Asexual lineages often exhibit broad distributions and can thrive in extreme habitats compared to their sexual counterparts. Several hypotheses can be proposed to explain this pattern. Asexual lineages could be versatile genotypes with wide environmental tolerance, enabling their dispersal and persistence across large geographic areas. Alternatively, asexual genotypes could be ecological specialists that thrive in specific environments and outcompete relatives colonizing distantly related areas with similar conditions in the process. Several aphid species feature widespread obligate asexual lineages, commonly known as “superclones”. Yet it is often unknown whether these clones are widespead ecological generalists or  successful specialists. To explore these hypotheses, we examined climatic niche differentiation among six globally distributed obligate asexual lineages of the cosmopolitan aphid pest, Brachycaudus helichrysi. To insure that we were investigating the aphid genotype niche and not a by-product of their association with endosymbionts mediating thermal tolerance, we first verified that clones hosted similar endosymbiont communities. Subsequently, we conducted multivariate analyses on clone occurrence data on a worldwide scale. Our results revealed that despite their global distribution, B. helichrysi superclones occupy different climatic niches. This study represents the first evidence that aphid superclones distribution can be mediated by distinctive ranges of climatic tolerance.

This data results from the sequencing of a 251 bp fragment of the 16S rDNA bacterial gene amplified in a worldwide sample of the leaf curl plum aphid pest (Brachycaudus helichrysi). The table with collection details is also attached to this data submission.

A total of 102 individuals, representative of six aphid clones and the diversity of their geographic distribution were used for characterising bacterial endosymbionts. Using DNA extracts from the individuals utilised for microsatellite genotyping in Piffaretti et al. (2013), we amplified a 251 bp portion of the V4 region of the 16S rRNA gene (Mizrahi-Man et al. 2013) and used targeted sequencing of indexed bacterial fragments on a MiSeq (Illumina) platform (Kozich et al. 2013) following the protocol described in Jousselin et al. (2016). Briefly, each DNA sample was amplified twice (replicates were conducted on distinct 96-well microplates). We also used negative controls (DNA extraction and PCR controls conducted on blank templates) to filter out bacterial contamination during laboratory procedures. A total of 216 PCR products (comprising DNA extracts and controls) were obtained. After purification of PCR products with a PCR clean-up and gel extraction kit (Macherey-Nagel), and quantified with the Kapa Library Quantification Kit (Kapa Biosystems). Paired-end sequencing of the DNA pool was carried out on a MISEQ (Illumina) FLOWCELL with a 500-cycle Reagent Kit v2 (Illumina).

We first applied sequence filtering criteria following Illumina’s quality control procedure. We then merged paired sequences into contigs with FLASH V.1.2.11 (Magoč and Salzberg 2011) and trimmed primers with CUTADAPT v.1.9.1 (Martin 2011). We then used the FROGS pipeline (Escudié et al. 2018)to generate an abundance table of symbiont lineages across samples.

Escudié, F., Auer, L., Bernard, M., Mariadassou, M., Cauquil, L., Vidal, K., Maman, S., Hernandez-Raquet, G., Combes, S. and Pascal, G. 2018. FROGS: find, rapidly, OTUs with galaxy solution. - Bioinformatics 34: 1287–1294.

Jousselin, E., Clamens, A.-L., Galan, M., Bernard, M., Maman, S., Gschloessl, B., Duport, G., Meseguer, A. S., Calevro, F. and Coeur D’Acier, A. 2016. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. - Mol Ecol Resour 16: 628–640.

Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. and Schloss, P. D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. - Appl Environ Microbiol 79: 5112–5120.

Mizrahi-Man, O., Davenport, E. R. and Gilad, Y. 2013. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. - PLoS One 8: e53608.

Piffaretti, J., Clamens, A.-L., Vanlerberghe-masutti, F., Gupta, R. K., Call, E., Halbert, S. and Jousselin, E. 2013a. Regular or covert sex defines two lineages and worldwide superclones within the leaf-curl plum aphid (Brachycaudus helichrysi, Kaltenbach). - Mol Ecol 22: 3916–3932.