Fig. 2

Phylogenomic analysis and demographic histories of the three Sinocyclocheilus species. a Phylogenomic relationships inferred from 3,181 orthologous genes of the three Sinocyclocheilus and six other teleost species (Homo sapiens was the outgroup), with the branch lengths scaled to estimated divergence times (numbers in blue show median and range values). The numbers besides the branch indicated expanded (green) and contracted (red) gene families since the split from a most recent common ancestor (MRCA). b Demographic histories were reconstructed using the pairwise sequentially Markovian coalescent (PSMC) model. The uplift process of the Qinghai-Tibet Plateau since 3.6 Ma was obtained from a published paper [11] and other significant environmental events, such as the atmospheric surface air temperature and Eurasian ice volume for the past 3 Ma, were taken from the National Centers for Environmental Information (NCEI; http://www.ncdc.noaa.gov/). The time range of three rounds of intense uplift (Qingzang, Kunhuang and Gonghe Movement) is highlighted in lilac. All three species have similar patterns of decrease under the Qingzang and Kunhuang Movement, but a subsequent divergent trend under the Gonghe Movement