Additional file 4. Partitioning scheme, evolutionary models and alignments used for phylogenetic and selection analyses. from Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of <i>Gammarus pisinnus</i> and <i>Gammarus lacustris</i>

We hypothesized that the mitogenome of <i>Gammarus lacustris</i> (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of <i>Gammarus pisinnus</i> (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% <i>atp8</i> to 76.1% <i>cox1</i>). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, <i>pisinnus</i> and <i>fossarum</i> exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in <i>atp8</i>) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining <i>Gammarus</i> species populating the same geographical range as GP.