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Phylogenetic relationships among Chinese species of  Morella  (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among  Morella rubra ,  M .  adenophora ,  M .  nana  and  M .  esculenta . Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of ((( M .  rubra ,  M .  adenophora ),  M .  nana ),  M .  esculenta ). Two species from North America ( M .  cerifera  and  M .  pensylvanica ) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of  M .  rubra  to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in  M .  rubra  occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for  M .  rubra ,  M .  nana  and  M .  esculenta  respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of  M .  rubra  and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing