Understanding how ecological and environmental changes, anthropogenic activities, and climate have driven and will direct animals’ development and predicting their prospective distribution profiles in the Quaternary are essential to making a tangible conservation strategy. Macaques (Macaca) distributed in mainland East Asia provide an ideal research model for such an effort. We reconstruct macaques’ geographic distribution profiles during the Quaternary, from the last inter-glaciation (LIG, 120,000 - 140,000 years BP), the Last Glacial Maximum (LGM, 22,000 years BP), and the present (1970-2000) – based on which we deduce their perspective distribution in the 2050s. The results show their suitable habitats during LIG and LGM were mainly in Southwest, Central, and Coastal China. A noticeable distribution reduction started in LIG and persisted until the current (1970-2000). Their distribution centroid would shift northward to mountainous regions, mainly in Southwest China, where more migration corridors would be reserved for their future development. Also, the results indicate that China’s Protected Area currently does not cover more than 87% of macaques’ habitats, a dismal situation for their conservation. Finally, this study proclaims that the conservation priority of the macaques in the years to come should focus on Southwest China – their future refuge region in Quaternary.

Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and dou-ble-reduction, diploid models of population genetic analysis cannot properly be ap-plied to polyploids. To overcome this problem, we developed a software package en-titled VCFPOP to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We make this soft-ware freely available, downloadable from http://github.com/huangkang1987/vcfpop.