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Abhari N, Colijn C, Mooers A, Tupper P. Capturing diversity: Split systems and circular approximations for conservation. J Theor Biol 2024; 578:111689. [PMID: 38061489 DOI: 10.1016/j.jtbi.2023.111689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/29/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023]
Abstract
We investigated the implications of employing a circular approximation of split systems in the calculation of maximum diversity subsets of a set of taxa in a conservation biology context where diversity is measured using Split System Diversity (SSD). We conducted a comparative analysis between the maximum SSD score and the maximum SSD set(s) of size k, efficiently determined using a circular approximation, and the true results obtained through brute-force search based on the original data. Through experimentation on simulated datasets and SNP data across 50 Atlantic Salmon populations, our findings demonstrate that employing a circular approximation can lead to the generation of an incorrect max-SSD set(s). We built a graph-based split system whose circular approximation led to a max-SSD set of size k=4 that was less than the true max-SSD set by 17.6%. This discrepancy increased to 25% for k=11 when we used a hypergraph-based split system. The same comparison on the Atlantic salmon dataset revealed a mere 1% difference. However, noteworthy disparities emerged in the population composition between the two sets. These findings underscore the importance of assessing the suitability of circular approximations in conservation biology systems. Caution is advised when relying solely on circular approximations to determine sets of maximum diversity, and careful consideration of the data characteristics is crucial for accurate results in conservation biology applications.
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Affiliation(s)
- Niloufar Abhari
- Department of Mathematics, Simon Fraser University, BC, Canada; Department of Biological Sciences, Simon Fraser University, BC, Canada.
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, BC, Canada
| | - Arne Mooers
- Department of Biological Sciences, Simon Fraser University, BC, Canada
| | - Paul Tupper
- Department of Mathematics, Simon Fraser University, BC, Canada
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2
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Zhu X, Zou R, Qin H, Chai S, Tang J, Li Y, Wei X. Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis. Evol Appl 2023; 16:1519-1530. [PMID: 37752963 PMCID: PMC10519411 DOI: 10.1111/eva.13584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 09/28/2023] Open
Abstract
Whether ex situ populations constructed in the limited nursery resources of botanical gardens can preserve enough genetic diversity of endangered plants in the wild remains uncertain. Here, a case study was conducted with Camellia tunghinensis, which is one of the species with the lowest natural distribution area in the sect. Chrysantha (golden camellia) of the family Theaceae. We investigated the genetic diversity and population structure of 229 samples from wild and ex situ populations using genotyping by sequencing (GBS). Core germplasm was constructed from these samples. The results showed that wild C. tunghinensis exhibited high genetic diversity, with observed heterozygosity of 0.257-0.293 and expected heterozygosity of 0.247-0.262. Compared with wild populations, the genetic diversity of ex situ populations established by transplanting wild seedlings was close to or even higher. However, the genetic diversity of those established by seed or cuttings of a few superior trees was lower. The Admixture analysis revealed that the structure of the ex situ populations derived from seeds and cuttings was relatively simple compared with the ex situ populations derived from transplanted wild seedlings and wild populations. These results suggested that direct transplanting of wild seedlings was more conducive to preserving the genetic diversity of endangered plants in the wild. In addition, wild populations demonstrated a small differentiation (mean F ST = 0.044) among themselves, possibly due to long-term and frequent gene flow between the wild populations. In contrast, moderate differentiation (mean F ST > 0.05) was detected among ex situ populations and between ex situ and wild populations. This may be the combined result of the absence of gene flow pathways and strong selection pressure in various ex situ environments. Finally, 77 core germplasms were extracted from 229, likely representing the genetic diversity of C. tunghinensis. This study provides future strategies for the ex situ conservation and management of the golden camellia species and other rare and endangered plants.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Huizhen Qin
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Yingying Li
- Institute of Forestry Economic Science, Guangdong Academy of ForestryGuangzhouChina
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable UtilizationGuangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
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3
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Zhu X, Tang J, Jiang H, Yang Y, Chen Z, Zou R, Xu A, Luo Y, Deng Z, Wei X, Chai S. Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum. BMC PLANT BIOLOGY 2023; 23:317. [PMID: 37316828 DOI: 10.1186/s12870-023-04285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs. METHODS In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level. RESULTS The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization. CONCLUSIONS Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Haidu Jiang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Yishan Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Zongyou Chen
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Aizhu Xu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, China
| | - Yajin Luo
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Zhenhai Deng
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
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Zhu X, Zou R, Tang J, Deng L, Wei X. Genetic diversity variation during the natural regeneration of Vatica guangxiensis, an endangered tree species with extremely small populations. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
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Jing Y, Bian L, Zhang X, Zhao B, Zheng R, Su S, Ye D, Zheng X, El-Kassaby YA, Shi J. Genetic diversity and structure of the 4 th cycle breeding population of Chinese fir ( Cunninghamia lanceolata (lamb.) hook). FRONTIERS IN PLANT SCIENCE 2023; 14:1106615. [PMID: 36778690 PMCID: PMC9911867 DOI: 10.3389/fpls.2023.1106615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi ) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.
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Affiliation(s)
- Yonglian Jing
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Bian
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuefeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Benwen Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Shunde Su
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Daiquan Ye
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Xueyan Zheng
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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6
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Zhu X, Liang H, Jiang H, Kang M, Wei X, Deng L, Shi Y. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. FRONTIERS IN PLANT SCIENCE 2022; 13:999964. [PMID: 36388513 PMCID: PMC9647136 DOI: 10.3389/fpls.2022.999964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hui Liang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Haolong Jiang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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7
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Figueroa‐Corona L, Moreno‐Letelier A, Ortega‐Del Vecchyo D, Peláez P, Gernandt DS, Eguiarte LE, Wegrzyn J, Piñero D. Changes in demography and geographic distribution in the weeping pinyon pine ( Pinus pinceana) during the Pleistocene. Ecol Evol 2022; 12:e9369. [PMID: 36225821 PMCID: PMC9534753 DOI: 10.1002/ece3.9369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying ecological communities. Here, we try to identify the processes underlying the demographic history of P. pinceana and characterize its genetic diversity using 3100 SNPs from genotyping by sequencing 90 adult individuals from 10 natural populations covering the species' entire geographic distribution. We inferred its population history and contrasted possible demographic scenarios of divergence that modeled the genetic diversity present in this restricted pinyon pine; in support, the past distribution was reconstructed using climate from the Last Glacial Maximum (LGM, 22 kya). We inferred that P. pinceana diverged into two lineages ~2.49 Ma (95% CI 3.28-1.62), colonizing two regions: the Sierra Madre Oriental (SMO) and the Chihuahuan Desert (ChD). Our results of population genomic analyses reveal the presence of heterozygous SNPs in all populations. In addition, low migration rates across regions are probably related to glacial-interglacial cycles, followed by the gradual aridification of the Chihuahuan Desert during the Holocene.
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Affiliation(s)
- Laura Figueroa‐Corona
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | | | - Diego Ortega‐Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoJuriquillaMexico
| | - Pablo Peláez
- Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavacaMorelosMexico
| | - David S. Gernandt
- Departamento de BotánicaInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Daniel Piñero
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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8
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Li L, Ou W, Wang Y, Peng J, Wang D, Xu S. Comparison of genetic diversity between ancient and common populations of Docynia delavayi (Franch.) Schneid. Gene X 2022; 829:146498. [PMID: 35447250 DOI: 10.1016/j.gene.2022.146498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/28/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022] Open
Abstract
Docynia delavayi (Franch.) Schneid. (D. delavayi), is a wild fruit tree which combines edible, medicinal, ecological and ornamental uses. In this study, ancient and common populations of D. delavayi were examined for genetic diversity and structure using SSR markers. As a result, a total of 136 alleles were detected at 18 SSR loci, with the mean of 7.56 alleles. The value of Na, Ne, I, He and Nm of the ancient populations were lower than those of the common populations except for Ho and Fst. It indicates that the genetic diversity of the common populations is higher than that in ancient populations. The genetic differences between ancient populations were slightly greater than those between common populations, which demonstrated less gene flow between ancient populations. According to the analysis of molecular variance (AMOVA), the genetic variation within the common population was greater than that in the ancient population, indicating that there was a higher genetic diversity within the common population. Also, the clustering heatmap results are partially consistent with the principal coordinate analysis (PCoA) results. Moreover, the mantel test showed an extremely significant correlation between genetic and geography distance (r = 0.214, p < 0.0001). Based on this work, we proposed strategies for protecting, which offers a theoretical basis for their effective utilization and conservation of D. delavayi ancient tree resources.
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Affiliation(s)
- Lianxing Li
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenli Ou
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Yuchang Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100083, China
| | - Dawei Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan 650224, China.
| | - Shuo Xu
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan 650224, China
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9
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Sousa F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Pinto Ricardo C, Batista D, Paulo OS. Population structure in Quercus suber L. revealed by nuclear microsatellite markers. PeerJ 2022; 10:e13565. [PMID: 35729909 PMCID: PMC9206845 DOI: 10.7717/peerj.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.
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Affiliation(s)
- Filipe Sousa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Joana Costa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,RAIZ, Herdade de Espirra, Pegões, Portugal
| | - Carla Ribeiro
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Marta Varandas
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Francisco Pina-Martins
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Polytechnic Institute of Setúbal, ESTBarreiro, Setúbal, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Maria Glushkova
- Forest Research Institute of B.A.S., Department of Forest Genetics, Physiology and Plantations, Sofia, Bulgaria
| | - Célia Miguel
- Faculdade de Ciências, Universidade de Lisboa, Biosystems & Integrative Sciences Institute, Lisboa, Portugal,iBET, Oeiras, Portugal
| | - Maria Manuela Veloso
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Margarida Oliveira
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cândido Pinto Ricardo
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Dora Batista
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Instituto Superior de Agronomia, Universidade de Lisboa, LEAF—Linking Landscape, Environment, Agriculture and Food (LEAF), Lisboa, Portugal
| | - Octávio S. Paulo
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
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10
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Tsumura Y. Genetic structure and local adaptation in natural forests of
Cryptomeria japonica
. Ecol Res 2022. [DOI: 10.1111/1440-1703.12320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba Ibaraki Japan
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11
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Wang M, Yuan M, Li X, Wu X, Ueno S, Cai M, Tsumura Y, Wen Y. Development and characterization of novel chloroplast microsatellite markers for Cryptomeria japonica var. sinensis (Cupressaceae) and their cross-species amplification. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00946-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Chen S, Guo W, Chen Z, Liao W, Fan Q. Strong Genetic Structure Observed in Primulina danxiaensis, a Small Herb Endemic to Mount Danxia With Extremely Small Populations. Front Genet 2021; 12:722149. [PMID: 34691147 PMCID: PMC8526925 DOI: 10.3389/fgene.2021.722149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Danxia landform occurring sporadically in southern China is a unique type of petrographic geomorphology. It has nurtured about 400 rare or threatened plant and animal species, whose diversity, endemism, and conservation have called increasing scientific and public attentions. Among them, Primulina danxiaensis (W. B. Liao, S. S. Lin, and R. J. Shen) W. B. Liao and K. F. Chung is a tiny perennial grass species recorded only in Mount Danxia, a natural World Heritage Site as part of China’s Danxia. In this study, restriction site-associated DNA sequencing (RAD-seq) was performed to investigate genetic diversity among these 12 populations of P. danxiaensis. A total of 432,041 variant sites were detected in 84,779 loci across 94 samples. The expected heterozygosity (HE) ranged from 0.017 to 0.139. Bottleneck signals were detected in most populations, Tajima’s D tests showed that most loci could be under recent positive selection, and one of the six positively selected loci identified by BayeScan was annotated as tRNAGlu, which may contribute to the species’ adaptation to shady environment. STRUCTURE analysis and phylogenetic tree showed that the 12 populations of P. danxiaensis could be divided into four gene pools (clades) corresponding to their geographic locations, and significant correlation was observed between genetic and geographic distances. Our study demonstrated that P. danxiaensis maintained a middle level of genetic diversity and strong population structure; geographic distance could be an important factor limiting gene flow among populations of P. danxiaensis, which were only sporadically recorded in Mount Danxia.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zaixiong Chen
- Administrative Commission of Danxiashan National Park, Shaoguan, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Lu Y, Ma Q, Chen C, Xu X, Zhang D. Effects of arbuscular mycorrhizal fungi on the nitrogen distribution in endangered Torreya jackii under nitrogen limitation. PLANTA 2021; 254:53. [PMID: 34402996 DOI: 10.1007/s00425-021-03704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhizal fungi regulated the distribution of nitrogen in the leaves, thereby facilitating the adaptation of the endangered plant Torreya jackii to a low-nitrogen environment. Rhizophagus irregularis was inoculated into sterilized soil to investigate its impact on the distribution ratio of leaf nitrogen in cell wall proteins, cell membrane proteins, water-soluble proteins, and photosynthetic systems which includes the carboxylation system (PC), energy metabolism (PB), and light-harvesting system in the endangered species Torreya jackii. The results showed that R. irregularis reduced the specific leaf weight and the distribution ratio of nitrogen in cell wall proteins in the leaves of T. jackii, whereas it enhanced the distribution ratio of nitrogen in cell membrane proteins and water-soluble proteins. R. irregularis enabled more nitrogen uptake for growth by decreasing the distribution of nitrogen to the structural substances. At low-nitrogen levels, inoculation with R. irregularis improved the plant height (18.78 ~ 36.04%), shoot dry weight (50.53 ~ 64.33%), total dry weight (42.86 ~ 52.82%), maximal net photosynthetic rate (Pmax) (16.83 ~ 20.11%), photosynthetic nitrogen use efficiency (PNUE) (40.01 ~ 43.14%), PC (33.56 ~ 38.59%) and PB (29.08 ~ 34.02%). However, it did not substantially affect the leaf nitrogen content per unit area or the leaf nitrogen content per unit mass. Moreover, Pmax exhibited a significant positive correlation with PC and PB, and all three parameters showed a significant positive correlation with the PNUE, thereby revealing that R. irregularis increased the photosynthetic capacity and PNUE of T. jackii through boosting PC and PB.
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Affiliation(s)
- Yin Lu
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China.
| | - Qing Ma
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Chuan Chen
- West Lake Scenic Spot Management Committee, Hangzhou, 310007, China
| | - Xiaolu Xu
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Deyong Zhang
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
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14
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Zheng Z, Li Y, Li M, Li G, Du X, Hongyin H, Yin M, Lu Z, Zhang X, Shrestha N, Liu J, Yang Y. Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species. FRONTIERS IN PLANT SCIENCE 2021; 12:581704. [PMID: 33643339 PMCID: PMC7902934 DOI: 10.3389/fpls.2021.581704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.
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Affiliation(s)
- Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guiting Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hu Hongyin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
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15
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Abstract
Forest tree improvement has mainly been implemented to enhance the productivity of artificial forests [...]
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