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He S, Yuan C, Zhang P, Wang H, Luo D, Dai X. Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers. BMC PLANT BIOLOGY 2024; 24:77. [PMID: 38287273 PMCID: PMC10823706 DOI: 10.1186/s12870-024-04759-5] [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: 11/14/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND Rhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources. RESULTS In the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity. CONCLUSIONS This is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.
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Affiliation(s)
- Shuang He
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China
| | - Congjun Yuan
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China.
| | - Panli Zhang
- Guizhou Forestry School, Guiyang, 550200, Guizhou, China
| | - Haodong Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Dali Luo
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Xiaoyong Dai
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Guizhou Libo Karst Forest Ecosystem National Observation and Research Station, Libo, 558400, Guizhou, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guiyang Guizhou, 55005, China
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Ul Islam S, Ahmed Mangral Z, Tariq L, Ahmad Bhat B, Waseem Tantray W, Ahmad R, Ahmad Khuroo A, Ul Hassan Dar T. Conservation genetics of endangered Trillium govanianum Wall. ex D. Don - A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery. Gene 2023; 888:147748. [PMID: 37652171 DOI: 10.1016/j.gene.2023.147748] [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: 03/26/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Understanding the genetic diversity and population structure of pharmaceutically important endangered plant species is crucial for their conservation and sustainable use. Despite the continuous population decline in Trillium govanianum Wall. ex D. Don, a highly prized medicinal plant endemic to the Himalaya, information regarding its conservation genetics has been lacking. Here, we employed a conservation genetics approach to investigate how drastically declining populations in natural habitats impact population genetic diversity and structure of this endangered species across the Kashmir Himalaya. We used Start codon targeted (SCoT) and Simple sequence repeat (SSR) markers to assess the intra- and inter-population genetic variation in seven sites across the study region. Based on these markers, we found a very low genetic diversity in T. govanianum populations. Very low levels of observed heterozygosity (Ho = 0.000) and that expected (He = 0.064) in the populations indicate high heterozygote deficiency and high levels of inbreeding depression (FIS = 1.000). A high genetic differentiation was observed among the populations for both SCoT (Gst = 0.719) and SSR (Fst = 0.707) markers. Both the markers showed low gene flow, SCoT (Nm = 0.195) and SSR (Nm = 0.119), depicting high among-population variation than within-population variation. Analysis of molecular variance also indicated a higher genetic variation between the populations than within populations. We also observed a significant positive correlation between genetic divergence and geographical distance, indicating that genetic differentiation in T. govanianum follows a pattern of isolation by distance. Bayesian structure and cluster analysis grouped the populations according to their geographical proximity. Further, redundancy analysis (RDA) revealed the presence of one polymorphic locus for each marker with high discriminatory power. Overall, our findings reveal a very low genetic diversity, high levels of inbreeding, and high genetic differentiation among the populations; likely resulting from habitat fragmentation, population isolation, bottleneck effect, low gene flow, and predominantly asexual reproduction currently operative in the species. Finally, based on the insights gained, we discuss the potential implications of our findings in guiding species recovery and habitat rehabilitation of T. govanianum in the Himalaya with conservation lessons for elsewhere in the world.
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Affiliation(s)
- Shahid Ul Islam
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Zahid Ahmed Mangral
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Lubna Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, Amar Singh College Campus, Cluster University Srinagar, Jammu and Kashmir, India
| | - Wajahat Waseem Tantray
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Rameez Ahmad
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Anzar Ahmad Khuroo
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India.
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Nakao M, Ishikawa T, Hibino Y, Ohari Y, Taniguchi R, Takeyama T, Nakamura S, Kakino W, Ikadai H, Sasaki M. Resolution of cryptic species complexes within the genus Metagonimus (Trematoda: Heterophyidae) in Japan, with descriptions of four new species. Parasitol Int 2022; 90:102605. [DOI: 10.1016/j.parint.2022.102605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/28/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022]
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Yang L, Hisoriev H, Kurbonova P, Boboev M, Bobokalonov K, Feng Y, Li W. High genetic diversity and low differentiation of endangered Ferula tadshikorum Pimenov in Tajikistan. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Telcİoğlu M, İbİş O, Aksöyek E, Özcan S, Moradİ M, Gürkan ÖFİ, Tez C. Genetic analysis of Iranian and Turkish red foxes ( Vulpes vulpes) based on mitochondrial DNA (D-loop) sequences. ETHOL ECOL EVOL 2019. [DOI: 10.1080/03949370.2019.1639079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Murat Telcİoğlu
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Osman İbİş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Eren Aksöyek
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
| | - Mohammad Moradİ
- Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Ömer Fİkret Gürkan
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Coşkun Tez
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
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Karssene Y, Nowak C, Chammem M, Cocchiararo B, Nouira S. Genetic diversity of the genus Vulpes (Red fox and Fennec fox) in Tunisia based on mitochondrial DNA and noninvasive DNA sampling. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Liu Y, Harris AJ, Gao Q, Su X, Ren Z. A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae). Ecol Evol 2019; 9:6014-6037. [PMID: 31161016 PMCID: PMC6540705 DOI: 10.1002/ece3.5186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/08/2022] Open
Abstract
We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among-species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.
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Affiliation(s)
- Yuping Liu
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - AJ Harris
- Department of BiologyOberlin College and ConservatoryOberlinOhio
| | - Qingbo Gao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
| | - Xu Su
- Key Laboratory of Medicinal Plant and Animal Resources of the Qinghai‐Tibet Plateau in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Environments and Resources in the Qinghai‐Tibet Plateau, School of Life ScienceQinghai Normal UniversityXiningChina
| | - Zhumei Ren
- School of Life ScienceShanxi UniversityTaiyuanChina
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Mohammad N, Dahayat A, Yadav M, Shirin F, Ansari SA. Genetic diversity and population structure of Litsea glutinosa (Lour.) in Central India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:655-663. [PMID: 30042620 PMCID: PMC6041236 DOI: 10.1007/s12298-018-0556-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 03/27/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Litsea glutinosa (Lour.), one of the most dwindling forest species in central India, is represented by highly fragmented populations that have been drastically reduced for the last 40 years, promulgating government ban on its extraction. For the first time with the help of ISSR markers, we investigated genetic variation and population structure of L. glutinosa in central Indian states. A total of 84 genotypes from 10 populations covering the entire potential pockets of the species in central India were collected. The percentage of polymorphic loci ranged from 44.79% (Rewa) to 94.79% (Marvahi) with a mean value of 70.10%. The sampled populations harbored high level of genetic diversity (mean h = 0.294 and I = 0.424) that was partitioned more within populations (73%) than between populations (27%). Bayesian structure analysis revealed the existence of four admixed genetic pools in L. glutinosa. The unsustainable extraction rather than genetic factor seems to be responsible for population fragmentation and dwindling status of this species. The dioecious nature of the species advocates an in-situ conservation to be the most suited approach for which Chhindwara, Jagdalpur, Balaghat and Jabalpur populations are appropriate.
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Affiliation(s)
- Naseer Mohammad
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Ankur Dahayat
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Manorama Yadav
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Fatima Shirin
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - S. A. Ansari
- Institute of Forest Productivity, Lalgutwa, Ranchi, Jharkhand 835 303 India
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Wang H, Wei B, Xiao H. Development of 15 microsatellite markers in Acer triflorum (Aceraceae) and cross-amplification in congeneric species. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01166. [PMID: 30131908 PMCID: PMC6055552 DOI: 10.1002/aps3.1166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Acer (Aceraceae) is an important genus in forest ecosystems in the Northern Hemisphere. In China, 151 species have been reported, and approximately 61 species are endemic. Thus, China is considered to host the greatest diversity of Acer, but markers are needed to evaluate the genetic structure and genetic diversity of these populations of wild Acer species. METHODS AND RESULTS Using an enriched genomic library, we developed and characterized 15 microsatellite primers for A. triflorum, 10 of which were polymorphic. The number of alleles varied from one to nine. The levels of observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 1.000 and 0.000 to 0.826, respectively. Most primers also successfully amplified in A. ginnala, A. griseum, A. mandshuricum, A. pseudosieboldianum, A. sinopurpurascens, A. tegmentosum, and A. ukurunduense. CONCLUSIONS These markers from A. triflorum will provide an opportunity to study genetic diversity and genetic structure in the genus Acer.
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Affiliation(s)
- Hua‐Ying Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of EducationNortheast Normal UniversityChangchun130024People's Republic of China
| | - Bai‐Ying Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of EducationNortheast Normal UniversityChangchun130024People's Republic of China
| | - Hong‐Xing Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of EducationNortheast Normal UniversityChangchun130024People's Republic of China
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Peng YQ, Fan LL, Mao FY, Zhao YS, Xu R, Yin YJ, Chen X, Wan DG, Zhang XH. Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd. C R Biol 2018; 341:152-159. [PMID: 29477283 DOI: 10.1016/j.crvi.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/30/2017] [Accepted: 01/25/2018] [Indexed: 11/15/2022]
Abstract
Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants.
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Affiliation(s)
- Yan Qun Peng
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Ling Ling Fan
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Fu Ying Mao
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Yun Sheng Zhao
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China; Ministry of Education Key Laboratory of Modern Hui Chinese Medicine, 750004 Yinchuan, Ningxia, China.
| | - Rui Xu
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Yu Jie Yin
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Xin Chen
- School of Pharmacy, Chengdu University of TCM, 611137 Chengdu, Sichuan, China.
| | - De Guang Wan
- School of Pharmacy, Chengdu University of TCM, 611137 Chengdu, Sichuan, China.
| | - Xin Hui Zhang
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
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Deiner K, Hull JM, May B. Range-wide phylogeographic structure of the vernal pool fairy shrimp (Branchinecta lynchi). PLoS One 2017; 12:e0176266. [PMID: 28472088 PMCID: PMC5417434 DOI: 10.1371/journal.pone.0176266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 04/07/2017] [Indexed: 12/02/2022] Open
Abstract
Wetland habitats across the world are experiencing rapid modification and loss due to accelerating habitat conversion. Impacts to wetland habitats are particularly acute in California where up to 90% of wetland habitats have been modified or lost. Vernal pool ecosystems have therefore undergone a dramatic loss in habitat and along with them an entire endemic fauna is under threat of extinction. Recent efforts to conserve vernal pool habitat and associated species have involved restoration and creation of vernal pools as well as translocations of threatened species. The vernal pool fairy shrimp, Branchinecta lynchi, is one of several endemic and federally listed species being targeted for translocations. To guide reintroduction and conservation, detailed information on range-wide population structure and diversity is needed. We collected genetic data from two mitochondrial genes throughout the known extant range of B. lynchi to elucidate population structure and diversity of the species. We found support for phylogeographic structure throughout the range of B. lynch associated with isolated watersheds and vernal pool regions previously identified in the recovery plan for the species. The underlying mechanisms responsible for this broad pattern of genetic structure have yet to be identified. However, the evidence of only a few haplotypes being shared across the species range and patterns of isolation by distance within vernal pool regions suggests dispersal limitation may play a role. These results stress that conservation programs, at a minimum, should consider using individuals from regional populations as sources for reintroductions to maintain historical patterns of genetic differentiation. Additionally, because genetic structure is associated with vernal pool regions which are based on local hydrology and geology, translocations should proceed considering the distance between donor and recipient sites.
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Affiliation(s)
- Kristy Deiner
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Joshua M. Hull
- Sacramento Fish and Wildlife Office, U.S. Fish and Wildlife Service, Sacramento, California, United States of America
| | - Bernie May
- Department of Animal Science, University of California Davis, Davis, California, United States of America
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Schierenbeck KA. Population-level genetic variation and climate change in a biodiversity hotspot. ANNALS OF BOTANY 2017; 119:215-228. [PMID: 28069633 PMCID: PMC5321061 DOI: 10.1093/aob/mcw214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 05/06/2023]
Abstract
INTRODUCTION Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. FACTORS INFLUENCING THE DISTRIBUTION OF GENETIC VARIATION Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant-insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. REGIONAL PRIORITIES AND EXAMPLES A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. CONCLUSIONS, SOLUTIONS AND RECOMMENDATIONS The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California's plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species.
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Affiliation(s)
- Kristina A Schierenbeck
- California State University, Chico Department of Biological Sciences, Chico, CA 95929-0515, USA
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Li CY, Chiang TY, Chiang YC, Hsu HM, Ge XJ, Huang CC, Chen CT, Hung KH. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing. Molecules 2016; 21:67. [PMID: 26751439 PMCID: PMC6273106 DOI: 10.3390/molecules21010067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1-4, the polymorphism information content ranged from 0.000-0.692, and the observed and expected heterozygosity were 0.000-1.000 and 0.080-0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.
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Affiliation(s)
- Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou 552, Taiwan.
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Mei Hsu
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Xue-Jun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | | | - Chaur-Tzuhn Chen
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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15
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Wu FQ, Shen SK, Zhang XJ, Wang YH, Sun WB. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron. AOB PLANTS 2014; 7:plu082. [PMID: 25477251 PMCID: PMC4294443 DOI: 10.1093/aobpla/plu082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/18/2014] [Indexed: 05/29/2023]
Abstract
Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction.
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Affiliation(s)
- Fu Qin Wu
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Shi Kang Shen
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Xin Jun Zhang
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Yue Hua Wang
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Wei Bang Sun
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, The People's Republic of China
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16
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Range-wide and local drivers of genetic structure in an endangered California vernal pool endemic crustacean. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0405-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Genetic diversity and structure in the annual vernal pool endemic Limnanthes vinculans Ornduff (Limnanthaceae): implications of breeding system and restoration practices. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0380-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Wang Y, Fu D, Xia J. The genetic diversity of the noble scallop (Chlamys nobilis, Reeve 1852) in China assessed using five microsatellite markers. Mar Genomics 2012; 9:63-7. [PMID: 23904061 DOI: 10.1016/j.margen.2012.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 05/31/2012] [Accepted: 06/06/2012] [Indexed: 11/18/2022]
Abstract
Five highly variable microsatellite loci were used to investigate the genetic diversity and population structure of the noble scallop Chlamys nobilis, in the South China Sea. A total of 200 individual scallops from 4 populations were genotyped. All of the 5 microsatellite loci screened in this study showed polymorphism. A total of 32 different alleles were observed over all loci. The number of alleles per locus ranged from 3 to 12. The average allelic number of these polymorphic markers was 6.4. The averages of observed (Ho) and expected heterozygosity (He) ranged from 0.07 to 0.32 and from 0.119 to 0.459, respectively. A highly significant deviation from the Hardy-Weinberg Law, owing primarily to heterozygote deficiency, was found in all populations studied. The Nanao population exhibited more genetic diversity than the other three populations in terms of allele richness and observed and expected heterozygosity.
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Affiliation(s)
- Yanhong Wang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, CAS, Guangdong key laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 Xingang West Road, Guangzhou, 510301, China.
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