by water). Although these plants are obviously exposed to hydrological changes, the degree of vulnerability may depend on the types of their reproduction and distribution, as well as the hydrological differences of habitats. The aim of this study was to investigate the genetic diversity of the cosmopolitan macrophyte Ceratophyllum demersum in hydrologically different aquatic habitats, i.e. rivers and backwaters separated from the main river bed to a different extent. For this purpose, the first microsatellite primer set was developed for this species. Using 10 developed primer pairs, a high level of genetic variation was explored in C. demersum populations. Overall, more than 80% of the loci were found to be polymorphic, a total of 46 different multilocus genotypes and 18 private alleles were detected in the 63 individuals examined. The results demonstrated that microsatellite polymorphism in this species depends on habitat hydrology. The greatest genetic variability was revealed in populations of rivers, where flowing water provides constant longitudinal connections with distant habitats. The populations of the hydrologically isolated backwaters showed the lowest microsatellite polymorphism, while plants from an oxbow occasionally flooded by the main river had medium genetic diversity. The results highlight that in contrast to species that spread independently of water flow or among hydrologically isolated water bodies, macrophytes with exclusive or dominant hydrochory may be most severely affected by habitat fragmentation, for example due to climate change.

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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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            Inference of Population Structure Using Multilocus Genotype Data

            We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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              STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/2407289Role: Role: Role: Role: Role: Role: Role: Role:
                Role: Role: Role:
                Role: Role: Role:
                URI : https://loop.frontiersin.org/people/2563081Role: Role: Role:
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                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                09 November 2023
                2023
                : 14
                : 1277916
                Affiliations
                [1] 1 Institute of Aquatic Ecology, Centre for Ecological Research , Budapest, Hungary
                [2] 2 Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network , Szeged, Hungary
                [3] 3 Department of Biotechnology, Faculty of Science and Informatics, Szeged University , Szeged, Hungary
                [4] 4 Aix Marseille University, Avignon University, French National Center for Scientific Research (CNRS), French National Research Institute for Sustainable Development (IRD), Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE) , Marseille, France
                [5] 5 Molecular Taxonomy Laboratory, Hungarian Natural History Museum , Budapest, Hungary
                Author notes

                Edited by: Guixiang Yuan, Hunan Agricultural University, China

                Reviewed by: Wei Li, Nanchang Institute of Technology, China; Beibei Hao, Guangdong Academy of Sciences, China; Qian Hu, Lushan Botanical Garden (CAS), China

                *Correspondence: Attila I. Engloner, engloner.attila@ 123456ecolres.hu
                Article
                10.3389/fpls.2023.1277916
                10665863
                36ddd75a-8329-414f-8f80-238452d0d6d0
                Copyright © 2023 Engloner, Németh, Kós, Meglécz and Bereczki

                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
                : 15 August 2023
                : 23 October 2023
                Page count
                Figures: 5, Tables: 2, Equations: 0, References: 67, Pages: 10, Words: 4440
                Funding
                This work was partially funded by the National Research, Development and Innovation Office (OTKA K106177).
                Categories
                Plant Science
                Original Research
                Custom metadata
                Aquatic Photosynthetic Organisms

                Plant science & Botany
                microsatellites,multilocus genotypes,vegetative dispersion,danube,river channel,backwaters

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