Bezault_LVRS-AFLP_EVOL-10-0838

Matrix of AFLP Genotypes. Individuals by lines and loci genotype (presence/absence) in column

Phenotypic data for Astatotilapia cf. bloyeti from Lake Chala

Phenotypic data for Astatotilapia cf. bloyeti from Lake Chala, fish were collected in fall 2014. Data includes individual ID number (column A), number of circuli (as an age estimate, column B), depth of capture (C), wet weight (D), genus (E), capture site (F), morph assignement (G), linear morphological distances (H to V), mitochondrial haplotype (W), stable isotopes (X-Y), intestine length (Z), volumetric proportion of prey items in the stomachs (AA-AL), fullness index of the stomachs from 1 (empty) to 5 (full, AM), and colouration (AN-AU)

ElectronicSupplementaryFiles from The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fish

Appendices, supplementary figures and supplementary table

MbipiaPundamilia_M1

MbipiaPundamilia_M

MbipiaPundamilia_M4

MbipiaPundamilia_M

Sampling site information.

<p>Sampling site information.</p

Nucleotide diversity inside and outside genomic islands for each population.

<p>Genomic islands of parallel differentiation (IPDs) show on average a slightly but not significantly higher diversity than both the genomic background and genomic islands of non-parallel differentiation (INDs) in all populations and diversity did not differ between populations. Nucleotide diversity was calculated in non-overlapping windows spanning multiple RAD-loci that together contained 2,500–2,685 sequenced bases. Windows were grouped into genomic background (n = 1,104 windows, filled violin plots), overlapping with non-parallel islands (n = 17, triangles) and with parallel islands (n = 25, circles) and tested for group differences in mean nucleotide diversity using t-tests (n.s.: not significant; *: Bonferroni-adjusted p-value < 0.05). Marker color indicates how extreme genomic island diversity is compared to the genomic background.</p

Allele frequencies of parallel lake-stream differentiation SNPs in 19 islands of parallel lake-stream differentiation.

<p>Pie charts represent allele frequencies at the sites S1, S2, L1 and L2 of parallel divergent SNPs within parallel islands. Light and dark blue segments show the respective proportions of stream-like and lake-like alleles at those sites. Star-like dots show SNPs indicative of parallel lake-stream differentiation, while color coding of dots and vertical bars are as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005887#pgen.1005887.g004" target="_blank">Fig 4</a>.</p

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