V12_OTU_biom_table

Biom Table for V1-2 16S amplico

V34_OTU_biom_table

Biom table for V3-4 16S amplico

V34_OTUs_alignment

OTU fasta alignment of V3-4 16S amplico

V12_OTUs_alignment

OTU fasta alignment for V1-2 16S amplico

Relative abundance of the seven cichlid core phyla in V12 (a) and V34 (b).

<p>Interquartile ranges (25th and 75th percentiles) and whiskers show data dispersion across species averages. Medians are shown as central horizontal lines. The two libraries returned a highly concordant pattern of core phyla abundance: the cichlid gut microbiota is dominated by Fusobacteria, Firmicutes and Proteobacteria, with the first two phyla largely fluctuating in relative abundance across species. Bacteroidetes, Planctomycetes, Actinobacteria and Verrucomicrobia are consistently less represented in all species (overall contributing less than 1% of the total reads).</p

Additional file 5: of Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes

qPCR results for P. philander. (XLSX 251 kb

Observed intraspecific core length (i.e. relative proportion of shared OTUs across 80% of conspecifics, shown as vertical lines), compared to random sampling of the whole dataset (barplots, 1000 permutations, p<0.05) for V12 (a) and V34 (B).

<p>There is a general trend for increase relative core length among conspecifics compared to random individuals, with few species carrying a significantly larger core in one or both libraries (<i>Astbur</i>, <i>Haptri</i>, <i>Hapmic</i> and <i>Permic</i>, p<0.05). <i>Perecc</i> was excluded from the analysis because it contributed with only one individual.</p

Principal coordinate analysis of beta diversity estimates for whole microbial communities of the 30 specimens analyzed (individual circles) based on binary Jaccard (a, b) and unweighted unifrac distances (c, d) for V12 (a, c) and V34 (b, d).

<p>Lines connect circles with the species centroid; species are colour-coded (see Legend). Despite few discrepancies between libraries, all plots illustrate two main clusters: the member of the tribe Tropheini, <i>Astbur</i> (in red), and the Perissodini species (<i>Haptri</i>, <i>Hapmic</i>, <i>Permic</i>, <i>Perecc</i> and <i>Plestr</i>), which largely superimpose in their microbiota space. The laboratory species <i>AstburLAB</i> carries a remarkably distinct microbiota from its wild conspecifics (<i>Astbur</i>).</p

Mean alpha diversity estimates per species (Chao1 (a), Shannon (b) and PD whole metric (c)), and standard deviation across conspecifics (bars).

<p>The two libraries significantly correlated in the pattern of diversity across-species for all three alpha indexes. <i>Astbur</i> carried the most biodiverse microbiota, significantly distinct from all other species and the same species kept in laboratory (i.e. <i>AstburLAB</i>) (p-value<0.05, all indexes, both libraries). Differences among Perissodini species were not statistically relevant (p-value>0.05, all indexes).</p

Cichlid core OTUs (80%).

<p>¹ OTUs from V12 (before semicolon), and OTUs from V34 (after semicolon). In case of OTUs returning the same best hit (putatively belonging to the same bacterial strain), only one AccNo is indicated.</p><p>² Correct classification was verified by concordance of sequence matches to several databases (RDPII, nt and Greengenes).</p><p>Cichlid core OTUs (80%).</p