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

Cite this dataset

Weeks, Andrea; Gostel, Morgan (2024). Data from: Can a Commiphora seedling germinated from an ancient seed solve a Biblical mystery? [Dataset]. Dryad. https://doi.org/10.5061/dryad.hqbzkh1n5

Abstract

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.

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


The dataset provides all files needed to reproduce testing the phylogenetic placement of an unknown Commiphora (Burseraceae) species and the results from the phylogenetic analyses.

Description of the data and file structure

DNA sequence data files:

  • Commiphora_Concatenated_Matrix_Final.nex: the aligned matrix of concatenated DNA sequences.
  • Data_Partition_Delimiters.nex: the description the partitioning of these concatenated DNA sequences by gene type.

Results from phylogenetic analysis of concatenated DNA sequences using maximum likelihood and 100 bootstrap replicates within iQtree.

  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.log: log file from iQtree analysis using 100 bootstrap replicates that specifies analytical parameters, their performance, and their output. Analyses are inclusive of all concatenated DNA sequences.
  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.iqtree: the full results from iQtree analysis using 100 bootstrap replicates.
  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.treefile: the maximum likelihood tree in NEWICK format
  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.contree: consensus tree from 100 best-fitting trees generated by analyses of 100 bootstrap replicates.
  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.boottrees: all trees generated from analyses using 100 bootstrap replicates.
  • iQtree_100reps_Commiphora_Concatenated_Matrix_Final.nex.best_scheme.nex: best fitting models for partitioning scheme.

Results from phylogenetic analysis of concatenated DNA sequences using maximum likelihood and 1000 ultra-fast bootstrap replicates within iQtree.

  • iQtree_1000UFreps_Commiphora_Concatenated_Matrix_Final.nex.log: log file from iQtree analysis using 1000 ultra-fast bootstrap replicates that specifies analytical parameters, their performance, and their output. Analyses are inclusive of all concatenated DNA sequences.
  • iQtree_1000UFreps_Commiphora_Concatenated_Matrix_Final.nex.iqtree: the full results from iQtree analysis using 1000 ultra-fast replicates.
  • iQtree_1000UFreps_Commiphora_Concatenated_Matrix_Final.nex.treefile: the maximum likelihood tree in NEWICK format.
  • iQtree_1000UFreps_Commiphora_Concatenated_Matrix_Final.nex.contree: consensus tree from 1000 best-fitting trees generated by analyses of 1000 ultra-fast bootstrap replicates.
  • iQtree_1000UFreps_Commiphora_Concatenated_Matrix_Final.nex.best_scheme.nex: best fitting models for partitioning scheme.

Results from phylogenetic analysis of chloroplast DNA sequences using maximum likelihood and 1000 ultra-fast bootstrap replicates within iQtree.

  • Commiphora_Concatenated_Matrix_Final_CP.nex.log: log file from iQtree analysis using 1000 ultra-fast bootstrap replicates that specifies analytical parameters, their performance, and their output. Analyses are inclusive of only chloroplast DNA sequences, referenced in the Supplementary Data section of the paper.
  • Commiphora_Concatenated_Matrix_Final_CP.nex.contree.tre: consensus tree from 1000 best-fitting trees generated by analyses of 1000 ultra-fast bootstrap replicates.
  • Commiphora_Concatenated_Matrix_Final_CP.nex.iqtree: the full results from iQtree analysis using 1000 ultra-fast bootstrap replicates.
  • Commiphora_Concatenated_Matrix_Final_CP.nex.treefile: the maximum likelihood tree in NEWICK format.

Results from phylogenetic analysis of nuclear DNA sequences using maximum likelihood and 1000 ultra-fast bootstrap replicates within iQtree.

  • Commiphora_Concatenated_Matrix_Final_ETS.nex.log: log file from iQtree analysis using 1000 ultra-fast bootstrap replicates that specifies analytical parameters, their performance, and their output. Analyses are inclusive of only nuclear DNA sequences, referenced in the Supplementary Data section of the paper.
  • Commiphora_Concatenated_Matrix_Final_ETS.nex.contree.tre: consensus tree from 1000 best-fitting trees generated by analyses of 1000 ultra-fast bootstrap replicates.
  • Commiphora_Concatenated_Matrix_Final_ETS.nex.iqtree: the full results from iQtree analysis using 1000 ultra-fast bootstrap replicates.
  • Commiphora_Concatenated_Matrix_Final_ETS.nex.treefile: the maximum likelihood tree in NEWICK format.

Any text editor can be used to inspect .log, .iqtree and .nex files. A phylogenetic tree editor is recommended to inspect .contree, .treefile, .boottrees files.

Sharing/Access information

Links to other publicly accessible locations of the data:

Data were derived from the following sources:

  • 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. 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/): OP96395, OP963952, OP963953, OP963954.

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)