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The complete mitogenome of Helixpomatia and the basal phylogeny of Helicinae (Gastropoda, Stylommatophora, Helicidae)
expand article infoOndřej Korábek, Adam Petrusek, Michail Rovatsos
‡ Charles University, Prague, Czech Republic
Open Access

Abstract

A complete mitochondrial genome of the Roman snail Helixpomatia Linnaeus, 1758 has been sequenced. The length and gene order correspond to that of other available helicid mitogenomes. We used the mitogenome sequence to reappraise the relationships among the four presumed principal groups of the helicid subfamily Helicinae. The results support the idea that the subfamily is divided between two western Palaearctic diversification centres: Iberian Peninsula and western Maghreb in the west, and Anatolia, the Aegean and Caucasus in the east. One group, the tribe Helicini, diversified in the east and the remaining three currently recognised tribes in the west. However, the exact relationships among lineages of the non-Helicini tribes could not be resolved.

Keywords

Allognathini , biogeography, Helicini , land snail, Mediterranean, mitochondrial genome, Otalini , phylogeny, Thebini

Introduction

Phylogenetic research on land snails has been thus far dominated by studies based on mitochondrial markers, mostly partial sequences of the cox1 (COI) and rrnL (16S rRNA) genes, not exceeding 2000 bp in total. These genes dominate not only in terms of the amount of sequences generated, but usually also by the variability of the sequences used if combined with sequences of nuclear loci. Although modern techniques targeting many loci simultaneously begin to advance also into the phylogenetics of pulmonate land snails (Teasdale et al. 2016), the mitochondrial markers will likely continue to be used not only due to relatively low costs and accessibility of the methods, but especially thanks to the wealth of previously published data. Mitochondrial genome sequences may then become handy for primer design, to facilitate assembly of further mitochondrial genomes from outputs of high-throughput sequencing, or directly as the data for phylogenetic analyses. In fact, one of the best resolved backbone phylogenies of Stylommatophora to date was reconstructed from mitochondrial genome sequences (Groenenberg et al. 2017).

We sequenced a complete mitogenome of Helixpomatia Linnaeus, 1758, a large and common European edible land snail species, to provide a reference for further work focused on the family Helicidae Rafinesque, 1815. We then used other helicid mitogenomic sequences to evaluate the support for the basal branching order in the subfamily Helicinae, which was reported by Neiber and Hausdorf (2015) from analyses based on partial sequences of rrnL and cox1 genes along with part of the nuclear rRNA gene cluster (5.8S rRNA, internal transcribed spacer 2, 28S rRNA).

The subfamily Helicinae includes several charismatic species, which are large, common, and edible. As the most prominent, we may mention Cepaeanemoralis (Linnaeus, 1758), famous for evolutionary studies of its colour polymorphism (e.g. Cain and Sheppard 1950, Jones et al. 1977, Silvertown et al. 2011), Cornuaspersum (Müller, 1774), the most commonly reared and consumed helicid species which became a pest in several regions around the globe (e.g. Rees 1955, Ansart et al. 2009), and Helixpomatia, a characteristic snail of Central Europe and the type species of the family’s type genus. Each of these three species represents a different lineage of the three presumed clades constituting the Helicinae, which were proposed and assigned a tribe status in the first comprehensive molecular phylogenetic study of Helicoidea by Razkin et al. (2015). Cepaea represents Allognathini Westerlund, 1902, HelixHelicini Rafinesque, 1815, and CornuOtalini Pfeffer, 1930. Razkin et al. (2015) also recognized a fourth tribe, the monotypic Thebini Wenz, 1923 represented by Theba Risso, 1826. The phylogenetic position of Theba has been contentious (Perrot 1939, Gittenberger and Ripken 1987, Bouchet and Rocroi 2005, Schileyko 2013, Razkin et al. 2015), but Helix, Cornu and Cepaea were generally considered closer to each other than to Theba, for which a separate tribe or even subfamily has been erected.

Neiber and Hausdorf (2015) used a more informative dataset than Razkin et al. (2015) and found Cepaea, Cornu and Theba to be more closely related to each other than to Helix and some other eastern Mediterranean genera. Their results suggest a principal biogeographic division within Helicinae, running approximately along the Apennine Peninsula and separating two equally old clades with centre of diversification in the western (Cornu, Cepaea and Theba, with their respective relatives) and the eastern (Helix and relatives; Korábek et al. 2015) Mediterranean basin, respectively. Considering the Paleogene/Neogene palaeogeographic evolution of the western Mediterranean (Giusti and Manganelli 1984, Rosenbaum et al. 2002, Advokaat et al. 2014, van Hinsbergen et al. 2014), it may be expected that the western taxa are indeed more closely related to each other.

Alternatively, the eastern group may be an offshoot of the western diversity, if the western group is paraphyletic. The systematic concept and monophyly of Otalini remains an open issue, as they (in the sense of Neiber and Hausdorf 2015) may be paraphyletic to both Thebini and Allognathini, and the east-west divide has not been unambiguously supported. The absence of an east-west divide in the phylogeny would lend support to a Western European origin of the whole subfamily Helicinae and to the north-western Maghreb being a refugium of its oldest and perhaps phylogenetically most distinctive lineages. Apart from biogeographic implications, the branching order at the base of the Helicinae has for us also a practical significance for the selection of appropriate outgroup taxa for analyses of relationships between Helix and related genera.

There are already published complete mitochondrial genome sequences of Ce.nemoralis (Terrett et al. 1996; NCBI accession number NC_001816), Co.apersum (Gaitán-Espitia et al. 2013; NCBI accession number NC_021747) and Thebapisana (Müller, 1774) (Wang et al. 2018b; Genbank accession number MH362760), as well as of a convenient outgroup species Cylindrusobtusus (Draparnaud, 1805) (Groenenberg et al. 2012; NC_017872). Combined with the newly sequenced mitogenome of Helixpomatia they offered an opportunity to verify the relationships between the four Helicinae tribes.

Methods

Sequencing and annotation

As a starting point we utilised mitochondrial sequences obtained from transcriptome sequencing (mRNA-Seq) performed for a different project, which included also a single H.pomatia individual (from Rožmitál pod Třemšínem, Czechia). In detail, 20 mg of foot tissue was homogenised with MagNA Lyser (Roche) and total RNA was extracted using the standard Trizol reagent protocol (Thermo Fisher Scientific). The barcoded and stranded mRNA-sequencing libraries were prepared using the Illumina TruSeq mRNA v2 sample preparation kit (Illumina, San Diego, CA, USA). The libraries were loaded on an Illumina NextSeq 500 sequencer and 75 bp were sequenced uni-directionally, resulting in approx. 87 million reads. The raw Illumina reads were trimmed for adapters and low-quality bases in GENEIOUS R7.1 (Kearse et al. 2012) with the trim utility using default parameters. Reads with a length of less than 50 bp were removed from the dataset. The trimmed reads were checked for quality in FASTQC (Andrews 2010) and MULTIQC (Ewels et al. 2016), and mapped with GENEIOUS R7.1 to the mitogenome of Co.aspersum. The partial sequences of 12 protein coding genes (all but atp8) of H.pomatia (GenBank acc. nos. MK400678-MK400689) were extracted from the alignment and were used to design primers for PCR amplification of the mitogenome of H.pomatia in few long overlapping fragments.

For amplification we used another individual sharing an identical cox1 sequence with the transcriptome data. The sample originated from Huldsessen, Bavaria, Germany (48.3978N, 12.7084E) and the shell voucher is deposited in the National Museum, Prague, lot P6M 29637. We designed specific primers with Primer BLAST (Ye et al. 2012) based on the transcriptome sequences and previous 16S data. Then, we amplified the mitogenome in several overlapping segments of ca. 4000–6000 bp with Platinum SuperFi proof-reading DNA polymerase (Invitrogen, Carlsbad, CA, USA) and sequenced ends of the fragments using the primers used for PCR. Resulting gaps were iteratively filled in further rounds of sequencing using new individual-specific primers flanking the gaps. The reads were aligned to the Co.aspersum sequence as reference and combined into a single 14070 bp contig. The sequence is available at GenBank (MK347426).

We used MITOS (Bernt et al. 2013b) to annotate the genome sequence, which identified the full set of the expected 2 rRNA, 22 tRNA, and 13 protein-coding genes (Table 1). However, we made manual adjustments to the MITOS output regarding the limits of rRNA and protein-coding genes, which were inconsistent between the MITOS annotation and the Ce.nemoralis, Co.aspersum, and Cy.obtusus RefSeq entries. To be more specific, we looked for start- and stop-codons whose positions would be compatible between H.pomatia and the other three species, and considered also the positions of adjacent genes. However, as gene overlap and alternative start- and incomplete stop-codons may occur in invertebrate mitogenomes (Bernt et al. 2013a) including land snails (Gaitán-Espitia et al. 2013), the start and end positions of the genes remain tentative until sequences of the coded proteins and rRNAs are known. The 16S gene was not recovered in one piece by MITOS, probably because the structure towards the 3’ end was too variable; so we combined the two fragments.

NCBI Transcriptome Shotgun Assembly database accession numbers of the Cepaeanemoralis sequences used in analysis.

cox1 GFLU01084822
nd6 GFLU01007552
nd5 GFLU01092360
nd1 GFLU01092360
nd4L GFLU01092360
cyb GFLU01076837
cox2 GFLU01076837
atp6 GFLU01122686
nd3 GFLU01014131
cox3 GFLU01122685
nd4 concatenated from GFLU01122684, GFLU01122687, GFLU01122688

Phylogenetic analyses

For the phylogenetic analysis we used a concatenated alignment of 12 protein-coding genes, excluding the short and fast evolving atp8. From annotated, previously published sequences (accession numbers NC_001816, NC_021747 and NC_017872), we extracted the individual genes following the annotation in the NCBI RefSeq database. However, previous studies, which used the sequence of Ce.nemoralis in mitogenomic phylogenetic analyses, repeatedly resulted in a spuriously long branch for this species (Knudsen et al. 2006, González et al. 2016, Minton et al. 2016, Groenenberg et al. 2017). A closer examination of the mitogenome sequence and translation of its protein coding regions revealed a very low quality of the sequence (see also White et al. 2011). Compared to newer Ce.nemoralis sequences there seemed to be frequent indels and suspect amino-acid changes were found in translated sequences. The very high number of errors in the sequence probably stems from the complex way it was obtained, which involved two rounds of cloning, and generally the immature methods of that time (Terrett et al. 1996). Therefore, we replaced the sequences of protein-coding genes of Ce.nemoralis by data retrieved from a transcriptome shotgun assembly (TSA) (Kerkvliet et al. 2017; NCBI BioProject PRJNA377398; see Table 1). To extract the mitochondrial genes from the transcriptome data, we performed for each gene a BLASTn search limited to Ce.nemoralis with the respective part of NC_001816 as the query in the NCBI TSA database. The sequence of T.pisana (MH362760) was not annotated, so we identified the individual genes by alignment with the extracted gene sequences of the other four species.

We performed the phylogenetic analyses in three stages, staring with the analysis of the nucleotide sequences. The protein coding genes were aligned with TRANSLATORX (Abascal et al. 2010), which aligns nucleotide sequences based on their amino acid translations. TRANSLATORX was run with the MAFFT 5 aligner (Katoh et al. 2005) and the invertebrate mitochondrial genetic code; other settings were left at their defaults. The resulting alignments were trimmed to a common length of the sequences. We specified a partitioning scheme consisting of the three codon positions and used IQTREE 1.6.5 to test the scheme against simpler scenarios, select substitution models (Kalyaanamoorthy et al. 2017) and to perform a maximum likelihood phylogenetic analysis (Nguyen et al. 2015, Chernomor et al. 2016). The model selection suggested the TIM2+F+I+Γ4, TVM+F+Γ4, and TIM2+F+Γ4 models for the three partitions. We used standard bootstrap and Shimodaira-Hasegawa-like approximate likelihood ratio tests (SH-aLRT; Guindon et al. 2010; both with 1000 replicates) to calculate branch supports. Then we translated the alignment into amino acid sequences, leaving it a single partition with 417 parsimony informative sites out of the total of 3489 sites, and run the model selection (selecting mtZoa+F+Γ4 as the best fit substitution model; Rota-Stabelli et al. 2009) and phylogenetic analysis as above.

The resulting topologies showed substantial differences in branch lengths between taxa. To explore if the resulting topology was influenced by long-branch attraction (LBA), we employed a site-heterogeneous mixture model using posterior mean site frequencies (PMSF; Wang et al. 2018a). This approach has been shown to effectively overcome LBA, and even to be somewhat prone to long-branch repulsion. Thus, if a grouping is due to LBA, this approach is likely to reveal that. We calculated the PMSF under the mtZoa+C60+F+Γ4 mixture model. As a guide tree we used successively all the three alternative topologies in the western group: Cornu+(Theba+Cepaea), (Cornu+Theba)+Cepaea, and (Cornu+Cepaea)+Theba.

Finally, to account for differences in nucleotide composition, we performed a Bayesian phylogenetic analysis of the nucleotide data with a branch-heterogeneous model allowing branches to have distinct compositions as implemented in P4 1.0 (Foster 2004; http://p4.nhm.ac.uk/). We performed the analysis in two runs of 1,000,000 generations with four heated chains each, using the same partitioning scheme as with IQTREE and the closest possible substitution models. For each data partition we allowed for three different nucleotide compositions to be assigned to tree branches randomly. We sampled each 1000th generation and discarded the first 20% of samples of each run as burn-in. To account for differences in results caused by the use of different inference algorithms in the methods, we repeated the analysis in P4 also assuming composition homogeneity.

Results

We have sequenced a complete mitogenome of H.pomatia, from a specimen representative of a common central-European lineage (Korábek et al. 2018) of this broadly distributed snail species. The length and gene content and order (Table 2) correspond with those of mitogenomes of Ce.nemoralis, T.pisana and Co.aspersum, the other Helicinae species with available mitogenome sequences.

Annotation of the mitogenome of Helixpomatia. The plus/minus strand refers to the position of the cox1 gene.

Gene Start position Start codon End position Stop codon Strand
cox1 1 ATG 1530 TAA plus
trnV 1527 1589 plus
rrnL (16S) 1657 2555 plus
trnL1 2566 2626 plus
trnA 2630 2691 plus
nd6 2692 TTG 3180 TAA plus
trnP 3177 3239 plus
nd5 3285 ATG 4955 TAA plus
nd1 4970 ATA 5842 TAG plus
nd4L 5842 GTG 6118 T-- plus
cyb 6119 ATG 7190 T-- plus
trnD 7234 7285 plus
trnC 7286 7345 plus
trnF 7346 7404 plus
cox2 7405 ATG 8071 T-- plus
trnY 8073 8119 plus
trnW 8121 8180 plus
trnG 8186 8233 plus
trnH 8237 8296 plus
trnQ 8296 8355 minus
trnL2 8356 8411 minus
atp8 8405 ATA 8578 TAG minus
trnN 8579 8638 minus
atp6 8637 ATG 9290 T-- minus
trnR 9291 9349 minus
trnE 9349 9411 minus
rrnS (12S) 9479 10173 minus
trnM 10173 10235 minus
nd3 10241 TTG 10581 T-- minus
trnS2 10579 10629 minus
trnT 10632 10693 minus
cox3 10693 ATG 11472 TAA minus
trnS1 11664 11719 plus
nd4 11720 ATA 13027 TAA plus
trnI 13030 13090 plus
nd2 13091 GTG 14021 T-- plus
trnK 14022 14070 plus

The phylogenetic analyses in all cases recovered the expected split between the eastern Helix and the western group of Theba, Cepaea, Cornu, assuming Cylindrus as an outgroup (Figure 1). This grouping received equivocal support in the analysis based on the nucleotide data, but it increased with amino acid data and further when using site-heterogeneous model. The support thus increased as the analyses got less sensitive to substitution saturation and among site heterogeneity. In the western group, the results united Theba and Cepaea to the exclusion of Cornu, but this branch received positive support only from bootstrap with the nucleotide data. Especially analyses of the amino-acid alignment with the site-heterogeneous model based on alternative guide trees resulted in very low support for the branch uniting Cepaea and Theba. The Bayesian analysis of nucleotide data with P4 recovered the same topology as the maximum likelihood analysis but with full support, regardless whether homo- or heterogeneous model was used.

Figure 1. 

The inferred phylogenetic relationships between the five helicid mitogenomes available. Branch supports are given for maximum likelihood analyses based on nucleotide data, amino acid data under homogeneous model, and amino acid data under site-heterogeneous model (in this order). The latter was run under alternative settings, see details in the text. Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-aLRT) and standard bootstrap percentages (BP) are reported. Values of SH-aLRT >90 % and BP >75 % are considered positive support. Cylindrus is included as an outgroup.

Discussion

Because Theba and Cepaea had the longest branches in the tree, which had short internal branches, and there is no independent indication of the relationship between Theba and Cepaea, we suspected the result to be caused by the LBA (Bergsten 2005). Theba is annual to biannual and semelparous (Heller 1982, Cowie 1984), unlike the other helicids, which are more long-lived (Pollard 1975, Bisenberger et al. 1999; Ansart et al. 2009). The genus may generally cause problems in phylogenetic inference if the difference in life history results in differece in substitution rate (Thomas et al. 2010; cf. Saclier et al. 2018). In addition, analysis of the nucleotide composition of the five taxa revealed substantial differences, where Cornu (GC 30.5%) and Cepaea (GC 41.6%) differed the most, which could obscure potential relationship between the two species. The low support with presumably more robust methods suggests that the relationship between Cepaea and Theba could be an artefact.

Our results are consistent with the hypothesis that Helicinae are principally divided into a western (mainly Iberia, western Maghreb, Macaronesia) and an eastern (Caucasus, Anatolia, Greece) group (Neiber and Hausdorf 2015). The split between these two lineages probably occurred no later than during the Late Eocene‒Early Oligocene (Neiber and Hausdorf 2015), but the east-west pattern in the distribution of the two lineages persists despite 30 million years having elapsed since the split. Only two Helix species naturally represent the eastern group west of ca 9°E (one in Europe, one in Africa; Neubert 2014, Korábek et al. 2018), and two species of Cepaea (Europe; Welter-Schultes 2012) and few species of Eremina Pfeiffer, 1855 (northern Africa; Ali et al. 2016) represent the western group east of 18°E.

Despite analysing a substantially higher number of genes than Razkin et al. (2015) and Neiber and Hausdorf (2015), we also could not resolve the relationships between Cornu, Cepaea and Theba. We assume that additional lineages should be analysed in order to resolve all the major phylogenetic and biogeographic problems within the western branch of Helicinae. These include Macularia Albers, 1850, whose phylogenetic position is equally problematic as that of Theba (Nordsieck 1987; Schileyko 2006; Neiber and Hausdorf 2015), the closest relative of Theba (perhaps Eremina, but see Holyoak et al. 2018), and the type genera of the tribes Otalini and Allognathini. Nevertheless, it is likely that only analyses of multiple nuclear loci will yield robust estimates of the basal relationships of Helicinae due to high and lineage-specific evolutionary rates of the mtDNA and the saturation of nucleotide substitutions.

Acknowledgements

We thank Tereza Kosová for help in the lab, Lucie Juřičková for financial support, and Marco T. Neiber for review and language polishing. Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures” (CESNET LM2015042) is greatly appreciated. MR was supported by Charles University Research Centre program (204069).

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