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Chen WH, Ko YZ, Chang HC, Chang CS, Hung KH, Shih HC, Ju LP, Shiao MS, Chiang YC. Comparative chemical profiling of leaf essential oils from Cinnamomum kanehirae and related species using steam distillation and solvent extraction: Implications for plant-based classification. Heliyon 2024; 10:e30628. [PMID: 38726167 PMCID: PMC11079393 DOI: 10.1016/j.heliyon.2024.e30628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Cinnamomum kanehirae Hayata, belonging to Lauraceae family, is an indigenous and endangered species of considerable economic importance in Taiwan. It plays a crucial role as the host for the economically valuable saprotrophic fungus, Taiwanofungus camphorates. However, accurate species identification poses a challenge due to the similarity in morphological features and frequent natural hybridization with closely related species. Acquiring high-quality and pure leaf oils becomes imperative for precise species identification and producing superior goods. In this study, our objective was to establish methodologies for analyzing the chemical composition of leaf essential oils and subsequently apply this knowledge to differentiate among three Cinnamomum species. Gas chromatography-mass spectrometry (GC/MS) was employed to scrutinize the chemical makeup of leaf essential oils from three closely related species: C. kanehirae, C. micranthum, and C. camphora. We utilized Steam Distillation (SD) and steam distillation-solvent extraction (SDSE) methods, with the SDSE-Hexane approach chosen for optimization, enhancing extraction efficiency and ensuring essential oil purity. Through the SDSE-Hexane method, we identified seventy-four compounds distributed across three major classes: monoterpenes hydrocarbons (0.0-7.0 %), oxygenated monoterpenes (3.8-90.9 %), sesquiterpenes hydrocarbons (0.0-28.3 %), and oxygenated sesquiterpenes (1.6-88.1 %). Our findings indicated the presence of more than one chemotype in both C. kanehirae and C. camphora, whereas no specific chemotype could be discerned in C. micranthum. Furthermore, clustering based on chemotypes allowed for the differentiation of samples from the three species. Notably, we demonstrated that the chemical compositions of grafted C. kanehirae remained largely unaffected by the rootstock. Conversely, natural hybrids between C. kanehirae and C. camphora exhibited profiles more closely aligned with C. kanehirae. The optimized extraction method and the chemotype-based classification system established in this study present valuable tools for essential oil preparation, species identification, and further exploration into the genetic variation of Cinnamomum.
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Affiliation(s)
- Wen-Hui Chen
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
- Pingtung County Central Laboratory, No.272, Je-Yu Road, Pingtung, 900, Taiwan
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Hsiu-Chun Chang
- Pingtung County Central Laboratory, No.272, Je-Yu Road, Pingtung, 900, Taiwan
| | - Chui-Shiang Chang
- Pingtung County Central Laboratory, No.272, Je-Yu Road, Pingtung, 900, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pintung, 912, Taiwan
| | - Huie-Chuan Shih
- Department of Nursing, Meiho University, Pingtung, 912, Taiwan
| | - Li-Ping Ju
- Forest Rrotection Division, Taiwan Forestry Research Institute, Taipei, 100, Taiwan
| | - Meng-Shin Shiao
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- The Multidisciplinary and Data Science Research Center(MDSRC), National Sun Yat-sen University, Kaohsiung, 804, Taiwan
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Zhao M, Ran X, Bai Y, Ma Z, Gao J, Xing D, Li C, Guo X, Jian X, Liu W, Liao Y, Chen K, Zhang H, Zhao T. Genetic diversity of Aedes aegypti and Aedes albopictus from cohabiting fields in Hainan Island and the Leizhou Peninsula, China. Parasit Vectors 2023; 16:319. [PMID: 37684698 PMCID: PMC10486073 DOI: 10.1186/s13071-023-05936-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Aedes aegypti and Ae. albopictus are important human arbovirus vectors that can spread arboviral diseases such as yellow fever, dengue, chikungunya and Zika. These two mosquito species coexist on Hainan Island and the Leizhou Peninsula in China. Over the past 40 years, the distribution of Ae. albopictus in these areas has gradually expanded, while Ae. aegypti has declined sharply. Monitoring their genetic diversity and diffusion could help to explain the genetic influence behind this phenomenon and became key to controlling the epidemic of arboviruses. METHODS To better understand the genetic diversity and differentiation of these two mosquitoes, the possible cohabiting areas on Hainan Island and the Leizhou Peninsula were searched between July and October 2021, and five populations were collected. Respectively nine and 11 microsatellite loci were used for population genetic analysis of Ae. aegypti and Ae. albopictus. In addition, the mitochondrial coxI gene was also selected for analysis of both mosquito species. RESULTS The results showed that the mean diversity index (PIC and SI values) of Ae. albopictus (mean PIC = 0.754 and SI = 1.698) was higher than that of Ae. aegypti (mean PIC = 0.624 and SI = 1.264). The same results were also observed for the coxI gene: the genetic diversity of all populations of Ae. albopictus was higher than that of Ae. aegypti (total H = 45 and Hd = 0.89958 vs. total H = 23 and Hd = 0.76495, respectively). UPGMA dendrogram, DAPC and STRUCTURE analyses showed that Ae. aegypti populations were divided into three clusters and Ae. albopictus populations into two. The Mantel test indicated a significant positive correlation between genetic distance and geographic distance for the Ae. aegypti populations (R2 = 0.0611, P = 0.001), but the correlation was not significant for Ae. albopictus populations (R2 = 0.0011, P = 0.250). CONCLUSIONS The population genetic diversity of Ae. albopictus in Hainan Island and the Leizhou Peninsula was higher than that of Ae. aegypti. In terms of future vector control, the most important and effective measure was to control the spread of Ae. albopictus and monitor the population genetic dynamics of Ae. aegypti on Hainan Island and the Leizhou Peninsula, which could theoretically support the further elimination of Ae. aegypti in China.
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Affiliation(s)
- Minghui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Xin Ran
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Yu Bai
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Zu Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian Gao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoxia Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xianyi Jian
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Liu
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Yun Liao
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Kan Chen
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Hengduan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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Xie B, Lai B, Chen L, Wei S, Tang S. Phylogeographic analysis of Siraitia grosvenorii in subtropical China provides insights into the origin of cultivated monk fruit and conservation of genetic resources. Ecol Evol 2023; 13:e10181. [PMID: 37304364 PMCID: PMC10256620 DOI: 10.1002/ece3.10181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/11/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
Siraitia grosvenorii, an economically important plant species with high medicinal value, is endemic to subtropical China. To determine the population structure and origin of cultivated S. grosvenorii, we examined the variation in three chloroplast DNA regions (trnR-atpA, trnH-psbA, trnL-trnF) and two orthologous nuclear genes (CHS and EDL2) of S. grosvenorii in 130 wild individuals (selected from 13 wild populations across its natural distribution range) and 21 cultivated individuals using a phylogeographic approach. The results showed three distinct chloroplast lineages, which were restricted to different mountain ranges, and strong plastid phylogeographic structure. Our findings suggest that S. grosvenorii likely experienced ancient range expansion and survived in multiple refuges in subtropical China during glacial periods, resulting in population fragmentation in different mountainous areas. Our results also demonstrated that wild populations in Guilin (Guangxi, China) share the same gene pool as cultivated S. grosvenorii, suggesting that current cultivars were collected directly from local wild resources, consistent with the principles of "nearby domestication." The results of this study provide insights into improving the efficiency of S. grosvenorii breeding using a genetic approach and outline measures for the conservation of its genetic resources.
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Affiliation(s)
- Bingbin Xie
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Bowen Lai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Liping Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Sujuan Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life ScienceGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life ScienceGuangxi Normal UniversityGuilinChina
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Hsien Li P, Shih YJ, Lu WC, Huang PH, Wang CCR. Antioxidant, antibacterial, anti-inflammatory, and anticancer properties of Cinnamomum kanehirae Hayata leaves extracts. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Singh B, Nathawat S, Avtar Sharma R. Antimicrobial potential of Indian Cinnamomum species. Saudi J Biol Sci 2023; 30:103549. [PMID: 36619679 PMCID: PMC9813755 DOI: 10.1016/j.sjbs.2022.103549] [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: 08/07/2022] [Revised: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022] Open
Abstract
Cinnamomum is the largest genus of Lauraceae family and has been used as spices, food, and food additives by the people. Total 15 Cinnamomum species are distributed in different parts of Indian sub-continent. Different parts (leaves, stem bark, stem wood, roots, flowers, and fruits) of these species were shade-dried and used for the determination of essential oils. A total of 19 essential oils were identified and quantified from the different parts of (leaf, stem bark, stem wood, root, flower, and fruit) of 15 Cinnamomum species. The stem bark of C. altissimum was rich in the presence of essential oils (52.2 %) whereas minimum levels of essential oils were recorded in roots (17.9 %). The γ-terpinene (11.1 %) was reported as the major component essential oil in C. subavenium flowers. Methanol extract of C. camphora stem wood showed stronger lowest minimum inhibitory concentration against S. aureus (25 ± 0.01 μg/ml), H. pylori (29 ± 0.05 μg/ml), B. subtilis (31 ± 0.03 μg/ml), E. faecalis (33 ± 0.01 μg/ml), C. albicans (38 ± 0.03 μg/ml) when compared to amoxycillin (S. aureus 56 ± 0.05 μg/ml; B. subtilis 27 ± 0.04 μg/ml, E. faecalis 22 ± 0.01 μg/ml), streptomycin (H. pylori 38 ± 0.02 μg/ml) and fluconazole (C. albicans 56 ± 0.01 μg/ml). Methanolic extract of C. camphora stem wood demonstrated maximum antimicrobial activity against S. aureus, H. pylori, B. subtilis, E. faecalis and C. albicans. The essential oil of C. altissimum stem bark displayed significant lowest MIC against S. aureus (21 ± 0.03 μg/ml), E. coli (22 ± 0.03 μg/ml), E. cloacae (37 ± 0.06 μg/ml), L. monocytogenes (47 ± 0.08 μg/ml), and P. chrysogenum (101 ± 0.07 μg/ml) when compared to amoxycillin (E. coli 18 ± 0.01 μg/ml, E. cloacae 21 ± 0.05 μg/ml, L. monocytogenes 31 ± 0.03 μg/ml), and fluconazole (P. chrysogenum 101 ± 0.07 μg/ml). The essential oil of C. altissimum stem bark displayed maximum antimicrobial activity against S. aureus, E. coli, E. cloacae, L. monocytogenes, and P. chrysogenum. Cinnamomum essential oils may be used as an alternative source of antibacterial and antifungal compounds in the treatment of various types of infections.
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Affiliation(s)
- Bharat Singh
- Amity of Biotechnology, Amity University Rajasthan, Jaipur 303 002, India,Corresponding author at: Amity of Biotechnology, Amity University Rajasthan, Jaipur 303 002, India.
| | - Sheenu Nathawat
- Amity of Biotechnology, Amity University Rajasthan, Jaipur 303 002, India
| | - Ram Avtar Sharma
- Department of Botany, University of Rajasthan, Jaipur 302 004, India
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Genetic Diversity of Two Globally Invasive Snails in Asia and Americas in Relation with Agricultural Habitats and Climate Factors. DIVERSITY 2022. [DOI: 10.3390/d14121069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The successful establishment of invasive populations is closely linked to environmental factors. It is unclear whether coexisting species in the native area follow the same genetic pattern in the invaded continents under the local climate factors. Two coexisting morphologically similar snails (Pomacea canaliculata and P. maculata), native to tropical and sub-tropical South America, have become invasive species for agriculture production and wetland conservation across five continents over 40 years. We analyzed the correlation between the genetic diversity of the two snails and the climate factors or habitat changes. Based on the 962 sequences from the invaded continents and South America, the nucleotide diversity in the agricultural habitat was low for P. canaliculata, whereas it was high for P. maculata, compared with that in the non-agricultural habitat. The two snails showed a divided population structure among the five continents. The P. canaliculata population in the invaded continents has remained stable, whereas the P. maculata population expanded suddenly. Seven main haplotype networks and two ancestral haplotypes (Pc3, Pm1) were found in the P. canaliculata and P. maculata populations. The haplotypes of the two snails were related to local climate factors. The overall fixation index of P. canaliculata and P. maculata was 0.2657 and 0.3097 between the invaded continents and South America. The population expansion of the two snails fitted the isolation-by-distance model. We discovered nine new sequences from the sampling locations. Overall, the genetic diversity and genetic differentiation of the two invasive snails were closely related to geographic separation, agricultural habitat, and climate factors.
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Genetic diversity, genetic structure, and demographic history of Cinnamomum chago, a plant species with extremely small populations in China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae). Sci Rep 2020; 10:16658. [PMID: 33028947 PMCID: PMC7542430 DOI: 10.1038/s41598-020-73748-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/22/2020] [Indexed: 11/23/2022] Open
Abstract
Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.
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Wu CC, Chang SH, Tung CW, Ho CK, Gogorcena Y, Chu FH. Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing. Sci Rep 2020; 10:15995. [PMID: 32994441 PMCID: PMC7525239 DOI: 10.1038/s41598-020-72775-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
Cinnamomum kanehirae Hayata and C. camphora (L.) Presl are important tree species in eastern Asia. The wood of C. kanehirae is in increasing demand for culturing Antrodia cinnamomea, a medicinal fungus that naturally grows inside the trunk of C. kanehirae. Putative hybrids between C. kanehirae and C. camphora were previously reported but with no scientific evidence, leading to confusion or misplanting. First, to identify the female parent of putative hybrids, the maternal inheritance InDel (insertion/deletion) markers were developed by using low-coverage sequencing. SNPs were developed by using genotyping-by-sequencing (GBS) approach in C. kanehirae, C. camphora and putative hybrids. The results indicated that the female parent of the studied hybrids was C. camphora. Eight hundred and forty of the 529,006 high-density SNPs were selected and used for analysis. Hybrids were classified as F1 (C. kanehirae × C. camphora), F2 and backcrosses. Hybridization has occurred in the human-developed area of eastern and southwestern Taiwan, and the introgression was bidirectional. For producing pure wood, buffering zones should be established around seed orchards to avoid cross-species pollination and to preserve the genetic purity of C. kanehirae. The DNA markers developed in this study will also be valuable for further wood identification, breeding and evolutionary research.
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Affiliation(s)
- Chia-Chen Wu
- Silviculture Division, Taiwan Forestry Research Institute, Council of Agriculture, Executive Yuan, Taipei, Taiwan.,School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Shu-Hwa Chang
- Silviculture Division, Taiwan Forestry Research Institute, Council of Agriculture, Executive Yuan, Taipei, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Cheng-Kuen Ho
- Silviculture Division, Taiwan Forestry Research Institute, Council of Agriculture, Executive Yuan, Taipei, Taiwan
| | - Yolanda Gogorcena
- Laboratory of Genomics, Genetics and Breeding of Fruit Trees and Grapevines, Experimental Station of Aula Dei-CSIC, Zaragoza, Spain
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
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Wang X, Liu XQ, Ko YZ, Jin XL, Sun JH, Zhao ZY, Yuan QJ, Chiang YC, Huang LQ. Genetic Diversity and Phylogeography of the Important Medical Herb, Cultivated Huang-Lian Populations, and the Wild Relatives Coptis Species in China. Front Genet 2020; 11:708. [PMID: 32719720 PMCID: PMC7350934 DOI: 10.3389/fgene.2020.00708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/10/2020] [Indexed: 12/04/2022] Open
Abstract
Huang-lian (Coptis plants in China) are essential medicinal plants in China, C. chinensis var. chinensis and C. deltoidea have been domesticated and cultivated for 700 years. In this study, the genetic diversity patterns and biogeographical information of cultivated Huang-lian and their wild relatives Coptis species were assessed using three plastids DNA regions. A total of 186 individuals from twenty-seven populations representing two species of cultivated Huang-lian and four species of wild relatives were collected and analyzed. Twenty-four haplotypes of six species were identified when three plastid spacers were combined. Historical biogeography inference revealed multiple dispersal events in the groups of cultivated Huang-lian and C. omeiensis. This evidence can infer that large initial population size and interbreeding with co-existing wild relatives in expanding new planting areas might be the main reason for maintaining the high genetic diversity of cultivated Huang-lian. Nevertheless, the multimodal curve of mismatch analysis and positive or negative differed among species and populations by neutrality tests indicated some groups of cultivated Huang-lian experienced genetic bottlenecks. Phylogeny analysis (NJ, MP, BI) showed that cultivated Huang-lian and C. omeiensis were clustered into a monophyletic group while C. chinensis var. brevisepala was paraphyletic, having earlier divergence time from C. chinensis var. chinensis (7.6 Ma) than C. omeiensis. Parsimony network demonstrated that C. deltoidea had more shared haplotypes with C. omeiensis than C. chinensis var. chinensis, and other haplotypes of C. deltoidea and C. omeiensis had less mutation steps than that of C. chinensis var. chinensis and C. omeiensis. This evidence suggests that C. omeiensis has a closer relationship with cultivated Huang-lian and might be a potential wild relative to C. deltoidea. The results reported here provide the baseline data for preserving genetic resources of Huang-lian and also evaluating the genetic impacts of long-term cultivation on medicinal plants, which could be instructive to future cultivation projects of traditional Chinese medicinal plants.
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Affiliation(s)
- Xin Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiao-Quang Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Xiao-Lei Jin
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Jia-Hui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhen-Yu Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qing-Jun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Lu-Qi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Md Naim D, Kamal NZM, Mahboob S. Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I. Saudi J Biol Sci 2020; 27:953-967. [PMID: 32127775 PMCID: PMC7042630 DOI: 10.1016/j.sjbs.2020.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 11/24/2022] Open
Abstract
The population genetics study is crucial as it helps in understanding the epidemiological aspects of dengue and help improving a vector control measures. This research aims to investigate the population genetics structure of two common species of Aedes mosquitoes in Penang; Aedes aegypti and Aedes albopictus using Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) marker. Molecular investigations were derived from 440 bp and 418 bp mtDNA COI on 125 and 334 larvae of Aedes aegypti and Aedes albopictus respectively, from 32 locations in Penang. All samples were employed in the BLASTn for species identification. The haplotype diversity, nucleotide diversity, neutrality test and mismatch distribution analysis were conducted in DnaSP version 5.10.1. AMOVA analysis was conducted in ARLEQUIN version 3.5 and the phylogenetic reconstructions based on maximum likelihood (ML) and neighbor-joining (NJ) methods were implemented in MEGA X. The relationships among haplotypes were further tested by creating a minimum spanning tree using Network version 4.6.1. All samples were genetically identified and clustered into six distinct species. Among the species, Ae. albopictus was the most abundant (67.2%), followed by Ae. aegypti (25.2%) and the rest were counted for Culex sp. and Toxorhynchites sp. Both Ae. aegypti and Ae. albopictus show low nucleotide diversity (π) and high haplotype diversity (h), while the neutrality test shows a negative value in most of the population for both species. There are a total of 39 and 64 haplotypes recorded for Ae. aegypti and Ae. albopictus respectively. AMOVA analysis revealed that most of the variation occurred within population for both species. Mismatch distribution analysis showed bimodal characteristic of population differentiation for Ae. aegypti but Ae. albopictus showed unimodal characteristics of population differentiation. Genetic distance based on Tamura-Nei parameter showed low genetic divergent within population and high genetic divergent among population for both species. The maximum likelihood tree showed no obvious pattern of population genetic structure for both Ae. aegypti and Ae. albopictus from Penang and a moderate to high bootstrap values has supported this conclusion. The minimum spanning network for Ae. aegypti and Ae. albopictus showed five and three dominant haplotypes respectively, which indicates a mixture of haplotypes from the regions analysed. This study revealed that there is no population genetic structure exhibited by both Ae. aegypti and Ae. albopictus in Penang. Mutation has occurred rapidly in both species and this will be challenging in controlling the populations. However, further analysis needed to confirm this statement.
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Affiliation(s)
- Darlina Md Naim
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
| | | | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Koohkanzadeh M, Pramual P, Fekrat L. Genetic Analysis of Populations of the Peach Fruit Fly, Bactrocera zonata (Diptera: Tephritidae), in Iran. NEOTROPICAL ENTOMOLOGY 2019; 48:594-603. [PMID: 30617740 DOI: 10.1007/s13744-018-0659-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Bactrocera zonata (Saunders) as one of the most devastating species of the genus Bactrocera is a notorious polyphagous fruit fly pest attacking lots of commercially important host plant species in many parts of the world including Iran. Despite economic importance, the population genetics of B. zonata have remained relatively unexplored in the country. In this study, the genetic structure, genetic diversity, and demographic history of this pest in Iran were investigated on the basis of cytochrome oxidase c subunit 1 (COI) sequences. A total of 21 haplotypes were identified from 66 individuals collected from seven locations. Genetic diversity indices (number of haplotypes, haplotype diversity, and nucleotide diversity) revealed high genetic diversity without any isolation by distance among the geographic areas. An overall low level of genetic differentiation between populations revealed by genetic structure analysis reinforces the hypothesis of free movement of flies throughout the geographic areas. Non-significant correlation between genetic distances and geographic distances was an indication of a high level of gene flow among the studied populations of the pest. In addition, the recent population expansion following a recent past bottleneck could be a factor that might be contributed to the overall low level of the genetic structure. Mismatch distribution analysis as well as Tajima's D and Fu's FS tests strengthens the likelihood of a recent expanded population following a population bottleneck.
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Affiliation(s)
- M Koohkanzadeh
- Dept of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - P Pramual
- Dept of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham, Thailand
| | - L Fekrat
- Dept of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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13
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Malini P, Ramasamy S, Schafleitner R, Muthukalingan K. Pheromone-binding proteins based phylogenetics and phylogeography of Maruca spp. from Asia, Africa, Oceania, and South America. Ecol Evol 2019; 9:9239-9272. [PMID: 31463019 PMCID: PMC6706176 DOI: 10.1002/ece3.5471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 11/17/2022] Open
Abstract
Variations in the functional response of legume pod borer (Maruca vitrata) populations to sex pheromone blends were observed in Asia and Africa. Hence, this study was carried out to understand the differences in pheromone-binding proteins (PBPs) among Maruca populations in Asia, Africa, Oceania, and South America. A de novo transcriptome assembly was adopted to sequence the entire transcribed mRNAs in M. vitrata from Taiwan. The raw-sequence data were assembled using homologous genes from related organisms in GenBank to detect M. vitrata PBPs (MvitPBPs). Sections of the cDNA of MvitPBP of different length were used to design primers to amplify the full-length cDNA of PBPs. All three PBP sequences comprised three exons interspersed by two introns. In total, 92 MvitPBP1 haplotypes, 77 MvitPBP2 haplotypes, and 64 MvitPBP3 haplotypes were identified in 105, 98, and 68 Maruca individuals, respectively. High pairwise F ST values (0.41-0.73) and phylogenetic analyses distinguished the putative Maruca species in South America from those occurring in rest of the world, and possibly two putative subspecies in Asia and Africa. The haplotype networks and Automatic Barcode Gap Discovery analyses also confirmed these results. The negative Tajima's D and Fu's F S values showed the recent demographic expansion of Maruca populations. Thus, this study confirmed the presence of different Maruca species and/or subspecies in different continents based on the diversity within PBP genes. Additional sampling and studies are suggested for Oceania and South America. The genetic differences among Maruca populations should be carefully considered while using sex pheromone lures and bio-control agents.
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Affiliation(s)
- Periasamy Malini
- World Vegetable CenterShanhuaTainanTaiwan
- Bharathidasan UniversityTiruchirappalliTamil NaduIndia
| | | | | | - Krishnan Muthukalingan
- Bharathidasan UniversityTiruchirappalliTamil NaduIndia
- Present address:
Madurai Kamaraj UniversityMaduraiTamil NaduIndia
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14
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Sajeela KA, Gopalakrishnan A, Basheer VS, Mandal A, Bineesh KK, Grinson G, Gopakumar SD. New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean. Mol Phylogenet Evol 2019; 136:53-64. [PMID: 30954588 DOI: 10.1016/j.ympev.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 03/09/2019] [Accepted: 04/03/2019] [Indexed: 01/03/2023]
Abstract
Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.
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Affiliation(s)
- K A Sajeela
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India.
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources (PMFGR) Centre-NBFGR, CMFRI, Kochi 682 018, Kerala, India
| | - A Mandal
- Rajiv Gandhi Centre for Aquaculture (RGCA), Sirkali 609 113, Nagapattinam, Tamil Nadu, India
| | - K K Bineesh
- Zoological Survey of India, Andaman and Nicobar Regional Centre, Haddo, Port Blair 744 102, India
| | - G Grinson
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
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15
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Baisvar VS, Singh M, Kumar R. Population structuring of Channa striata from Indian waters using control region of mtDNA. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:414-423. [PMID: 30905237 DOI: 10.1080/24701394.2018.1532416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (FST = 0.56, p < .00) among the populations. The pattern of genetic differentiation was not consistent with geographical distributions. AMOVA identified three genetically heterogeneous clades. The significant finding of Imphal and Chaliyar was that they were found genetically close to each other, but geographically much isolated from each other. The inference of the study suggests that the hypothesis of the single panmictic population of C. striata in Indian waters is rejected.
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Affiliation(s)
- Vishwamitra Singh Baisvar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Mahender Singh
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Ravindra Kumar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
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16
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Chaw SM, Liu YC, Wu YW, Wang HY, Lin CYI, Wu CS, Ke HM, Chang LY, Hsu CY, Yang HT, Sudianto E, Hsu MH, Wu KP, Wang LN, Leebens-Mack JH, Tsai IJ. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. NATURE PLANTS 2019; 5:63-73. [PMID: 30626928 PMCID: PMC6784883 DOI: 10.1038/s41477-018-0337-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/26/2018] [Indexed: 05/19/2023]
Abstract
We present reference-quality genome assembly and annotation for the stout camphor tree (Cinnamomum kanehirae (Laurales, Lauraceae)), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry than monocots. Two whole-genome duplication events were inferred within the magnoliid lineage: one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small-scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of the terpenoid synthase gene subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.
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Affiliation(s)
- Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Han-Yu Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chan-Yi Ivy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Lo-Yu Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Yao Hsu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Ting Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Min-Hung Hsu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Kun-Pin Wu
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ling-Ni Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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17
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Chen YA, Tzeng DTW, Huang YP, Lin CJ, Lo UG, Wu CL, Lin H, Hsieh JT, Tang CH, Lai CH. Antrocin Sensitizes Prostate Cancer Cells to Radiotherapy through Inhibiting PI3K/AKT and MAPK Signaling Pathways. Cancers (Basel) 2018; 11:cancers11010034. [PMID: 30602706 PMCID: PMC6356781 DOI: 10.3390/cancers11010034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/20/2018] [Accepted: 12/25/2018] [Indexed: 02/07/2023] Open
Abstract
Radiotherapy is one of the most common treatment options for local or regional advanced prostate cancer (PCa). Importantly, PCa is prone to radioresistance and often develops into malignancies after long-term radiotherapy. Antrocin, a sesquiterpene lactone isolated from Antrodia cinnamomea, possesses pharmacological efficacy against various cancer types; however, its therapeutic potential requires comprehensive exploration, particularly in radioresistant PCa cells. In this study, we emphasized the effects of antrocin on radioresistant PCa cells and addressed the molecular mechanism underlying the radiosensitization induced by antrocin. Our results showed that a combination treatment with antrocin and ionizing radiation (IR) synergistically inhibited cell proliferation and induced apoptosis in radioresistant PCa cells. We further demonstrated that antrocin downregulated PI3K/AKT and MAPK signaling pathways as well as suppressed type 1 insulin-like growth factor 1 receptor (IGF-1R)-mediated induction of β-catenin to regulate cell cycle and apoptosis. Using xenograft mouse models, we showed that antrocin effectively enhanced radiotherapy in PCa. Our study demonstrates that antrocin sensitizes PCa to radiation through constitutive suppression of IGF-1R downstream signaling, revealing that it can be developed as a potent therapeutic agent to overcome radioresistant PCa.
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Affiliation(s)
- Yu-An Chen
- Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung 40402, Taiwan.
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Microbiology and Immunology, Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
| | - David T W Tzeng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China.
| | - Yi-Ping Huang
- Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung 40402, Taiwan.
| | - Chun-Jung Lin
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - U-Ging Lo
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Chia-Lin Wu
- Department of Microbiology and Immunology, Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Department of Neurology, Chang Gung Memorial Hospital, Linkou 33305, Taiwan.
| | - Ho Lin
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Chih-Hsin Tang
- Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung 40402, Taiwan.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40202, Taiwan.
| | - Chih-Ho Lai
- Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung 40402, Taiwan.
- Department of Microbiology and Immunology, Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Department of Nursing, Asia University, Taichung 41354, Taiwan.
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou 33305, Taiwan.
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18
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Manin BO, Drakeley CJ, Chua TH. Mitochondrial variation in subpopulations of Anopheles balabacensis Baisas in Sabah, Malaysia (Diptera: Culicidae). PLoS One 2018; 13:e0202905. [PMID: 30138386 PMCID: PMC6107281 DOI: 10.1371/journal.pone.0202905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima's D and Fu's Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.
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Affiliation(s)
- Benny Obrain Manin
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Chris J. Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tock H. Chua
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- * E-mail:
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19
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Palraju M, Paulchamy R, Sundaram J. Population genetic structure and molecular diversity of Leucinodes orbonalis based on mitochondrial COI gene sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1231-1239. [PMID: 29421947 DOI: 10.1080/24701394.2018.1436169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Leucinodes orbonalis is a destructive pest found throughout eggplant cultivating fields of Tamil Nadu, India. The genetic diversity and its population structure were investigated in this pest using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from 20 populations of L. orbonalis collected from various agro-climatic conditions. The study indicated almost no genetic diversity among various populations. The COI nucleotide sequence based haplotype analysis also revealed no significant genetic variation among various populations. However, haplotype network analysis with three clades was nearly matching with the structure of phylogenetic analysis that showed geographical separations induced distribution of some genetic variation. The PCA and nMDS Shephard's plot analyses were also illustrated that the populations sampled were nearly matched with phylogenetic tree and haplotype network. This study on phylogeographical structure using the mitochondrial COI sequence diversity of L. orbonalis therefore suggested presence of few genetically distinct populations due to some specific habitat requirements.
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Affiliation(s)
- Murali Palraju
- a Department of Zoology, Unit of Entomology , University of Madras , Chennai , India
| | - Ramaraj Paulchamy
- a Department of Zoology, Unit of Entomology , University of Madras , Chennai , India
| | - Janarthanan Sundaram
- a Department of Zoology, Unit of Entomology , University of Madras , Chennai , India
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20
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Al-Araimi NA, Al-Atiyat RM, Gaafar OM, Vasconcelos R, Luzuriaga-Neira A, Eisa MO, Amir N, Benaissa MH, Alfaris AA, Aljumaah RS, Elnakhla SM, Salem MM, Ishag IA, El Khasmi M, Beja-Pereira A. Maternal genetic diversity and phylogeography of native Arabian goats. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption. Sci Rep 2017; 7:16227. [PMID: 29176629 PMCID: PMC5701162 DOI: 10.1038/s41598-017-16430-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/03/2017] [Indexed: 11/28/2022] Open
Abstract
Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected increase in variation in C. sociabilis. To explore this outcome further, we used targeted gene capture to sequence over 2,000 putatively neutral regions for both species. Our data revealed that, contrary to the microsatellite analyses, the eruption was associated with a small but significant decrease in genetic variation in both species. We suggest that genome-level analyses provide greater power than traditional molecular markers to detect the genetic consequences of population size changes, particularly changes that are recent, short-term, or modest in size. Consequently, genomic analyses promise to generate important new insights into the effects of specific environmental events on demography and genetic variation.
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Phylogeographic studies of schizothoracine fishes on the central Qinghai-Tibet Plateau reveal the highest known glacial microrefugia. Sci Rep 2017; 7:10983. [PMID: 28887534 PMCID: PMC5591315 DOI: 10.1038/s41598-017-11198-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 08/15/2017] [Indexed: 11/26/2022] Open
Abstract
Pleistocene climatic oscillations have greatly influenced the evolutionary history and distribution pattern of most extant species. However, their effects on species on the Qinghai-Tibet Plateau (QTP) are not well understood. To investigate the effects of past climatic shifts, particularly the Last Glacial Maximum (LGM), on plateau fish, we analysed the phylogeographic structure and demographic history of five closely related taxa of the subfamily Schizothoracinae, a representative endemic taxon of the QTP, from nine endorheic lakes on the central QTP and three peripheral exorheic rivers using the mitochondrial control region (D-loop) sequence and 12 microsatellite (SSR) markers. Phylogram from D-loop haplotypes revealed two well-supported lineages (North and South) separated by the Tanggula Mountains. The results from the D-loop and SSR revealed that endorheic populations possess high genetic diversity and a unique genetic structure. The most recent demographic expansion occurred post-LGM for most endorheic populations and in the last interglacial period for Siling Co and all exorheic populations. Phylogeographic structure, together with species distribution modelling, supports the scenario of multiple glacial refugia on the QTP during the LGM and suggests that Siling Co (4540 m asl) is a cryptic glacial microrefugia for plateau fish, which would be the highest glacial microrefugia known.
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23
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Low VL, Tan TK, Prakash BK, Vinnie-Siow WY, Tay ST, Masmeatathip R, Hadi UK, Lim YAL, Chen CD, Norma-Rashid Y, Sofian-Azirun M. Contrasting evolutionary patterns between two haplogroups of Haematobia exigua (Diptera: Muscidae) from the mainland and islands of Southeast Asia. Sci Rep 2017; 7:5871. [PMID: 28724923 PMCID: PMC5517420 DOI: 10.1038/s41598-017-05921-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022] Open
Abstract
Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.
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Affiliation(s)
- Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia.
| | - Tiong Kai Tan
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Batah Kunalan Prakash
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Yin Vinnie-Siow
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Roungthip Masmeatathip
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Kamphaeng Saen, Thailand
| | - Upik Kesumawati Hadi
- Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Bogor, Indonesia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Dhang Chen
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yusoff Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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24
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Huang BH, Huang CW, Huang CL, Liao PC. Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants. Sci Rep 2017; 7:5465. [PMID: 28710389 PMCID: PMC5511155 DOI: 10.1038/s41598-017-05900-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/06/2017] [Indexed: 01/11/2023] Open
Abstract
Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson's metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, 11677, Taiwan.
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25
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Chen JH, Huang CL, Lai YL, Chang CT, Liao PC, Hwang SY, Sun CW. Postglacial range expansion and the role of ecological factors in driving adaptive evolution of Musa basjoo var. formosana. Sci Rep 2017; 7:5341. [PMID: 28706224 PMCID: PMC5509723 DOI: 10.1038/s41598-017-05256-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/25/2017] [Indexed: 02/03/2023] Open
Abstract
Genetic variation evolves during postglacial range expansion of a species and is important for adapting to varied environmental conditions. It is crucial for the future survival of a species. We investigate the nuclear DNA sequence variation to provide evidence of postglacial range expansion of Musa basjoo var. formosana, a wild banana species, and test for adaptive evolution of amplified fragment length polymorphic (AFLP) loci underlying local adaptation in association with environmental variables. Postglacial range expansion was suggested by phylogeographical analyses based on sequence variation of the second intron of copper zinc superoxide dismutase 2 gene. Two glacial refugia were inferred by the average FST parameter (mean FST of a population against the remaining populations). Using variation partitioning by redundancy analysis, we found a significant amount of explained AFLP variation attributed to environmental and spatially-structured environmental effects. By combining genome scan methods and multiple univariate logistic regression, four AFLP loci were found to be strongly associated with environmental variables, including temperature, precipitation, soil moisture, wet days, and surface coverage activity representing vegetation greenness. These environmental variables may have played various roles as ecological drivers for adaptive evolution of M. basjoo var. formosana during range expansion after the last glacial maximum.
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Affiliation(s)
- Jui-Hung Chen
- Department of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei, 11677, Taiwan
| | - Chun-Lin Huang
- Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, 1 Guanchien Road, Taichung, 40453, Taiwan
| | - Yu-Long Lai
- Department of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei, 11677, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei, 10617, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei, 11677, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei, 11677, Taiwan.
| | - Chih-Wen Sun
- Department of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei, 11677, Taiwan.
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26
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Alam MMM, Westfall KM, Pálsson S. Historical demography and genetic differentiation of the giant freshwater prawn Macrobrachium rosenbergii in Bangladesh based on mitochondrial and ddRAD sequence variation. Ecol Evol 2017. [PMID: 28649344 PMCID: PMC5478082 DOI: 10.1002/ece3.3023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Macrobrachium rosenbergii, the giant freshwater prawn, is an important source of high quality protein and occurs naturally in rivers as well as commercial farms in South and South‐East Asia, including Bangladesh. This study investigated the genetic variation and population structure of M. rosenbergii sampled from four rivers in Bangladesh (sample size ranged from 19 to 20), assessing sequence variation, both in the mitochondrial cytochrome oxidase subunit 1 (CO1) gene and in 106 single nucleotide polymorphisms (SNPs) sampled randomly from the genome with double digest RAD sequencing (ddRADseq). The mitochondrial variation presented a shallow genealogy with high haplotype diversity (h = 0.95), reflecting an expansion in population size for the last ~82 kyr. Based on the CO1 variation the current effective population size (Ne) was 9.7 × 106 (CI: 1.33 × 106 – 35.84 × 106) individuals. A significant population differentiation was observed with the mitochondrial CO1 sequence variation and based on the ddRADseq variation, which could be traced to the divergence of the population in the Naf River in the South‐East border with Myanmar from the other populations. A differentiation in mtDNA haplotype frequencies was also observed between the Biskhali River and the Karnaphuli Rivers in eastern Bangladesh. This study demonstrated the use of high‐throughput genotyping based on the ddRADseq method to reveal population structure at a small geographical scale for an important freshwater prawn. The information from this study can be utilized for management and conservation of this species in Bangladesh.
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Affiliation(s)
- M M Mahbub Alam
- Department of Life and Environmental Sciences University of Iceland Reykjavik Iceland.,Faculty of Fisheries Sylhet Agricultural University Sylhet Bangladesh
| | - Kristen M Westfall
- Department of Life and Environmental Sciences University of Iceland Reykjavik Iceland.,Pacific Biological Station Fisheries and Oceans Canada Nanaimo BC Canada
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences University of Iceland Reykjavik Iceland
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27
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Behera BK, Baisvar VS, Rout AK, Pakrashi S, Kumari K, Panda D, Das P, Parida PK, Meena DK, Bhakta D, Das BK, Jena J. The population structure and genetic divergence of Labeo gonius (Hamilton, 1822) analyzed through mitochondrial DNA cytochrome b gene for conservation in Indian waters. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:543-551. [DOI: 10.1080/24701394.2017.1320992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Bijay Kumar Behera
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Vishwamitra Singh Baisvar
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Ajaya Kumar Rout
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sudip Pakrashi
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Kavita Kumari
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Debabrata Panda
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Pronob Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Pranaya Kumar Parida
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Dharmendra Kumar Meena
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - D. Bhakta
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Joykrushna Jena
- Fisheries Division – Indian Council of Agricultural Research, New Delhi, India
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28
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Liu T, Sun K, Park YC, Feng J. Phylogenetic relationships and evolutionary history of the greater horseshoe bat, Rhinolophus ferrumequinum, in Northeast Asia. PeerJ 2016; 4:e2472. [PMID: 27761309 PMCID: PMC5068396 DOI: 10.7717/peerj.2472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/22/2016] [Indexed: 11/20/2022] Open
Abstract
The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations.
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Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Yung Chul Park
- Department of Forest Environment Protection, College of Forest and Environmental Science, Kangwon National University , Chuncheon , South Korea
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
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Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Sci Rep 2016; 6:31044. [PMID: 27534981 PMCID: PMC4989166 DOI: 10.1038/srep31044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/06/2016] [Indexed: 11/24/2022] Open
Abstract
Subtropical evergreen broad-leaved forest (EBLF) is one of the most important vegetation types in China. Inferences from palaeo-biome reconstruction (PBR) and phylogeography regarding range shift history of EBLF during the late Quaternary are controversial and should be reconciled. We compared phylogeographic patterns of three EBLF constituents in China, Castanopsis tibetana, Machilus thunbergii and Schima superba. Contrary to a chorus of previous phylogeographic studies and the results of species distribution modelling (SDM) of this study (in situ survival during the LGM), the three species displayed three different phylogeographic patterns that conform to either an in situ survival model or an expansion-contraction model. These results are partially congruent with the inference of PBR that EBLF was absent to the north of 24° N at the LGM. This study suggests that the constituents of EBLF could have responded idiosyncratically to climate changes during the Late Quaternary. The community assemblages of EBLF could have been changing over time, resulting in no palaeo-analogs to modern-day EBLF, which may be the main reason responsible for the failure of PBR to detect the occurrence of EBLF north of 24° N at the LGM.
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30
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Kibegwa F, Githui K, Jung'a J, Badamana M, Nyamu M. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J Anim Breed Genet 2015; 133:238-47. [DOI: 10.1111/jbg.12182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 02/01/2015] [Indexed: 11/30/2022]
Affiliation(s)
- F.M. Kibegwa
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - K.E. Githui
- Molecular Genetics Laboratory; National Museums of Kenya; Nairobi Kenya
| | - J.O. Jung'a
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - M.S. Badamana
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - M.N. Nyamu
- Molecular Genetics Laboratory; National Museums of Kenya; Nairobi Kenya
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Amaral MRX, Albrecht M, McKinley AS, de Carvalho AMF, de Sousa Junior SC, Diniz FM. Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic. Molecules 2015; 20:15158-74. [PMID: 26295384 PMCID: PMC6332107 DOI: 10.3390/molecules200815158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/11/2015] [Accepted: 07/13/2015] [Indexed: 11/26/2022] Open
Abstract
The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA). Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97) within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.
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Affiliation(s)
| | - Marc Albrecht
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA.
| | - Alan Shane McKinley
- National Park Service, 18001 Old Cutler Bay Rd Suite 419, Palmetto Bay, FL 33190, USA.
| | | | | | - Fabio Mendonça Diniz
- Molecular Biology & Biotechnology Laboratory, EMBRAPA Meio-Norte, CP 01, Teresina, PI 64049-550, Brazil.
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32
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Wu CC, Ho CK, Chang SH. The complete chloroplast genome of Cinnamomum kanehirae Hayata (Lauraceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2681-2. [PMID: 26053940 DOI: 10.3109/19401736.2015.1043541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome of Cinnamomum kanehirae (Hayata), the first to be completely sequenced of Lauraceae family, is presented in this study. The total genome size is 152,700 bp, with a typical circular structure including a pair of inverted repeats (IRa/b) of 20,107 bp of length separated by a large single-copy region (LSC) and a small single-copy region (SSC) of 93,642 bp and 18,844 bp of length, respectively. The overall GC content of the genome is 39.1%. The nucleotide sequence shows 91% identities with Liriodendron tulipifera in the Magnoliaceae. In total, 123 annotated genes consisted of 79 coding genes, eight rRNA genes, and 36 tRNA genes. Among all 79 coding genes, seven genes (rpoC1, atpF, rpl2, ndhB, ndhA, rps16, and rpl2) contain one intron, while two genes (ycf3 and clpP) contain two introns. The maximum likelihood phylogenetic analysis revealed that C. kanehirae chloroplast genome is closely related to Calycanthus fertilis within Laurales order.
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Affiliation(s)
- Chia-Chen Wu
- a Silviculture Division , Taiwan Forestry Research Institute , Taipei , Taiwan
| | - Cheng-Kuen Ho
- a Silviculture Division , Taiwan Forestry Research Institute , Taipei , Taiwan
| | - Shu-Hwa Chang
- a Silviculture Division , Taiwan Forestry Research Institute , Taipei , Taiwan
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33
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Periasamy M, Schafleitner R, Muthukalingan K, Ramasamy S. Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa. PLoS One 2015; 10:e0124057. [PMID: 25893977 PMCID: PMC4404340 DOI: 10.1371/journal.pone.0124057] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
This study was undertaken to assess the genetic diversity and host plant races of M. vitrata population in South and Southeast Asia and sub-Saharan Africa. The cytochrome c oxidase subunit 1 (cox1) gene was used to understand the phylogenetic relationship of geographically different M. vitrata population, but previous studies did not include population from Southeast Asia, the probable center of origin for Maruca, and from east Africa. Extensive sampling was done from different host plant species in target countries. Reference populations from Oceania and Latin America were used. An amplicon of 658 bp was produced by polymerase chain reaction, and 64 haplotypes were identified in 686 M. vitrata individuals. Phylogenetic analysis showed no difference among the M. vitrata population from different host plants. However, the results suggested that M. vitrata has formed two putative subspecies (which cannot be differentiated based on morphological characters) in Asia and sub-Saharan Africa, as indicated by the high pairwise FST values (0.44–0.85). The extremely high FST values (≥0.93) of Maruca population in Latin America and Oceania compared to Asian and African population seem to indicate a different species. On the continental or larger geographical region basis, the genetic differentiation is significantly correlated with the geographical distance. In addition, two putative species of Maruca, including M. vitrata occur in Australia, Indonesia and Papua New Guinea. The negative Tajima’s D and Fu’s FS values showed the recent demographic expansion of Maruca population. The haplotype network and Automatic Barcode Gap Discovery analyses confirmed the results of phylogenetic analysis. Thus, this study confirmed the presence of three putative Maruca species, including one in Latin America, one in Oceania (including Indonesia) and M. vitrata in Asia, Africa and Oceania. Hence, the genetic differences in Maruca population should be carefully considered while designing the pest management strategies in different regions.
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Affiliation(s)
- Malini Periasamy
- Asian Vegetable Research and Development Center (AVRDC)—The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Roland Schafleitner
- Asian Vegetable Research and Development Center (AVRDC)—The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan
| | - Krishnan Muthukalingan
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Srinivasan Ramasamy
- Asian Vegetable Research and Development Center (AVRDC)—The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan
- * E-mail:
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Awotunde EO, Bemji MN, Olowofeso O, James IJ, Ajayi OO, Adebambo AO. Mitochondrial DNA Sequence Analyses and Phylogenetic Relationships Among Two Nigerian Goat Breeds and the South African Kalahari Red. Anim Biotechnol 2015; 26:180-7. [DOI: 10.1080/10495398.2014.977907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Ho PT, Kwan YS, Kim B, Won YJ. Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria. Ecol Evol 2015; 5:419-35. [PMID: 25691968 PMCID: PMC4314273 DOI: 10.1002/ece3.1374] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/19/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022] Open
Abstract
To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000-19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.
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Affiliation(s)
- Phuong-Thao Ho
- Division of EcoCreative, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
| | - Ye-Seul Kwan
- Division of EcoScience, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
| | - Boa Kim
- Division of EcoScience, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
| | - Yong-Jin Won
- Division of EcoCreative, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
- Division of EcoScience, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
- Department of Life Science, Ewha Womans University52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 120-750, Korea
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36
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Qi XS, Yuan N, Comes HP, Sakaguchi S, Qiu YX. A strong 'filter' effect of the East China Sea land bridge for East Asia's temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae). BMC Evol Biol 2014; 14:41. [PMID: 24593236 PMCID: PMC4015774 DOI: 10.1186/1471-2148-14-41] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/25/2014] [Indexed: 11/27/2022] Open
Abstract
Background In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters. Results Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles. Conclusions Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment for certain species and their biological (e.g., recruitment) properties.
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Affiliation(s)
| | | | | | | | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China.
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Chang JC, Ponnath DW, Ramasamy S. Phylogeographical structure in mitochondrial DNA of eggplant fruit and shoot borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae) in South and Southeast Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:198-204. [PMID: 24491107 DOI: 10.3109/19401736.2014.880890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Leucinodes orbonalis is the most detrimental South and Southeast Asian insect pest of eggplant. To help reduce the impact of this pest, population genetic diversity and structure of L. orbonalis were examined in eight populations from six countries using mitochondrial cytochrome c oxidase subunit I DNA sequences. No correlation between genetic diversity and geographic distance was detected among populations. Low levels of haplotype and nucleotide diversities were observed in the Philippines population, suggesting recent colonization. No significant gene flow was found among local populations in different countries. The Vietnam population is highly differentiated, indicated by significant pairwise FST values, and may be ascribed to a new subspecies or race. India was confirmed to be the source of genetic variation in L. orbonalis populations. Our study showed that L. orbonalis formed subpopulations for each local region, and the corresponding pest management technology should be developed at the country scale.
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Affiliation(s)
- Jian-Cheng Chang
- a Unit of Entomology , AVRDC - The World Vegetable Center , Shanhua , Taiwan and
| | - Daniel W Ponnath
- b Faculty Geisenheim , RheinMain University of Applied Sciences Wiesbaden, Rüsselsheim , Geisenheim , Germany
| | - Srinivasan Ramasamy
- a Unit of Entomology , AVRDC - The World Vegetable Center , Shanhua , Taiwan and
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38
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Rosly HAAM, Nor SAM, Yahya K, Naim DM. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment. Mol Biol Rep 2013; 40:6407-18. [PMID: 24062076 DOI: 10.1007/s11033-013-2755-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 09/14/2013] [Indexed: 11/30/2022]
Abstract
A primary factor in population management and wildlife conservation is the delineation of population units derived from descriptions of population genetic structure. Yet, predicting factors that influence the patterns of gene flow in a population particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the mud crab Scylla olivacea examined based on a 542 bp segment of the mitochondrial DNA cytochrome c oxidase I gene among 91 individuals from six localities in the west and east coast of Peninsular Malaysia. In total 55 unique haplotypes were distinguished with 45 private haplotypes and a single common haplotype shared among all populations studied. The other ten haplotypes were shared among various populations. The sharing of this haplotype reflects the connection of the mangrove areas between east and west coast of Peninsular Malaysia. High haplotype diversity (h = 0.968 ± 0.021; mean ± SD) and low nucleotide diversity (π = 0.120 ± 0.015; mean ± SD) were displayed, which may be indicative of genetic bottleneck events. No significant phylogenetic lineages were recognized using neighbour-joining and maximum parsimony methods. Hierarchical AMOVA analysis indicated that 99.33 % of the genetic variation was contained within populations and 0.67 % occurred among populations, suggesting no geographical patterning among populations studied, supported by F st test. Mismatch distribution analysis showed that the observed distribution of the pairwise mutation differences among haplotypes was multimodal, which is not concordant with a sudden range expansion scenario. However, neutrality tests showed non-significant negative values suggesting that the populations studied may have experienced past population growth, but the expansion may have been restricted to separate local areas that resulted in the non-significant negative Fu's Fs and Tajima's D value. Overall, this present preliminary study was able to be a reference on the phylogenetic relationships and assessment of genetic structure of Scylla sp. in Malaysia.
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Fan DM, Yue JP, Nie ZL, Li ZM, Comes HP, Sun H. Phylogeography ofSophora davidii(Leguminosae) across the ‘Tanaka-Kaiyong Line’, an important phytogeographic boundary in Southwest China. Mol Ecol 2013; 22:4270-4288. [DOI: 10.1111/mec.12388] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Deng Mei Fan
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
- Laboratory of Subtropical Biodiversity; Jiangxi Agricultural University; Nanchang Jiangxi 330045 China
| | - Ji Pei Yue
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Ze Long Nie
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - Zhi Min Li
- School of Life Science; Yunnan Normal University; Kunming 650092 Yunnan China
| | - Hans Peter Comes
- Department of Organismic Biology; University of Salzburg; Hellbrunnerstrasse 34 A-5020 Salzburg Austria
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
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Lu MC, El-Shazly M, Wu TY, Du YC, Chang TT, Chen CF, Hsu YM, Lai KH, Chiu CP, Chang FR, Wu YC. Recent research and development of Antrodia cinnamomea. Pharmacol Ther 2013; 139:124-56. [DOI: 10.1016/j.pharmthera.2013.04.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 03/14/2013] [Indexed: 12/20/2022]
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Ting N, Astaras C, Hearn G, Honarvar S, Corush J, Burrell AS, Phillips N, Morgan BJ, Gadsby EL, Raaum R, Roos C. Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus). Ecol Evol 2012; 2:550-61. [PMID: 22822434 PMCID: PMC3399144 DOI: 10.1002/ece3.98] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/29/2011] [Indexed: 11/24/2022] Open
Abstract
It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.
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Affiliation(s)
- Nelson Ting
- Department of Anthropology, University of Oregon,308 Condon Hall, Eugene, Oregon 97403
| | - Christos Astaras
- Wildlife Conservation Research Unit, University of Oxford,Abingdon Road, Tubney, Oxfordshire, OX13 5QL, United Kingdom
| | - Gail Hearn
- Department of Biology and Bioko Biodiversity Protection Program, Drexel University,3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Shaya Honarvar
- Department of Biology and Bioko Biodiversity Protection Program, Drexel University,3141 Chestnut Street, Philadelphia, Pennsylvania 19104
| | - Joel Corush
- Department of Anthropology, University of Oregon,308 Condon Hall, Eugene, Oregon 97403
| | - Andrew S Burrell
- Department of Anthropology, New York University,25 Waverly Place, New York, New York 10003
| | - Naomi Phillips
- Department of Biology, Arcadia University,450 South Easton Road, Glenside, Pennsylvania 19038-3295
| | - Bethan J Morgan
- San Diego Zoo Global Institute for Conservation Research,15600 San Pasqual Valley Road, Escondido, California 92027
- Department of Psychology, University of Stirling,FK9 4LA, Stirling, Scotland, United Kingdom
| | | | - Ryan Raaum
- Department of Anthropology, Lehman College and City University of New York Graduate Center,250 Bedford Park Blvd., West Bronx, New York 10468
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center,Kellnerweg 4, 37077 Göttingen, Germany
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