Identifying evolutionarily significant units for conservation of the endangered Malus sieversii using genome-wide RADseq data

13 March 2018

Zhang, Hong-Xiang; Li, Hai-Yan ; Li, Yu-Xiu

Malus sieversii, a wild progenitor of the domesticated apple, is an endangered species and is designated as the second conservation priority by the China Plant Red Data Book. It is urgent to carry out in situ conservation due to its survival crisis, but previous studies have not yet identified evolutionarily significant units (ESUs) for conservation management. In this study, we investigated the genetic diversity and phylogenetic relationships of six M. sieversii populations from China using an integrated analysis of microsatellite (nSSR) data, genome-wide SNPs and previous results in order to propose reasonable conservation management. The results showed that the levels of genetic diversity for the six sampled populations were not consistent among our nSSR and previous studies. We suggest that the genetic diversity index is not an effective method to identify priority conservation areas for M. sieversii. Based on the selection criteria of ESUs for endangered species conservation, ESUs should indicate lineage divergence, geographical separation and different adaptive variation. Here, our phylogenetic tree based on genome-wide SNPs yielded a clear relationship of divergent lineages among the six M. sieversii populations, which provides new conclusions that are different from the phylogenetic relationships of these populations in previous studies. Three independent lineages, including the pairs of populations Huocheng-Yining, Gongliu-Xinyuan and Tuoli-Emin, were determined. Geographical distances of pairwise populations among the different phylogenetic lineages were much greater than those within the same phylogenetic lineage. A clustering analysis on environmental variables showed that the three independent lineages of population pairs inhabited similar environmental conditions, which indicates that they have adapted to different environments. Finally, we propose that three independent ESUs should be recognized for conservation of M. sieversii in its Chinese distribution.