Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China
Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by d...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/12/7/1579 |
| _version_ | 1797607225096667136 |
|---|---|
| author | Xue-Ying Wei Ting Wang Jin Zhou Wei-Yue Sun Dong-Mei Jin Jian-Ying Xiang Jian-Wen Shao Yue-Hong Yan |
| author_facet | Xue-Ying Wei Ting Wang Jin Zhou Wei-Yue Sun Dong-Mei Jin Jian-Ying Xiang Jian-Wen Shao Yue-Hong Yan |
| author_sort | Xue-Ying Wei |
| collection | DOAJ |
| description | Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of <i>Aleuritopteris grevilleoides</i>, an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified. Through the reconstruction and analysis of genetic diversity, population structure, population dynamics, evolution time, and ancestral geographical distribution, combined with geological historical events such as the formation of dry-hot valleys, this study explores the formation history, current situation, reasons for endangerment and scientifically sound measures for the protection of <i>A. grevilleoides</i>. In our study, <i>A. grevilleoides</i> had low genetic diversity (Obs_Het = 0.16, Exp_Het = 0.32, Pi = 0.33) and a high inbreeding coefficient (Fis = 0.45). The differentiation events were 0.18 Mya, 0.16 Mya, and 0.11 Mya in the <i>A. grevilleoides</i> and may have been related to the formation of terraces within the dry-hot valleys. The history of population dynamics results shows that the diversion of the river resulted in a small amount of gene flow between the two clades, accompanied by a rapid increase in the population at 0.8 Mya. After that, the effective population sizes of <i>A. grevilleoides</i> began to contract continuously due to topographic changes resulting from the continuous expansion of dry-hot valleys. In conclusion, we found that the environmental changes caused by geological events might be the main reason for the changing population size of <i>A. grevilleoides</i>. |
| first_indexed | 2024-03-11T05:27:12Z |
| format | Article |
| id | doaj.art-d8d3c5b43127412b9e82510b68fcae5b |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T05:27:12Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-d8d3c5b43127412b9e82510b68fcae5b2023-11-17T17:24:36ZengMDPI AGPlants2223-77472023-04-01127157910.3390/plants12071579Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, ChinaXue-Ying Wei0Ting Wang1Jin Zhou2Wei-Yue Sun3Dong-Mei Jin4Jian-Ying Xiang5Jian-Wen Shao6Yue-Hong Yan7College of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, ChinaCollege of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaYunnan Academy of Biodiversity, Southwest Forestry University, Kunming 650224, ChinaCollege of Life Sciences, Anhui Normal University, Wuhu 241000, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, ChinaUnderstanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of <i>Aleuritopteris grevilleoides</i>, an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified. Through the reconstruction and analysis of genetic diversity, population structure, population dynamics, evolution time, and ancestral geographical distribution, combined with geological historical events such as the formation of dry-hot valleys, this study explores the formation history, current situation, reasons for endangerment and scientifically sound measures for the protection of <i>A. grevilleoides</i>. In our study, <i>A. grevilleoides</i> had low genetic diversity (Obs_Het = 0.16, Exp_Het = 0.32, Pi = 0.33) and a high inbreeding coefficient (Fis = 0.45). The differentiation events were 0.18 Mya, 0.16 Mya, and 0.11 Mya in the <i>A. grevilleoides</i> and may have been related to the formation of terraces within the dry-hot valleys. The history of population dynamics results shows that the diversion of the river resulted in a small amount of gene flow between the two clades, accompanied by a rapid increase in the population at 0.8 Mya. After that, the effective population sizes of <i>A. grevilleoides</i> began to contract continuously due to topographic changes resulting from the continuous expansion of dry-hot valleys. In conclusion, we found that the environmental changes caused by geological events might be the main reason for the changing population size of <i>A. grevilleoides</i>.https://www.mdpi.com/2223-7747/12/7/1579GBS datapopulation geneticsdivergence timereconstruct ancestral state |
| spellingShingle | Xue-Ying Wei Ting Wang Jin Zhou Wei-Yue Sun Dong-Mei Jin Jian-Ying Xiang Jian-Wen Shao Yue-Hong Yan Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China Plants GBS data population genetics divergence time reconstruct ancestral state |
| title | Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China |
| title_full | Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China |
| title_fullStr | Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China |
| title_full_unstemmed | Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China |
| title_short | Simplified Genomic Data Revealing the Decline of <i>Aleuritopteris grevilleoides</i> Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China |
| title_sort | simplified genomic data revealing the decline of i aleuritopteris grevilleoides i population accompanied by the uplift of dry hot valley in yunnan china |
| topic | GBS data population genetics divergence time reconstruct ancestral state |
| url | https://www.mdpi.com/2223-7747/12/7/1579 |
| work_keys_str_mv | AT xueyingwei simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT tingwang simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT jinzhou simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT weiyuesun simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT dongmeijin simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT jianyingxiang simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT jianwenshao simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina AT yuehongyan simplifiedgenomicdatarevealingthedeclineofialeuritopterisgrevilleoidesipopulationaccompaniedbytheupliftofdryhotvalleyinyunnanchina |