Genetic Diversity in the Paramecium aurelia Species Complex

Department of Biology, Indiana University, USA.
Molecular Biology and Evolution (Impact Factor: 9.11). 12/2008; 26(2):421-31. DOI: 10.1093/molbev/msn266
Source: PubMed


Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.

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Available from: Francesco Catania,
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    • "Based on macronuclear genome sequences analyses, McGrath et al. showed that P. sexaurelia diverged immediately following or concurrently with the recent WGD. Similarly, that species was revealed to occupy the most distant position in previous studies (Catania et al. 2009; Coleman 2005) as well as in the present work. Although currently there are no genome data for P. sonneborni , P. jenningsi and P. schewiakoffi, on the basis of the nuclear marker analysis (Fig. 4) and assumptions concerning the time of P. sexaurelia separation (McGrath et al. 2014), we hypothesize that these three species (P. "
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    ABSTRACT: The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.
    Protist 07/2015; 166(4):438-456. DOI:10.1016/j.protis.2015.07.001 · 3.05 Impact Factor
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    • "Many DNA sequencing methods are available to analyse protist community composition (Hajibabaei et al. 2011; Zufall, Dimon & Doerder 2013), to characterize genetic diversity of species complexes (e.g. Catania et al. 2009), or to understand the evolution of genes and genomes (e.g. Brunk et al. 2003; Moradian et al. 2007). "
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    ABSTRACT: 1.Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are measured in order to study processes and patterns at different spatiotemporal scales and across all levels of biological organization. This includes measurements of body size, mobility, or abundance, in order to understand population dynamics, dispersal behaviour, and ecosystem processes. Also, a variety of manipulations are employed, such as temperature changes or varying connectivity in spatial microcosm networks. 2.Past studies, however, have used varying methods for maintenance, measurement, and manipulation, which hinders across-study comparisons and meta-analyses, and the added value they bring. Furthermore, application of techniques such as flow-cytometry, image and video analyses, and in-situ environmental probes provide novel and improved opportunities to quantify variables of interest at unprecedented precision and temporal resolution. 3.Here, we take the first step towards a standardization of well-established and novel methods and techniques within the field of protist microcosm experiments. We provide a comprehensive overview of maintenance, measurement, and manipulation methods. An extensive supplement contains detailed protocols of all methods, and these protocols also exist in a community updateable online repository. 4.We envision that such a synthesis and standardization of methods will overcome shortcomings and challenges faced by past studies, and also promote activities such as meta-analyses and distributed experiments conducted simultaneously across many different laboratories at a global scale.
    Methods in Ecology and Evolution 02/2015; 6(2). DOI:10.1111/2041-210X.12312 · 6.55 Impact Factor
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    • "The choice of these two species was motivated by their different evolutionary distances from P. tetraurelia (Catania et al. 2009), with P. sexaurelia being one of the earliest diverging aurelias following the most recent WGD and P. biaurelia diverging from P. tetraurelia much later (Fig. 1). "
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    ABSTRACT: The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are presented and compared to the published sequence of P. tetraurelia. Levels of duplicate-gene retention from the recent WGD differ by >10% across species, with P. sexaurelia losing significantly more genes than P. biaurelia or P. tetraurelia. In addition, historically high rates of gene conversion have homogenized WGD paralogs, probably extending paralogs lifetime. The probability of duplicate retention is positively correlated with GC content and expression level; ribosomal proteins, transcription factors, and intracellular signaling proteins are overrepresented among maintained duplicates. Finally, multiple sources of evidence indicate that P. sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species. Additionally, though P. biaurelia and P. tetraurelia diverged from each other much later, there are still over 100 cases of divergent resolution between these two species. Taken together, these results indicate that divergent resolution of duplicate genes between lineages acts to reinforce reproductive isolation between species in the Paramecium aurelia complex.
    Genome Research 08/2014; 24(10). DOI:10.1101/gr.173740.114 · 14.63 Impact Factor
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