data_Bontempsetal2016

data_Bontempsetal201

C_atl_RADseq_de_novo_assembly

Species: Cedrus atlantica Manetti Number of individuals: one single adult individual coming from the Luberon forest(43°47' N / 5°12' E, France) Plant tissue: needles (diploid) Sequencing method: Restriction site Associated DNA sequencing, paired-end sequencing using the Illumina HiSeq2000 platform (Illumina Inc., San Diego, CA) (2 x 101 bp) Data description: 66,656 contigs generated by de novo assembly Assembly tool: Velvet 1.2.06 (Zerbino & Birney 2008

C_atl_mRNAseq_de_novo_assembly

Species: Cedrus atlantica Manetti Number of indiivudals: one single 2-year-old seedling that originated from the the Luberon forest (43°47' N / 5°12' E, France) and was grown in a greenhouse in a pot Plant tissues: needles and roots (diploid) Sequencing method: transcriptome sequencing, paired-end sequencing using the Illumina HiSeq2000 platform (Illumina Inc., San Diego, CA) (2 x 101 bp) Data description: 130,184 contigs generated by de novo assembly Assembly tool: CLC Genomics Workbench 4.8 (CLC bio, Cambridge, MA

Sample locations of the 16 <i>M. schimitscheki</i> populations used in this study.

<p>Informations associated with the site codes below are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070818#pone-0070818-t001" target="_blank">Table 1</a>.</p

Genetic clustering of ten successive cohorts of <i>M. schimitscheki</i> (1999–2008).

<p>This Bayesian analysis implemented in STRUCTURE <b>used</b> a model allowing admixture and assumed two population clusters (K = 2). A: Graphical representation of the two genetic clusters, where each vertical line represents an individual and each color represents a cluster. Individuals are grouped by year of cohort production and diapause phenotype (SD = 2-year diapause, PD = 4-year prolonged diapause). B: Curve of Evanno's DeltaK corresponding to the STRUCTURE simulations. C: Assignment frequencies of individuals to each cluster in each group (in green and red according to the colors of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070818#pone-0070818-g003" target="_blank">Figure 3a</a>). Frequencies of admixed individuals are in blue.</p

Pairwise Fst divergence between successive cohorts of a natural invasive population of <i>M. schimitscheki</i> in southeastern France.

<p>Sample size for each genotyped cohort is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070818#pone-0070818-t002" target="_blank">Table 2</a>. The 2000 cohort was excluded due to low sample size (N = 5). Pairwise Fst matrix was obtained using all microsatellite loci after applying the correction for null alleles implemented in GENEPOP. Fst values in bold were significantly different from 0 (P<0.05).</p

Adult emergences from seeds of <i>C. atlantica</i> in southern French cohorts of <i>M. schimitscheki</i> over the five consecutive years following their productions (1999–2007).

<p>Emergences occurring beyond the 2-year obligatory diapause due to host cone maturation reflect propensities to prolonged diapause. Nc: number of cohorts surveyed per year of production on which mean emergence percentages and their standard errors (bars) were estimated. In 2008, only one population (Mont Ventoux) was surveyed for genetic purposes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070818#pone-0070818-t002" target="_blank">Table 2</a>).</p

Pairwise Fst divergence between 12 groups of <i>M. schimitscheki</i> produced between 1999 and 2008, expressing either a short (2 years: SD) or a prolonged diapause (4 years: PD) phenotype.

<p>Individuals of the n-SD group were produced at a year n and emerged at year n+2. Individuals of the n-PD group were produced at a year n and emerged at year n+4. Both 2000-PD and 2002-PD groups were excluded from this analysis due to low sample sizes (N<10).This pairwise Fst matrix was obtained using eight microsatellite loci after applying the correction for null alleles implemented in GENEPOP. Fst values in bold were significantly different from 0 (P<0.05). The numbers of genotyped individuals in each group are in subscript.</p

Propensity to prolonged diapause and indices of population genetics of ten successive cohorts (1999–20008) in a natural invasive population of <i>M. schimitscheki</i> collected at Mont Ventoux, France.

<p>SD: individuals (males and females) emerging after the obligatory 2-year diapause; 4-year PD: individuals (males and females) emerging after a 4-year prolonged diapause; N: number of genotyped females in the cohort; Na: average number of alleles; He: expected heterozygosity; Ho: observed heterozygosity; AR: allelic richness (minimum sample size of 5); PAR: private allelic richness estimated after a rarefaction procedure; St (P): probabilities associated with the rejection of the mutation–drift equilibrium using a sign test at the 0.05 threshold (probabilities lower than 0.05 are in bold).</p

Invasiveness assay of LL-BLG and LL-FnBPA+ BLG strains <i>in vivo</i>.

<p>Mice were orally administered with LL-BLG and LL-FnBPA+ BLGpre-incubated in FCS. One hour after the gavage mice were sacrificed. The internalized lactococci were enumerated in the whole small intestine 60 min after infection (after gentamicin treatment to kill extracellular bacteria from the intestinal lumen).</p