Lake Constance (47° 38’ N, 9° 22’ E) is a deep (max. depth 251m) and large (surface area 536 km²) postglacial lake in Central Europe. Originally, it harboured two charr species – Salvelinus umbla and S. profundus. The first is a medium-sized, colorful, winter spawning charr, which is widespread across Central European lakes, the second a small, pale, summer spawning, deepwater charr, which is endemic to Lake Constance (Schillinger 1901, Kottelat and Freyhof 2007). S. profundus has exceptionally large eyes and the upper jaw strongly overlaps the lower jaw. These traits are both considered adaptations to its life in the deep where it mostly feeds on profundal benthos (Schillinger 1901). During the second half of the last century, Lake Constance became eutrophic, resulting in oxygen-depletion in deep waters (IGKB 2004). The anoxic conditions harmed the development of eggs by profundal spawning fish (Baer et al. 2017). Thanks to strict management interventions, the lake has returned to an oligotrophic state, and oxygen is again available in the water column down to the greatest depth (IGKB 2004).

Individual measures of morphological distances, gill raker numbers, age, capture depth as well as microsatellite genotypes. Linear morphometric distances (TL-jaw_overlap) were measured on the preserved fish using a digital caliper, are given in mm, and are described in Figure S1 in the Appendix. Alleles of the 9 microsatellite markers are coded as retention time, missing data is indicated with 999.