Can a Commiphora seedling germinated from an ancient seed solve a Biblical mystery?

A seed recovered during archaeological excavations of a cave in the Judean desert was germinated, with radiocarbon analysis indicating an age of 993 CE– 1202 calCE. DNA sequencing and phylogenetic analysis identified the seedling as belonging to the angiosperm genus Commiphora Jacq., sister to three Southern African Commiphora species, but unique from all other species sampled to date. The germinated seedling was not closely related to Commiphora species commonly harvested for their fragrant oleoresins including Commiphora gileadensis (L.) C.Chr., candidate for the locally extinct “Judean Balsam” or “Balm of Gilead” of antiquity. GC-MS analysis revealed minimal fragrant compounds but abundance of those associated with multi-target bioactivity and a previously undescribed glycolipid compound series. Several hypotheses are offered to explain the origins, implications and ethnobotanical significance of this unknown Commiphora sp., the first discovered at an archaeological site in this region, including identification with a resin producing tree mentioned in Biblical sources and a possible agricultural relationship with the historic Judean Balsam.

Methods
All of the DNA sequence data, with the exception of the sequences from the unknown Commiphora species, were derived from a previously published study: Gostel, M., Phillipson, P. and A. Weeks. 2016. Phylogenetic reconstruction of the myrrh genus, Commiphora (Burseraceae), reveals multiple radiations in Madagascar and clarifies infrageneric relationships. Systematic Botany 41(1): 67  81.  [http://dx.doi.org/10.1600/036364416X690598](http://dx.doi.org/10.1600/036364416X690598). The DNA sequence data for the unknown Commiphora species were generated by the present study and were also accessioned within GenBank ([https://www.ncbi.nlm.nih.gov/genbank/](https://www.ncbi.nlm.nih.gov/genbank/)): OP96395, OP963952, OP963953, OP963954.

The phylogeny was inferred from the gene-partioned matrix of DNA sequence data using maximum likelihood algorithms as implemented by IQ-Tree (multicore version 1.6.12) web-interface (Trifinoupolis et al. 2014). Within IQ-Tree, the best-fitting model of sequence evolution for the was estimated and applied to the partitioned matrix (Chernomor et al. 2016) in 1000 ultrafast (Hoang et al. 2018) and 100 standard maximum likelihood bootstrap replicates using 1000 iterations and a 0.99 minimum correlation coefficient. Tree search parameters included a perturbation strength of 0.5 and an IQ-stopping rule of 100. The final tree topology was generated from the majority rule consensus of the bootstrapped trees, which did not differ between the results of the two analyses.

Trifinopoulos, J. et al.W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis, Nucleic Acids Research, 44, W232W235 (2016) [https://doi.org/10.1093/nar/gkw256](https://doi.org/10.1093/nar/gkw256)

D.T. Hoang et al. UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35, 518522. (2018) [https://doi.org/10.1093/molbev/msx281](https://doi.org/10.1093/molbev/msx281)

O. Chernomor et al. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65, 997-1008. (2016) [https://doi.org/10.1093/sysbio/syw037](https://doi.org/10.1093/sysbio/syw037)