Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Endemic species flocks inhabiting ancient lakes, oceanic islands and other
long-lived isolated habitats are often interpreted as adaptive radiations.
Yet molecular evidence for directional selection during species flocks
radiation is scarce. Using partial transcriptomes of 64 species of Lake
Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups,
we report a revised phylogeny of this species flock, and analyze evidence
for positive selection within the endemic lineages. We confirm two
independent invasions of amphipods into Baikal and demonstrate that
several morphological features of Baikal amphipods, such as body armor and
reduction of appendages and sensory organs, evolved in several lineages in
parallel. Radiation of Baikal amphipods has been characterized by short
phylogenetic branches and frequent episodes of positive selection which
tended to be more frequent in the early phase of the second invasion of
amphipods into Baikal when the most intensive diversification occurred.
Notably, signatures of positive selection are frequent in genes encoding
mitochondrial membrane proteins with electron transfer chain and ATP
synthesis functionality. In particular, subunits of both the membrane and
substrate-level ATP synthases show evidence of positive selection in the
plankton species Macrohectopus branickii, possibly indicating adaptation
to active plankton lifestyle and to survival under conditions of low
temperature and high hydrostatic pressures known to affect membranes
functioning. Other functional categories represented among genes likely to
be under positive selection include Ca-binding muscle-related proteins,
possibly indicating adaptation to Ca-deficient low mineralization Baikal
waters.