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AFLP Reveals Low Genetic Diversity of the Bryozoan Pectinatella Magnifica

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AFLP Reveals Low Genetic Diversity of the Bryozoan Pectinatella Magnifica Moravcová et al. J of Biol Res-Thessaloniki (2017) 24:12 DOI 10.1186/s40709-017-0069-8 Journal of Biological Research-Thessaloniki SHORT REPORT Open Access AFLP reveals low genetic diversity of the bryozoan Pectinatella magnifca (Leidy, 1851) in the Czech Republic Vendula Moravcová1, Jana Moravcová1, Vladislav Čurn1, Zuzana Balounová1, Josef Rajchard1 and Lenka Havlíčková1,2* Abstract Background: Non-native species have aroused scientifc interest because of their ability to successfully colonise areas to which they have been introduced, despite their sometimes limited genetic variation compared to their native range. These species establish themselves with the aid of some pre-existing features favouring them in the new envi- ronment. Pectinatella magnifca (Leidy, 1851), the freshwater magnifcent bryozoan, is non-native in Europe and Asia. This study was designed to determine the genetic diversity and population structure of P. magnifca colonies collected from the Protected Landscape Area (PLA) and UNESCO Biosphere Reserve Třeboňsko (the Czech Republic) in the 2009 and 2011–2014 periods using Amplifed Fragment Length Polymorphism (AFLP). Findings: The vast majority of the examined non-native colonies, except three colonies sampled in 2012, expressed very low levels of genetic variation, not diferentiating from the USA native colony. The Bayesian clustering approach grouped the 28 accessions into two genetically diferent populations. Conclusions: The data suggest relatively low gene diversity within all colonies, which might refect the recent expan- sion of P. magnifca in the Czech Republic. Keywords: Invasive species, Non-native species, Pectinatella magnifca, Bryozoan Findings containing 12–18 genetically identical zooids and can Background lead to considerable dimension and weight, as in the Pectinatella magnifca (Leidy, 1851), a freshwater bryo- case of nearly 1 m diameter and 70 kg colony described zoan species that naturally inhabits lakes and rivers in by Balounová et al. [7]. Recent studies have focused on eastern North America [1, 2], has been recently spread- the determination of evolutionary relationships within ing in Europe and western Asia [3–5]. Its colonies begin P. magnifca, incorporating morphological traits (such life from a germinated statoblast (a product of asexual as the morphology of the statoblasts, white spots on reproduction) or settled larva (the result of sexual repro- lophophora, pigmented mouth), molecular approaches, duction). Once formed, colonies exude a protective gel- or a combination of both morphological traits and atin-like matrix of exopolymers, enabling attachment to genetic data [8]. Most systematic (phylogenetic) stud- diferent submerged natural or artifcial substrates [6] ies including P. magnifca have used nuclear ribosomal as fat sheets (in the form of thin flms), as sessile globu- (ssrDNA, lsrDNA) and mitochondrial (rrnL, rrnS, cox1, lar colonies, or as gelatinous balls foating in water. Te cox3, cytb) genes [9–13]. However, to determine intraspe- colonies are covered on their surface with rosettes, each cifc relatedness, ribosomal and mitochondrial genes are not sufcient, as demonstrated for instance in the case of using mitochondrial cytochrome c oxidase subunit I gene *Correspondence: [email protected] (cox1) for intraspecifc analysis of geographically distinct 2 Department of Biology, University of York, York YO10 5DD, UK colonies of P. magnifca in Korea [8]. AFLP markers are Full list of author information is available at the end of the article © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Moravcová et al. J of Biol Res-Thessaloniki (2017) 24:12 Page 2 of 6 considered as one of the most popular tools for genetic CA, USA) according to the manufacturer’s protocol. analysis in the felds of evolutionary genetics, ecology Te quality and quantity of obtained DNA was veri- and conservation of genetic resources [14]. Te tech- fed by using a spectrophotometer BioSpec Nano (Shi- nique combines a high-information content and fdelity madzu, Tokyo, Japan). Te DNA was tested by using with the possibility of carrying out genome wide scans. specifc primers (Pm28SF: 5′-CTTTTCAGCCAA However, a potential problem with this technique is the GCACATGA-3′ and Pm28SR: 5′-AAACCTCGCGTA lack of homology of bands with the same electrophoretic GAGCAAAA-3′), designed for this study with Primer3 mobility, what is known as fragment-size homoplasy [15]. software [16], amplifying a fragment of 398 bp. Prim- Tis study is the frst of its kind, where the random whole ers were designed based on the unique P. magnifca 28S genome AFLP analysis was applied to determine relat- rRNA gene sequence available in GenBank (FJ409576.1), edness of geographically and time-distant colonies of P. and were chosen on the basis of their performance and magnifca. Te results provide the frst comprehensive specifcity against alternative primers. Te specifcity summary of the methodology used. was confrmed by sequencing. PCR was performed with 3 ng of DNA template, mixed with 1 µl (10 µM) of each Methods primer, 12.5 µl PPP MM (TopBio, Prague, Czech Repub- A total of 29 samples from colonies of Pectinatella mag- lic) and distilled water to make a fnal volume of 20 µl. nifca were collected between July and September in PCR was performed using the following programme: pre- 2009 and 2011–2014. From these, 28 colonies were sam- denaturation for 5 min at 95 °C, 35 cycles of 30 s at 95 °C, pled from seven diferent locations within the Protected 1 min 60 °C and 40 s at 72 °C, fnally, 10 min at 72 °C. Landscape Area and Biosphere Reservation of Třeboňsko PCR products were subjected to electrophoresis on 1.5% (in the Czech Republic) (Fig. 1) and one representative agarose gel in 1 × TBE bufer, and detected through eth- sample was collected from the native region of P. mag- idium bromide staining. nifca, in the Pacifc Northwest of the USA (Additional AFLP analysis was carried out as described by Vos fle 1: Table S1). For each geographic location, up to eight et al. [17] with four primer combinations: fuores- 2 transects of 20 m (10 m along the coast by 2 m into the cent dye-labelled primer EcoRI + ACG/MseI + AGT, water) were used to search for and sample statoblasts EcoRI + ACG/MseI + ACC, EcoRI + ACG/MseI + AAC from colonies. Te samples were fxed in 96% ethanol and EcoRI + ACG/MseI + ATT. and stored at 4 °C, or were directly stored without fxa- One microliter of selective PCR amplicons, 0.4 μl of ™ ® tion in − 20 °C. the GeneScan 500 LIZ (Life Technologies, USA) and Total genomic DNA was extracted from statoblasts 11 μl of formamide, were denatured at 95 °C for 5 min, by using DNeasy ® Blood & Tissue kit (Qiagen, Valencia, cooled on ice immediately and directly forwarded to an 1. Veselí I. 2. Vlkov 3. Podřezaný 4. Cep I. 5. Nový 6. Kanclíř 7. Hejtman 0 20 40 80 120 160 0 5.5 11 16.5 22 Kilometers Kilometers Fig. 1 Map representing the sampled locations from the Třeboňsko region in the Czech Republic Moravcová et al. J of Biol Res-Thessaloniki (2017) 24:12 Page 3 of 6 capillary electrophoresis on an ABI 3500 genetic analyzer (7.42%), 8d and 6.1e (7.75%), and same distance of 7.94% (Life Technologies, USA) and data were analysed by Gen- was observed between samples 5.2c and 8d and also 2a eMapper 5.0 software (Life Technologies, USA). Signals and 1.1c. obtained from fragment analyzer were transformed into Te STRUCTURE results divided samples into two a binary character matrix with 1 for the presence or 0 for groups (K = 2) with no consistent trend diferentiating the absence of a band at a particular position. individual localities or years of collection by using these Cluster and principal component analysis (PCA) were groups (Additional fle 2: Table S2). performed. Tese analyses were calculated by using R software (cran.r-project.org, version 3.2.3, accessed in Discussion 2015). Analysis of the genetic structure of the popula- Recent studies show that the level of expansion of the tion was carried out assigning samples to K populations non-native Pectinatella magnifca is increasing not only according to allele frequencies of each locus by using in Europe and Asia, but also within the country of its Bayesian model-based clustering method with Struc- native origin [2, 4, 5, 8, 20]. Te AFLP technique is very ture 2.3.4 [18]. Te program was run 10 times at each of popular in population and evolutionary genetic studies 10 diferent K values (1–10) with a period of 5000 burn- of organisms with no prior sequence knowledge, aiming in steps followed by 50,000 iterations. Te admixture to assess the degree of variability and genetic structure model with independent allele frequencies was used in among tested individuals. Te advantage of this tech- all analyses. Te number of populations was inferred by nique is genome wide screening, which provides a high plotting the log probability of the data [Ln P(D)] for each information content. However, every methodology can K value. Also, in order to determine the most appropriate number of K, ΔK was calculated as described by Evanno et al. [19]. Results AFLP analysis with four primer combinations ampli- fed 496 bands, ranging in size of 36–480 bp, from which 79.4% were polymorphic (394 bands).
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