Intra-population genetic diversity and its effects on outlining genetic diversity of ciliate populations: Using Paramecium multimicronucleatum as an example |
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| Affiliation: | 1. Laboratory of Protozoology, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China;2. School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand;3. Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China;1. Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków 31-016, Sławkowska 17, Poland;2. Laboratory of Protistology and Experimental Zoology, Faculty of Biology and Soil Science, St. Petersburg State University, Saint Petersburg 199034, Universitetskaya nab. 7/9, Russia;1. Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea;2. Department of Biological Sciences, Inha University, Incheon 22212, South Korea;3. Institute of Life Science & Natural Resources, Korea University, Seoul 02841, South Korea;4. Department of Biology, Gangneung-Wonju National University, Gangneung 25457, South Korea;5. Consulting Engineering Office for Ecology, Radetzkystrasse 10, 5020 Salzburg, Austria;1. Department of Biological Science, College of Natural Sciences, University of Ulsan, Ulsan 680-749, South Korea;2. Department of Zoology, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, 842 15 Bratislava, Slovak Republic;1. College of Life Science, Northwest Normal University, Lanzhou 730070, China;2. Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China;3. College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China;4. Department of Zoology, King Saud University, Riyadh 11451, Saudi Arabia;5. Department of Biology, North Carolina Central University, Durham, 1801 Fayetteville St., NC 27707, USA;1. Key Laboratory for Space Bioscience and Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, PR China;2. Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an 710119, PR China;1. Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil;2. Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany;3. Dipartimento di Biologia, Università di Pisa, via A. Volta 4-6, Pisa, Italy;4. Department of Invertebrate Zoology, St. Petersburg State University, Russia;5. Laboratório de Genética Molecular de Eucariontes e Simbiontes, Departamento de Genética, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil |
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| Abstract: | Questions regarding ciliate distribution (endemism vs. cosmopolitanism) and degree of genetic diversity (high vs. low) remain unsettled, even when the same organism is under investigation. Presence of genes with high copy number and amplification of non-dominant haplotypes might account for the observed discordance in these studies. Herein, we used direct PCR and cloning sequencing to examine intra-population sequence diversity and its effect on assessments of phylogeography of Paramecium multimicronucleatum. Totally, 381 ITS1-5.8S rDNA-ITS2-28S rDNA and 304 mitochondrial cytochrome oxidase subunit I (COI) gene sequences were generated for 18 populations of P. multimicronucleatum. The following results were obtained: (1) Direct sequencing of PCR products captured the dominant ITS and LSU haplotypes, indicating that it is an appropriate strategy for constructing phylogeography of large-scale spatial populations. (2) Deep cloning was deemed more appropriate for the COI gene for population level studies, as direct sequencing could not easily capture the dominant haplotypes. (3) No endemic populations of P. multinucleatum were noted, indicating origin from a single founder population. (4) Nuclear genetic diversity within temporal populations was high, but only the dominant haplotypes seemed to be passed on to subsequent generations. |
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| Keywords: | Eukaryotic microbes Genetic polymorphisms Geography Sequencing strategy Spatial populations Temporal populations |
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