To explore the influence of vicariance on differentiation patterns of taxa in arid regions, we
systematically assessed the genetic diversity and variability of Capparis spinosa, a typical
xerophyte that is widely distributed in the Tianshan Mountains and adjacent areas. In total,
300 individuals from 25 populations were sampled, and 14 haplotypes were identified
using two cpDNA sequences (rpS12-rpL20 and ndhF). A high level of total genetic diversity
(HT ¼ 0.859) was detected, and this was attributed to the extensive distribution range,
which included numerous large populations. The SAMOVA results suggested that the 25
populations were clustered into 4 major geographical groups; a similar divergence trend
was found by constructing a BEAST phylogenetic tree and a network diagram. The AMOVA
results revealed that significant genetic differentiation occurred among groups. Our results
indicated a considerable correlation between genetic divergence and geographical distribution.
Isolation due to complex mountain and desert geography might limit gene exchange
between disjunct populations, resulting in high differentiation between
geographical groups.