Intra-population genetic diversity and its effects on outlining genetic diversity of ciliate populations: Using Paramecium multimicronucleatum as an example.

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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