A detailed description of materials and methods is provided in SI Appendix, SI Materials and Methods . Briefly, we obtained varieties of P. dactylifera and Phoenix wild relatives from various sources, including collections from wild populations, germplasm collections, research facilities, and ornamental gardens (SI Appendix, Table S1 ). Whole-genome 2 100 paired-end sequencing was conducted on an Illumina HiSeq 2500 Sequencer with one-half to one lane per sample. Data were aligned to the date palm draft assembly (28 (link)) available at the National Center for Biotechnology Information (NCBI) with Burrows–Wheeler aligner (59 ). SNPs were called following standard protocols (60 ) and filtered accordingly.
Phylogenomic analysis was conducted on a subset of SNPs separately for nuclear, cpDNA, and mtDNA genomes using a combination of randomized axelerated maximum likelihood (RAxML) (61 (link)) and R packages phangorn (62 (link)) and ape (63 (link)). Model-based clustering of population genomic data was conducted with STRUCTURE (29 (link)). A model of population splits and mixtures was fitted to the data using TreeMix (36 (link)). Admixture tests with and D statistics were conducted with Popstats (64 (link)). Estimates of ancestry proportions were obtained from TreeMix mixture weights and with the -ratio approach as implemented in Popstats. Population and introgression summary statistics were estimated directly from sample alignments with analysis of next generation sequencing data (ANGSD) (65 (link)) or from SNPs with vcftools (66 (link)) and a script from Martin et al. (37 (link)). Statistical analysis was conducted with the R Statistical Programing Language (67 ).
Archaeobotanical records of date palm were gathered from published reports, based on finding monograph chapters based on previous regional reviews (e.g., refs. 68 and 69 ), a database search of “literature on archaeological remains of cultivated plants 1981–2004” (70 ), and a Google scholar search for additional recent journal articles. It includes all reports, most of which are dated based on associated artifactal and archaeological evidence (indicated as “ass.”), in some cases by associated radiocarbon dates (C14) or direct accelerator mass spectrometry (AMS) dates on crop remains. Few of these are directly dated Phoenix stones themselves, but those available are indicated as “AMS*.” Calibrated radiocarbon dates have been summed and the 1-sigma range has been taken to represent the phase of the sample, from a which a median has been calculated. In the case of associated dating evidence a standard period age range has been taken from recent archaeological literature (based on the expertise of D.Q.F.) and a median taken from this range. Where there are concerns over the true antiquity of remains, such as uncarbonized Phoenix stones of large size from Takrakori, Libya, attributed to a 8,000-yBP context (38 ), these are flagged in our database (Dataset S1 ) and excluded from the synthesis of date palm spread. Additional details are provided in SI Appendix, SI Text .
DNA sequence data new to this study have been deposited in the Sequence Read Archive (71 (link)). SNP data have been deposited in the Dryad Digital Repository (72 ).
Phylogenomic analysis was conducted on a subset of SNPs separately for nuclear, cpDNA, and mtDNA genomes using a combination of randomized axelerated maximum likelihood (RAxML) (61 (link)) and R packages phangorn (62 (link)) and ape (63 (link)). Model-based clustering of population genomic data was conducted with STRUCTURE (29 (link)). A model of population splits and mixtures was fitted to the data using TreeMix (36 (link)). Admixture tests with and D statistics were conducted with Popstats (64 (link)). Estimates of ancestry proportions were obtained from TreeMix mixture weights and with the -ratio approach as implemented in Popstats. Population and introgression summary statistics were estimated directly from sample alignments with analysis of next generation sequencing data (ANGSD) (65 (link)) or from SNPs with vcftools (66 (link)) and a script from Martin et al. (37 (link)). Statistical analysis was conducted with the R Statistical Programing Language (67 ).
Archaeobotanical records of date palm were gathered from published reports, based on finding monograph chapters based on previous regional reviews (e.g., refs. 68 and 69 ), a database search of “literature on archaeological remains of cultivated plants 1981–2004” (70 ), and a Google scholar search for additional recent journal articles. It includes all reports, most of which are dated based on associated artifactal and archaeological evidence (indicated as “ass.”), in some cases by associated radiocarbon dates (C14) or direct accelerator mass spectrometry (AMS) dates on crop remains. Few of these are directly dated Phoenix stones themselves, but those available are indicated as “AMS*.” Calibrated radiocarbon dates have been summed and the 1-sigma range has been taken to represent the phase of the sample, from a which a median has been calculated. In the case of associated dating evidence a standard period age range has been taken from recent archaeological literature (based on the expertise of D.Q.F.) and a median taken from this range. Where there are concerns over the true antiquity of remains, such as uncarbonized Phoenix stones of large size from Takrakori, Libya, attributed to a 8,000-yBP context (38 ), these are flagged in our database (
DNA sequence data new to this study have been deposited in the Sequence Read Archive (71 (link)). SNP data have been deposited in the Dryad Digital Repository (72 ).
