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Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species

Population genetic structure can provide valuable insights for conserving genetic resources and understanding population evolution, but it is often underestimated when using the most popular method and software, STRUCTURE and delta K, to assess. Although the hierarchical STRUCTURE analysis has been...

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Autores principales: Zhang, Chaoqiang, Tang, Yiwei, Tian, Defeng, Huang, Yanyan, Yang, Guanghui, Nan, Peng, Wang, Yuguo, Li, Lingfeng, Song, Zhiping, Yang, Ji, Zhong, Yang, Zhang, Wenju
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9624186/
https://www.ncbi.nlm.nih.gov/pubmed/36330273
http://dx.doi.org/10.3389/fpls.2022.962364
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author Zhang, Chaoqiang
Tang, Yiwei
Tian, Defeng
Huang, Yanyan
Yang, Guanghui
Nan, Peng
Wang, Yuguo
Li, Lingfeng
Song, Zhiping
Yang, Ji
Zhong, Yang
Zhang, Wenju
author_facet Zhang, Chaoqiang
Tang, Yiwei
Tian, Defeng
Huang, Yanyan
Yang, Guanghui
Nan, Peng
Wang, Yuguo
Li, Lingfeng
Song, Zhiping
Yang, Ji
Zhong, Yang
Zhang, Wenju
author_sort Zhang, Chaoqiang
collection PubMed
description Population genetic structure can provide valuable insights for conserving genetic resources and understanding population evolution, but it is often underestimated when using the most popular method and software, STRUCTURE and delta K, to assess. Although the hierarchical STRUCTURE analysis has been proposed early to overcome the above potential problems, this method was just utilized in a few studies and its reliability needs to be further tested. In this study, the genetic structure of populations of Wikstroemia monnula was evaluated by sequencing 12 nuclear microsatellite loci of 905 individuals from 38 populations. The STRUCTURE analysis suggested the most likely number of clusters was two, but using multi-hierarchical structure analysis, almost every population was determined with an endemic genetic component. The latter result is consistent with the extremely low gene flow among populations and a large number of unique cpDNA haplotypes in this species, indicating one level of structure analysis would extremely underestimate its genetic component. The simulation analysis shows the number of populations and the genetic dispersion among populations are two key factors to affect the estimation of K value using the above tools. When the number of populations is more than a certain amount, K always is equal to 2, and when a simulation only includes few populations, the underestimation of K value also may occur only if these populations consist of two main types of significantly differentiated genetic components. Our results strongly support that the hierarchical STRUCTURE analysis is necessary and practicable for the species with lots of subdivisions.
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spelling pubmed-96241862022-11-02 Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species Zhang, Chaoqiang Tang, Yiwei Tian, Defeng Huang, Yanyan Yang, Guanghui Nan, Peng Wang, Yuguo Li, Lingfeng Song, Zhiping Yang, Ji Zhong, Yang Zhang, Wenju Front Plant Sci Plant Science Population genetic structure can provide valuable insights for conserving genetic resources and understanding population evolution, but it is often underestimated when using the most popular method and software, STRUCTURE and delta K, to assess. Although the hierarchical STRUCTURE analysis has been proposed early to overcome the above potential problems, this method was just utilized in a few studies and its reliability needs to be further tested. In this study, the genetic structure of populations of Wikstroemia monnula was evaluated by sequencing 12 nuclear microsatellite loci of 905 individuals from 38 populations. The STRUCTURE analysis suggested the most likely number of clusters was two, but using multi-hierarchical structure analysis, almost every population was determined with an endemic genetic component. The latter result is consistent with the extremely low gene flow among populations and a large number of unique cpDNA haplotypes in this species, indicating one level of structure analysis would extremely underestimate its genetic component. The simulation analysis shows the number of populations and the genetic dispersion among populations are two key factors to affect the estimation of K value using the above tools. When the number of populations is more than a certain amount, K always is equal to 2, and when a simulation only includes few populations, the underestimation of K value also may occur only if these populations consist of two main types of significantly differentiated genetic components. Our results strongly support that the hierarchical STRUCTURE analysis is necessary and practicable for the species with lots of subdivisions. Frontiers Media S.A. 2022-10-07 /pmc/articles/PMC9624186/ /pubmed/36330273 http://dx.doi.org/10.3389/fpls.2022.962364 Text en Copyright © 2022 Zhang, Tang, Tian, Huang, Yang, Nan, Wang, Li, Song, Yang, Zhong and Zhang https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Plant Science
Zhang, Chaoqiang
Tang, Yiwei
Tian, Defeng
Huang, Yanyan
Yang, Guanghui
Nan, Peng
Wang, Yuguo
Li, Lingfeng
Song, Zhiping
Yang, Ji
Zhong, Yang
Zhang, Wenju
Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title_full Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title_fullStr Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title_full_unstemmed Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title_short Population genetic structure of Wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
title_sort population genetic structure of wikstroemia monnula highlights the necessity and feasibility of hierarchical analysis for a highly differentiated species
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9624186/
https://www.ncbi.nlm.nih.gov/pubmed/36330273
http://dx.doi.org/10.3389/fpls.2022.962364
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