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Banerjee P, Dey G, Maity JP, Stewart KA, Sharma RK, Chan MWY, Lee K, Chen C. The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden apple snails) across Taiwan. Ecol Evol 2024; 14:e11268. [PMID: 38646006 PMCID: PMC11027011 DOI: 10.1002/ece3.11268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024] Open
Abstract
The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.
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Affiliation(s)
- Pritam Banerjee
- Department of Environmental Science, Policy and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Gobinda Dey
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
- Department of Agricultural ChemistryNational Taiwan UniversityTaipeiTaiwan
| | - Jyoti Prakash Maity
- Environmental Science Laboratory, Department of Chemistry, Biological Laboratory, School of Applied SciencesKIIT Deemed to be UniversityBhubaneswarOdishaIndia
| | - Kathryn A. Stewart
- Institute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Raju Kumar Sharma
- Doctoral Program in Science, Technology, Environment and Mathematics, Department of Earth and Environmental SciencesNational Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Michael W. Y. Chan
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Kuanhsuen Lee
- Department of Emergency MedicineDitmanson Medical Foundation Chia‐Yi Christian HospitalChiayiTaiwan
| | - Chien‐Yen Chen
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
- Center for Nano Bio‐Detection, Center for Innovative Research on Aging SocietyAIM‐HI, National Chung Cheng UniversityChiayiTaiwan
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Jiang S, Li Z, Li J, Xu K, Ye Y. Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene. Animals (Basel) 2024; 14:718. [PMID: 38473102 DOI: 10.3390/ani14050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/14/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.
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Affiliation(s)
- Senping Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhenhua Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Khatun MF, Hwang HS, Kang JH, Lee KY, Kil EJ. Genetic Diversity and DNA Barcoding of Thrips in Bangladesh. Insects 2024; 15:107. [PMID: 38392526 PMCID: PMC10888972 DOI: 10.3390/insects15020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Thrips are economically important pests, and some species transmit plant viruses that are widely distributed and can damage vegetables and cash crops. Although few studies on thrips species have been conducted in Bangladesh, the variation and genetic diversity of thrips species remain unknown. In this study, we collected thrips samples from 16 geographical locations throughout the country and determined the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene in 207 thrips individuals. Phylogenetic analysis revealed ten genera (Thrips, Haplothrips, Megalothrips, Scirtothrips, Frankliniella, Dendrothripoides, Astrothrips, Microcephalothrips, Ayyaria, and Bathrips) and 19 species of thrips to inhabit Bangladesh. Among these, ten species had not been previously reported in Bangladesh. Intraspecific genetic variation was diverse for each species. Notably, Thrips palmi was the most genetically diverse species, containing 14 haplotypes. The Mantel test revealed no correlation between genetic and geographical distances. This study revealed that thrips species are expanding their host ranges and geographical distributions, which provides valuable insights into monitoring the diversity of and control strategies for these pests.
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Affiliation(s)
- Mst Fatema Khatun
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
- Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Hwal-Su Hwang
- Department of Plant Medicine, College of Agriculture and Life Science, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 37224, Republic of Korea
| | - Jeong-Hun Kang
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
| | - Kyeong-Yeoll Lee
- Department of Plant Medicine, College of Agriculture and Life Science, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 37224, Republic of Korea
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 37224, Republic of Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
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Huang A, Ma J, Yang J, Chen B, Zhou J, Yi L. Genetic diversity and population structure of the Asian citrus psyllid in China. J Insect Sci 2024; 24:2. [PMID: 38195069 PMCID: PMC10776205 DOI: 10.1093/jisesa/iead120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024]
Abstract
The Asian citrus psyllid (ACP) is the main vector of Citrus Huanglongbing, the most damaging citrus disease, causing significant financial losses in the citrus industry. Global warming has expanded the habitat of this pest, allowing it to continue its northward migration to China. Population genetic information of ACP is fundamentally essential for species management. This study investigated the genetic diversity and population structure of Chinese ACP using the mitochondrial cytochrome oxidase subunit I gene by dataset comprised 721 sequences from 27 geographic sites in China. Low haplotype diversity (0.323 ± 0.022) and low nucleotide diversity (0.00071 ± 0.00007) were observed in the entire population, which may indicate recent founder events. Twenty-three haplotypes were identified and clustered into 2 haplogroups: haplogroup I and haplogroup II. Haplogroup II included only 2 unique haplotypes, which occurred exclusively in the Southwest China ACP population. Genetic differentiation analyses were also indicative of Southwest China population was significantly differentiated from the remaining populations. Demographic history analysis showed that ACP population in China has experienced demographic expansion. Our results provided a better understanding of the genetic distribution patterns and structures of ACP populations in China.
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Affiliation(s)
- Aijun Huang
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
- National Navel Orange Engineering Research Center, Ganzhou 341000, China
| | - Jiayu Ma
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
| | - Jin Yang
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
| | - Bo Chen
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
| | - Jun Zhou
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
- National Navel Orange Engineering Research Center, Ganzhou 341000, China
| | - Long Yi
- College of Life Science, Gannan Normal University, Ganzhou 341000, China
- National Navel Orange Engineering Research Center, Ganzhou 341000, China
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Wang X, Wang W, Qin Y, Wang M, Li Y, Liu H. Population Genetic Diversity of Two Blue Oat Mite Species on Triticum Hosts in China. Insects 2023; 14:377. [PMID: 37103192 PMCID: PMC10143575 DOI: 10.3390/insects14040377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Blue oat mite species, including Penthaleus major and P. tectus, are pests widely distributed across China that cause damage to winter wheat. This study evaluated the genetic diversity of P. major and P. tectus on Triticum hosts collected from 23 geographic locations based on mitochondrial cytochrome c oxidase subunit I (COI) sequences. We identified nine haplotypes in 438 P. major individuals from 21 geographic locations and five haplotypes in 139 P. tectus individuals from 11 geographic locations. Meanwhile, P. major exhibits high values of haplotype diversity (Hd) and nucleotide diversity (Pi) (Hd = 0.534 > 0.5 and Pi = 0.012 > 0.005), representing a large stable population with a long evolutionary history. P. tectus shows low values of Hd and Pi (Hd = 0.112 < 0.5 and Pi = 0 < 0.005), which suggest recent founder events. Moreover, demographic analysis suggested that P. major and P. tectus have not undergone a recent population expansion. The lowest genetic variation was observed in Xiangzhou (XZ-HB), Zaoyang (ZY-HB), Siyang (SY-JS), and Rongxian (RX-SC), with only one species and one haplotype identified in over 30 individuals. Robust genetic differentiation was found in P. major compared to P. tectus, which provides a theoretical basis for the widespread distribution of P. major in China.
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Sruoga V, Havelka J. Review of the Neotropical Species of the Elachista praelineata Species Group (Lepidoptera, Elachistidae, Elachistinae) with Identification Keys and Description of a New Species from Bolivia. Insects 2023; 14:62. [PMID: 36661990 PMCID: PMC9863831 DOI: 10.3390/insects14010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Neotropical species of the Elachista praelineata species group are reviewed. Five species are recognized in the Neotropics. A new species, Elachista stonisi sp. nov., and female of E. albisquamella Zeller, 1877 are described and illustrated with photographs of the adults, some of the immature stages, female genitalia, and leaf mines. The female of E. lata Sruoga, 2010 is associated with the male based on morphology and the comparison of partial mitochondrial COI sequences. Identification keys to the Neotropical species of E. praelineata species group, based on male and female genitalia, are provided.
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Watanabe HK, Senokuchi R, Nomaki H, Kitahashi T, Uyeno D, Shimanaga M. Distribution and Genetic Divergence of Deep-Sea Hydrothermal Vent Copepods (Dirivultidae: Siphonostomatoida: Copepoda) in the Northwestern Pacific. Zoolog Sci 2021; 38:223-230. [PMID: 34057346 DOI: 10.2108/zs200153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/17/2021] [Indexed: 11/17/2022]
Abstract
Copepods in the family Dirivultidae are one of the most successful meiofauna in deep-sea hydrothermal vent fields and are abundant near venting fluid. Although vents are spatially limited ocean habitats, they are distributed widely in the Atlantic, Pacific, and Indian Oceans. However, knowledge of dirivultid biogeography and phylogeography remains limited, especially in the northwestern Pacific. Here, we obtained partial mitochondrial COI gene sequences of three dirivultids from the northwestern Pacific-Stygiopontius senokuchiae and an unidentified Chasmatopontius species from vent fields in the Izu-Bonin Arc and Stygiopontius senckenbergi associated with the squat lobster Shinkaia crosnieri in the Okinawa Trough-and analyzed them in comparison with existing data. The among-species sequence diversity exceeded 80 out of 560 bp (14% or 0.166 in Kimura 2-parameter distance), whereas the within-species diversity was less than 10 bp (2% or 0.018 in Kimura 2-parameter distance), with no genetic saturation. Each species formed a monophyletic clade and the genetic region targeted is deemed reliable for identifying species and populations for these copepods. Among the three genera targeted, only Chasmatopontius formed a monophyletic cluster, while Aphotopontius and Stygiopontius did not. Species delimitation analyses suggested the existence of cryptic species in Chasmatopontius. Subdivision among local populations was observed in Aphotopontius, but not in Stygiopontius in the same distribution, implying potential differences in dispersal ability among different genera of dirivultids. Further sampling is required, to fill the spatial gaps to elucidate the biogeography and evolution of dirivultids in the global deep ocean.
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Affiliation(s)
- Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan,
| | - Reina Senokuchi
- Aitsu Marine Station, Kumamoto University, Matsushima, Kami-amakusa, Kumamoto 861-6102, Japan
| | - Hidetaka Nomaki
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Tomo Kitahashi
- RIGC, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Daisuke Uyeno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima 980-0065, Japan
| | - Motohiro Shimanaga
- Aitsu Marine Station, Kumamoto University, Matsushima, Kami-amakusa, Kumamoto 861-6102, Japan
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Hikosaka-Katayama T, Watanuki N, Niiho S, Hikosaka A. Geographical Distribution and Genetic Diversity of Praesagittifera naikaiensis (Acoelomorpha) in the Seto Inland Sea, Japan. Zoolog Sci 2021; 37:314-322. [PMID: 32729709 DOI: 10.2108/zs190119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/25/2020] [Indexed: 11/17/2022]
Abstract
Acoel flatworms are simple bilaterians that lack digestive lumens and coelomic cavities. Although they are a significant taxon for evaluating the evolution of metazoans, suitable species for biological experiments are not available in Japan. We recently focused on Praesagittifera naikaiensis, which inhabits the sandy shores of intertidal zones in the Seto Inland Sea in Japan, as a candidate for a representative acoel species to be used in experiments. However, reports on its distribution range remain limited. Here, we surveyed the habitats of P. naikaiensis on 108 beaches along the Seto Inland Sea. Praesagittifera naikaiensis is reported here from 37 sites (six previously known and 31 newly discovered sites) spread over a wide area of the Seto Inland Sea, from Awaji Island in Hyogo Prefecture to Fukuoka Prefecture (364 km direct distance). Based on the mitochondrial cytochrome oxidase subunit I (COI) gene haplotypes, we evaluated the genetic diversity of 145 individuals collected from 33 sites. Out of 42 COI haplotypes, 13 haplotypes were shared by multiple individuals. The most frequent haplotype was observed in 67 individuals collected from 31 sites. Eight other haplotypes were detected at geographically distant locations (maximum of 299 km direct distance). Multiple haplotypes were found at 32 sites. These results demonstrate that sufficient genetic flow exists among P. naikaiensis populations throughout the Seto Inland Sea. Molecular phylogenetic analysis of the COI haplotypes of P. naikaiensis revealed that all specimens were grouped into one clade. The genetic homogeneity of the animals in this area favors their use as an experimental animal.
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Affiliation(s)
- Tomoe Hikosaka-Katayama
- Center for Gene Science, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Nanami Watanuki
- Faculty of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Saki Niiho
- Faculty of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akira Hikosaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan,
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Li X, Zhang Z, Zhang J, Huang J, Wang L, Li Y, Hafeez M, Lu Y. Population Genetic Diversity and Structure of Thrips tabaci (Thysanoptera: Thripidae) on Allium Hosts in China, Inferred From Mitochondrial COI Gene Sequences. J Econ Entomol 2020; 113:1426-1435. [PMID: 31982906 DOI: 10.1093/jee/toaa001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Thrips tabaci Lindeman is a widely distributed agricultural pest China, which causes damage to many vegetables and cash crops. However, the population genetic variation of this pest in China remains unknown. In this study, the genetic diversity and structure of T. tabaci on Allium hosts collected from 12 geographic locations were evaluated based on mitochondrial cytochrome oxidase subunit I (COI) sequences. Six haplotypes were identified in 247 T. tabaci individuals from 12 geographic locations. All the identified T. tabaci haplotypes were thelytokous populations. The strongest genetic differentiation and relatively low gene flow were found between QHXN and other locations, which might be due to geographic barriers, such as high altitude Qinghai-Tibet Plateau. The lowest genetic variation was found in eastern and southern regions, with only one haplotype identified. The Mantel test showed no correlation between genetic distance and geographical distances. High gene flow between locations with substantial geographical distances suggested that migration of T. tabaci across China might be facilitated through human activities. The results of demographic analysis suggested that T. tabaci in China have undergone a recent demographic expansion. The possible influences of T. tabaci invasion history and human activities on the current haplotype geographical distribution were interpreted and the implications of these findings for T. tabaci management were discussed.
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Affiliation(s)
- Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jinming Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Likun Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yehua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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Rattanawannee A, Duangphakdee O, Chanchao C, Teerapakpinyo C, Warrit N, Wongsiri S, Oldroyd BP. Genetic Characterization of Exotic Commercial Honey Bee (Hymenoptera: Apidae) Populations in Thailand Reveals High Genetic Diversity and Low Population Substructure. J Econ Entomol 2020; 113:34-42. [PMID: 31769836 DOI: 10.1093/jee/toz298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 06/10/2023]
Abstract
Domestication of animal species is often associated with a reduction in genetic diversity. The honey bee, Apis mellifera Linnaeus, 1758, has been managed by beekeepers for millennia for both honey and wax production and for crop pollination. Here we use both microsatellite markers and sequence data from the mitochondrial COI gene to evaluate genetic variation of managed A. mellifera in Thailand, where the species is introduced. Microsatellite analysis revealed high average genetic diversity with expected heterozygosities ranging from 0.620 ± 0.184 to 0.734 ± 0.071 per locus per province. Observed heterozygosities were generally lower than those expected under Hardy-Weinberg equilibrium, both locally and across the population as a whole. Mitochondrial sequencing revealed that the frequency of two evolutionary linages (C-Eastern European and O-Middle Eastern) are similar to those observed in a previous survey 10 yr ago. Our results suggest that Thai beekeepers are managing their A. mellifera in ways that retain overall genetic diversity, but reduce genetic diversity between apiaries.
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Affiliation(s)
- Atsalek Rattanawannee
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Orawan Duangphakdee
- King Mongkut's University of Technology Thonburi, Ratchaburi Campus, Bangmod, Thung Khru, Bangkok, Thailand
| | - Chanpen Chanchao
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nattapot Warrit
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Siriwat Wongsiri
- Agricultural Interdisciplinary Program, Graduate School, Maejo University, Chiang Mai, Thailand
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, Macleay Building A12, University of Sydney, Sydney, NSW, Australia
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Zhan Z, Li J, Xu K. Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora). Microorganisms 2019; 7:microorganisms7110493. [PMID: 31717798 PMCID: PMC6920991 DOI: 10.3390/microorganisms7110493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/03/2022] Open
Abstract
Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.
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Affiliation(s)
- Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ju Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.Z.); (J.L.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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12
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Veeraragavan S, Duraisamy R, Mani S. Mitochondrial cytochrome oxidase (COI) sequence-based identification of pod borer of Thylacoptila sp. AA isolated from Senna alata (L.) Roxb. for the first time in India. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:407-413. [PMID: 30732502 DOI: 10.1080/24701394.2018.1532415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the present study, two pod borer larvae were found to damage pods of the host plant Senna alata. As pods (seeds) are commercially important, it prompted the investigators to find out the adult of pod borer larvae by molecular sequencing and reported in this article for the first time from S. alata. Successful amplification was achieved for chloroplast DNA isolated from leaves of host plant S. alata and tissue DNA from unknown larvae and sequenced. The sequences were submitted to NCBI domain, and the taxonomic position of host plant of pod borer larvae was confirmed as S. alata (L.) Roxb. Of the two sequences belonging to pod borer larvae, specimen 1 (S1) matched with already available three sequences of Thylacoptila sp. AA. But, specimen 2 (S2) showed significant variation in its genetic distance in Neighborhood Joining tree and maximum likelihood tree; these factors imply that specimen 2 (S2) is distinct from Thylacoptila sp. AA. Therefore, it is reported that specimen 2 may be represented as Thylacoptila sp. BB where in BB indicates variant from other available sequences. Nonetheless, reporting species of Thylacoptila as insect pest in pods of S. alata is an important contribution to the annals of insect-pest-plant interaction more importantly in medicinally important plant species S. alata.
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Affiliation(s)
- Savitha Veeraragavan
- a Department of Ecology and Environmental Sciences , Pondicherry University , Puducherry , India
| | - Ramamoorthy Duraisamy
- a Department of Ecology and Environmental Sciences , Pondicherry University , Puducherry , India
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Hu J, Zhang X, Jiang Z, Zhang F, Liu Y, Li Z, Zhang Z. New putative cryptic species detection and genetic network analysis of Bemisia tabaci (Hempitera: Aleyrodidae) in China based on mitochondrial COI sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:474-484. [PMID: 28366102 DOI: 10.1080/24701394.2017.1307974] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex and widely distributed throughout tropical and subtropical regions. To understand the B. tabaci cryptic species diversity in China more comprehensively, in the year 2014 and 2016, a large-scale sampling was conducted from the famous biodiversity hotspot of China, Yunnan province. Mitochondrial cytochrome oxidase I gene sequences were used to identify new putative cryptic species. Phylogenetic analyses were performed using Bayesian methods to evaluate the position of new cryptic species in the context of the B. tabaci diversity in Asia. Two new cryptic species, China 5 and Asia V were identified. In total, 19 B. tabaci cryptic species are present in China, two invasive (MED and MEAM1) and 17 indigenous. A new sibling species of B. tabaci was first defined and reported. Based on the mtCOI sequences and haplotype network analyses, the genetic diversity of MED was far higher than MEAM1. We confirmed the exotic MED was originated from the western Mediterranean regions and first invaded into Yunnan, China. The genetic structures of other four indigenous species (Asia I, Asia II 1, Asia II 6, and China 1) with relatively wide distribution ranges in China were also discussed.
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Affiliation(s)
- Jian Hu
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | - Xiaoyun Zhang
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | - Zhilin Jiang
- b School of Biology and Chemistry, Pu'er University , Pu'er , China
| | - Feifei Zhang
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | - Yuanyuan Liu
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | - Zhan Li
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | - Zhongkai Zhang
- a Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation , Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
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14
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Sridhar J, Chinna Babu Naik V, Ghodke A, Kranthi S, Kranthi KR, Singh BP, Choudhary JS, Krishna MSR. Population genetic structure of cotton pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) using mitochondrial cytochrome oxidase I (COI) gene sequences from India. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:941-948. [PMID: 27607604 DOI: 10.1080/24701394.2016.1214727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Pink bollworm (PBW), Pectinophora gossypiella is one of the most destructive pest's globally inflicting huge economic losses in cotton even during later stages of crop growth. In the present investigation, the population genetic structure, distribution, and genetic diversity of P. gossypiella in cotton growing zones of India using partial mitochondrial DNA cytochrome oxidase-I (COI) gene was addressed. The overall haplotype (Hd), number of nucleotide differences (K), and nucleotide diversity (π) were 0.3028, 0.327, and 0.00047, respectively which suggest that entire population exhibited low level of genetic diversity. Zone-wise clustering of population revealed that central zone recorded low level of Hd (0.2730) as compared to north (0.3619) and south (0.3028) zones. The most common haplotype (H1) reported in all 19 locations could be proposed as ancestral/original haplotype. This haplotype with one mutational step formed star-like phylogeny connected with 11 other haplotypes. The phylogenetic relationship studies revealed that most haplotypes of populations are closely related to each other. Haplotype 5 was exclusively present in Dharwad (South zone) shared with populations of Hanumangarh and Bathinda (North zone). The result indicated that there is no isolation by distance effect among the Indian populations of PBW. The present study reports a low genetic diversity among PBW populations of India and H1, as ancestral haplotype from which other haplotypes have evolved suggests that the migration and dispersal over long distance and invasiveness are major factors.
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Affiliation(s)
- J Sridhar
- a Division of Plant Protection , ICAR-Central Potato Research Institute , Shimla , Himachal Pradesh , India
| | - V Chinna Babu Naik
- b Division of Crop Protection , ICAR-Central Institute for Cotton Research , Nagpur , Maharashtra , India
| | - A Ghodke
- b Division of Crop Protection , ICAR-Central Institute for Cotton Research , Nagpur , Maharashtra , India
| | - S Kranthi
- b Division of Crop Protection , ICAR-Central Institute for Cotton Research , Nagpur , Maharashtra , India
| | - K R Kranthi
- b Division of Crop Protection , ICAR-Central Institute for Cotton Research , Nagpur , Maharashtra , India
| | - B P Singh
- a Division of Plant Protection , ICAR-Central Potato Research Institute , Shimla , Himachal Pradesh , India
| | - J S Choudhary
- c Division of Entomology, ICAR Research Complex for Eastern Region, Research Centre , Plandu Ranchi , Jharkhand , India
| | - M S R Krishna
- d Department of Biotechnology , KL University , Guntur , Andhra Pradesh , India
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15
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Mutanen M, Kivelä SM, Vos RA, Doorenweerd C, Ratnasingham S, Hausmann A, Huemer P, Dincă V, van Nieukerken EJ, Lopez-Vaamonde C, Vila R, Aarvik L, Decaëns T, Efetov KA, Hebert PDN, Johnsen A, Karsholt O, Pentinsaari M, Rougerie R, Segerer A, Tarmann G, Zahiri R, Godfray HCJ. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Syst Biol 2016; 65:1024-1040. [PMID: 27288478 PMCID: PMC5066064 DOI: 10.1093/sysbio/syw044] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/14/2022] Open
Abstract
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Affiliation(s)
- Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Finland;
| | | | - Rutger A Vos
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | - Axel Hausmann
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Vlad Dincă
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Carlos Lopez-Vaamonde
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.,Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leif Aarvik
- Natural History Museum University of Oslo, Norway
| | - Thibaud Decaëns
- Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | | | - Ole Karsholt
- Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | | | - Rodolphe Rougerie
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Andreas Segerer
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Gerhard Tarmann
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Reza Zahiri
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada
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16
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Qin L, Pan LL, Liu SS. Further insight into reproductive incompatibility between putative cryptic species of the Bemisia tabaci whitefly complex. Insect Sci 2016; 23:215-24. [PMID: 27001484 DOI: 10.1111/1744-7917.12296] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/18/2015] [Indexed: 05/26/2023]
Abstract
The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex.
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Affiliation(s)
- Li Qin
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Li-Long Pan
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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17
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Batovska J, Blacket MJ, Brown K, Lynch SE. Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia. Ecol Evol 2016; 6:3001-11. [PMID: 27217948 PMCID: PMC4863023 DOI: 10.1002/ece3.2095] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 01/11/2023] Open
Abstract
DNA barcoding is a modern species identification technique that can be used to distinguish morphologically similar species, and is particularly useful when using small amounts of starting material from partial specimens or from immature stages. In order to use DNA barcoding in a surveillance program, a database containing mosquito barcode sequences is required. This study obtained Cytochrome Oxidase I (COI) sequences for 113 morphologically identified specimens, representing 29 species, six tribes and 12 genera; 17 of these species have not been previously barcoded. Three of the 29 species ─ Culex palpalis, Macleaya macmillani, and an unknown species originally identified as Tripteroides atripes ─ were initially misidentified as they are difficult to separate morphologically, highlighting the utility of DNA barcoding. While most species grouped separately (reciprocally monophyletic), the Cx. pipiens subgroup could not be genetically separated using COI. The average conspecific and congeneric p‐distance was 0.8% and 7.6%, respectively. In our study, we also demonstrate the utility of DNA barcoding in distinguishing exotics from endemic mosquitoes by identifying a single intercepted Stegomyia aegypti egg at an international airport. The use of DNA barcoding dramatically reduced the identification time required compared with rearing specimens through to adults, thereby demonstrating the value of this technique in biosecurity surveillance. The DNA barcodes produced by this study have been uploaded to the ‘Mosquitoes of Australia–Victoria’ project on the Barcode of Life Database (BOLD), which will serve as a resource for the Victorian Arbovirus Disease Control Program and other national and international mosquito surveillance programs.
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Affiliation(s)
- Jana Batovska
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR) BioSciences Research AgriBio Centre for AgriBioscience Bundoora Victoria 3083 Australia
| | - Mark J Blacket
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR) BioSciences Research AgriBio Centre for AgriBioscience Bundoora Victoria 3083 Australia
| | - Karen Brown
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR) BioSciences Research AgriBio Centre for AgriBioscience Bundoora Victoria 3083 Australia
| | - Stacey E Lynch
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR) BioSciences Research AgriBio Centre for AgriBioscience Bundoora Victoria 3083 Australia
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Laskar BA, Kumar V, Kundu S, Tyagi K, Singha D, Chakraborty R, Chatterjee S, Saha S. DNA barcoding of Gobiid fishes (Perciformes: Gobiidae) from eastern and northeastern India with new record of a Gobionellinae species for the region. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:584-587. [PMID: 27159693 DOI: 10.3109/24701394.2016.1143470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three species clades in the neighbor-joining tree. The results confirmed the identification of five sample sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous congeners. This is a new subfamily record for the northeastern region. Another 15 sample sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15 sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one sample sequence cladded with G. giuris sequences of South African specimens. This indicated the presence of either a hidden species or a previously synonymized species in the G. giuris complex.
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Affiliation(s)
- Boni Amin Laskar
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Vikas Kumar
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Shantanu Kundu
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Kaomud Tyagi
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Devkant Singha
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Rajasree Chakraborty
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Sumantika Chatterjee
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
| | - Soumitra Saha
- a Centre for DNA Taxonomy, Molecular Systematics Division , Zoological Survey of India , Kolkata , India
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Zhong B, Chen TT, Gong RY, Zhao ZX, Wang B, Fang C, Mao HL. Classification of Pelteobagrus fish in Poyang Lake based on mitochondrial COI gene sequence. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4635-4637. [PMID: 26643194 DOI: 10.3109/19401736.2015.1101592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We use DNA molecular marker technology to correct the deficiency of traditional morphological taxonomy. Totality 770 Pelteobagrus fish from Poyang Lake were collected. After preliminary morphological classification, random selected eight samples in each species for DNA extraction. Mitochondrial COI gene sequence was cloned with universal primers and sequenced. The results showed that there are four species of Pelteobagrus living in Poyang Lake. The average of intraspecific genetic distance value was 0.003, while the average interspecific genetic distance was 0.128. The interspecific genetic distance is far more than intraspecific genetic distance. Besides, phylogenetic tree analysis revealed that molecular systematics was in accord with morphological classification. It indicated that COI gene is an effective DNA molecular marker in Pelteobagrus classification. Surprisingly, the intraspecific difference of some individuals (P. e6, P. n6, P. e5, and P. v4) from their original named exceeded species threshold (2%), which should be renewedly classified into Pelteobagrus fulvidraco. However, another individual P. v3 was very different, because its genetic distance was over 8.4% difference from original named Pelteobagrus vachelli. Its taxonomic status remained to be further studied.
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Affiliation(s)
- Bin Zhong
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
| | - Ting-Ting Chen
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
| | - Rui-Yue Gong
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
| | - Zhe-Xia Zhao
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
| | - Binhua Wang
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
| | - Chunlin Fang
- b Institute of Fisheries Science of Jiangxi Province , Nanchang , China
| | - Hui-Ling Mao
- a Department of Bioscience , College of Life Science, Nanchang University , Nanchang , China and
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Hu J, Chen YD, Jiang ZL, Nardi F, Yang TY, Jin J, Zhang ZK. Global haplotype analysis of the whitefly Bemisia tabaci cryptic species Asia I in Asia. ACTA ACUST UNITED AC 2014; 26:232-41. [PMID: 24460161 DOI: 10.3109/19401736.2013.830289] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidiae), is a cryptic species complex comprising a minimum of 24 cryptic species. Some members of this complex are important agricultural pests, causing considerable damage to vegetable as well as ornamental and horticultural crops. Asia I, one of the cryptic species of B. tabaci, is widely distributed in Asia. One hundred and sixty mitochondrial cytochrome oxidase I (COI) sequences from eight countries have been analyzed to investigate the geographic origin and current genetic structure of this cryptic species. Sixty different haplotypes were identified, with levels of genetic distances ranging from 0.001 to 0.021. A sign of possible genetic differentiation emerges from the differential distribution of dominant haplotypes in Indonesia and India compared to China. A possible ancient separation between Asia I in India and Indonesia and secondary contact in China has been hypothesized.
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Affiliation(s)
- Jian Hu
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
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Rakauskas R, Havelka J, Zaremba A. Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp.) collected from different hosts in Europe (Hemiptera, Aphididae). Zookeys 2013:255-67. [PMID: 24039523 PMCID: PMC3764526 DOI: 10.3897/zookeys.319.4251] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/27/2013] [Indexed: 11/23/2022] Open
Abstract
Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. Hyalopterus pruni and Hyalopterus persikonus emerged as a sister species, whilst Hyalopterus amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of Hyalopterus amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of Hyalopterus pruni and Hyalopterus persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.
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Affiliation(s)
- Rimantas Rakauskas
- Department of Zoology, Vilnius University, M. K. Čiurlionio 21/27, LT-03101, Vilnius, Lithuania
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