Coalescence-based mtDNA control region mismatch analysis of the six Lake Apoyo <i>Amphilophus</i> species showing different demographic histories.

<p>Expansions ca. two mutations ago occurred in <i>A</i><i>. chancho</i> and <i>A</i><i>. supercilius</i> and ongoing population expansions are detected in <i>A. astorquii</i><i>, </i><i>A</i><i>. globosus</i> and <i>A</i><i>. zaliosus</i>.</p

Results of STRUCTURE clustering analyses.

<p>Top: on complete AFLP matrix for K6 with group information, GENSBACK 2 and MIGPRIOR 0.05; Middle: same as top but on the 49 AFLP outlier loci only; Bottom: on the 49 outlier loci for K6 without group information. Species of sample origin given above, sample IDs of individuals given below.</p

AFLP neighbor-network based on Link’s genetic distances.

<p>AFLP neighbor-network based on Link’s genetic distances.</p

Neighbor-joining tree based on Link et al. distance measure using 2297 AFLP loci with bootstrap values ≥ 50 given above nodes.

<p>Neighbor-joining tree based on Link et al. distance measure using 2297 AFLP loci with bootstrap values ≥ 50 given above nodes.</p

Median-joining parsimony-network based on the mitochondrial control-region, containing nine equal parsimonious trees.

<p>Circle size corresponds to sample size, branch length correlates with number of mutational steps.</p

GERFWF_Alignment_1056

This alignment comprises 1056 DNA barcodes belonging to 93 species of freshwater fishes and lampreys from Germany

COI sequence alignment

DNA sequence alignment containing all 3165 individuals. Sequence labels contain genus, species, drainage system, country of origin, field or museum ID, and sample ID