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Table 1 O. europaea genomes used in the analysis. The columns show the sample origin, analysis in which it was used, plastid group [17], nuclear group [12], ploidy level, and the source of the data. *Cultivars that are duplicated and are excluded from the main analysis (see “Methods”)

From: Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

O. europaea subsp. Origin Analysis Plastid group Nuclear group Ploidy level Source
europaea var. europaea cv. “Farga” Spain (Boadilla/La Senia) Nuclear, plastid, mitochondrial E3.1 Central MB (Q2) 2x ENA (PRJEB4992)
europaea var. europaea cv. “Arbequina” Spain (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Central MB (Q2) 2x This study
europaea var. europaea cv. “Picual” Spain (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Western MB (Q1) 2x This study
europaea var. europaea cv. “Beladi” Lebanon (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Eastern MB (Q3) 2x This study
europaea var. europaea cv. “Sorani” Syria (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Eastern MB (Q3) 2x This study
europaea var. europaea cv. “Manzanilla” Spain Plastid E1.1 – 2x NCBI (FN996972)
europaea var. europaea cv. “Bianchera” Italy Plastid E1.1 – 2x NCBI (NC_013707)
europaea var. europaea cv. “Chemlal de Kabilye” Algeria (BGMO_UCO) Nuclear, plastid, mitochondrial E3.2 Mosaic (Q2 + Q1) 2x This study
europaea var. europaea cv. “Megaritiki” Greece (BGMO_UCO) Nuclear, plastid, mitochondrial E2.2 Central (Q2) 2x This study
europaea var. europaea cv. “Lechin de Sevilla” Spain (BGMO_UCO) Nuclear, plastid, mitochondrial E2.3 Mosaic (Q1 + Q2) 2x This study
europaea var. europaea cv. “Lechin de Granada” Spain (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Western MB (Q1) 2x This study
europaea var. europaea cv. “Frantoio” Italy (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Central (Q2) 2x This study
europaea var. europaea cv. “Koroneiki” Greece (BGMO_UCO) Nuclear, plastid, mitochondrial E1.1 Central (Q2) 2x This study
europaea var. sylvestris “sylvestris-T” Turkey Nuclear, plastid, mitochondrial E1.1 – 2x NCBI (PRJNA417827)
europaea var. sylvestris “sylvestris-S” Spain (Pechón) Nuclear, plastid, mitochondrial E3 – 2x This study
europaea var. sylvestris “W7R224” Morocco Nuclear, plastid, mitochondrial E3 – 2x SRR9860491
europaea var. sylvestris “W11R37” Spain Nuclear, plastid, mitochondrial E3 – 2x SRR9860496
europaea var. sylvestris “W9R302” Albania Nuclear, plastid, mitochondrial E2 – 2x SRR9860497
europaea var. sylvestris “W8R225” Morocco Nuclear, plastid, mitochondrial E1 – 2x SRR9860498
europaea var. sylvestris “W4R183” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860503
europaea var. sylvestris “W3R78” Spain (Menorca island) Nuclear, plastid, mitochondrial E2 – 2x SRR9860505
europaea var. sylvestris “W2R74” Spain Nuclear, plastid, mitochondrial E3 – 2x SRR9860532
europaea var. sylvestris “W1R198” Croatia Nuclear, plastid, mitochondrial E2 – 2x SRR9860533
europaea var. europaea cv. “Myrtolia” Greece Nuclear, plastid, mitochondrial E1 – 2x SRR9860492
europaea var. europaea cv. “Klon-14-1812” Albania Nuclear, plastid, mitochondrial E1 – 2x SRR9860493
europaea var. europaea cv. “Barri” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860494
europaea var. europaea cv. “Grappolo” Italy Nuclear, plastid, mitochondrial E1 – 2x SRR9860495
europaea var. europaea cv. “Mari” Iran Nuclear, plastid, mitochondrial E1 – 2x SRR9860499
europaea var. europaea cv. “Lianolia Kerkyras” Greece Nuclear, plastid, mitochondrial E2 – 2x SRR9860500
europaea var. europaea cv. “Piñonera” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860501
europaea var. europaea cv. “Mavreya” Greece Nuclear, plastid, mitochondrial E1 – 2x SRR9860502
europaea var. europaea cv. “Royal” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860504
europaea var. europaea cv. “Llumeta” Spain Nuclear, plastid, mitochondrial E3 – 2x SRR9860506
europaea var. europaea cv. “Barnea” Israel Nuclear, plastid, mitochondrial E1 – 2x SRR9860507
europaea var. europaea cv. “Majhol-1013” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860508
europaea var. europaea cv. “Mastoidis” Greece Nuclear, plastid, mitochondrial E1 – 2x SRR9860509
europaea var. europaea cv. “Abbadi Abou Gabra-842” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860510
europaea var. europaea cv. “Fishomi” Iran Nuclear, plastid, mitochondrial E1 – 2x SRR9860511
europaea var. europaea cv. “Abou Satl Mohazam” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860512
europaea var. europaea cv. “Forastera de Tortosa” Spain Nuclear, plastid, mitochondrial E3 – 2x SRR9860514
europaea var. europaea cv. “Dokkar” Tunisia Nuclear, plastid, mitochondrial E3 – 2x SRR9860516
europaea var. europaea cv. “Jabali” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860517
europaea var. europaea cv. “Majhol-152” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860518
europaea var. europaea cv. “Picudo” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860519
europaea var. europaea cv. “Maarri” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860520
europaea var. europaea cv. “Temprano” Spain Nuclear, plastid, mitochondrial E2 – 2x SRR9860521
europaea var. europaea cv. “Menya” Spain Nuclear, plastid, mitochondrial E2 – 2x SRR9860522
europaea var. europaea cv. “Koroneiki”* Greece Nuclear, plastid, mitochondrial E1.1 – 2x SRR9860523
europaea var. europaea cv. “Manzanilla de Sevilla” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860524
europaea var. europaea cv. “Uslu” Turkey Nuclear, plastid, mitochondrial E1 – 2x SRR9860525
europaea var. europaea cv. “Lechin de Sevilla”* Spain Nuclear, plastid, mitochondrial E2.3 – 2x SRR9860526
europaea var. europaea cv. “Ocal” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860527
europaea var. europaea cv. “Abou Kanani” Syria Nuclear, plastid, mitochondrial E1 – 2x SRR9860528
europaea var. europaea cv. “Verdial de Velez-Malaga-1” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860529
europaea var. europaea cv. “Arbequina”* Spain Nuclear, plastid, mitochondrial E1.1 – 2x SRR9860530
europaea var. europaea cv. “Chemlal de Kabylie”* Algeria Nuclear, plastid, mitochondrial E3.2 – 2x SRR9860531
europaea var. europaea cv. “Leccino” Italy Nuclear, plastid, mitochondrial E1 – 2x SRR9860534
europaea var. europaea cv. “Manzanillera de Huercal Overa” Spain Nuclear, plastid, mitochondrial E2 – 2x SRR9860535
europaea var. europaea cv. “Hojiblanca” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860536
europaea var. europaea cv. “Kalamon” Greece Nuclear, plastid, mitochondrial E1 – 2x SRR9860537
europaea var. europaea cv. “Picual”* Spain Nuclear, plastid, mitochondrial E1.1 – 2x SRR9860538
europaea var. europaea cv. “Zarza” Spain Nuclear, plastid, mitochondrial E2 – 2x SRR9860539
europaea var. europaea cv. “Morrut” Spain Nuclear, plastid, mitochondrial E1 – 2x SRR9860540
europaea var. europaea cv. “Frantoio”* Italy Nuclear, plastid, mitochondrial E1.1 – 2x SRR9860541
europaea var. sylvestris “Stavrovouni 11” Cyprus Plastid E1.4 – 2x NCBI (HF558645)
europaea var. sylvestris “Haut Atlas 1” Morocco (High Atlas) Plastid E2 – 2x NCBI (NC_015401)
europaea var. sylvestris “Gue de Constantine 20” Algeria: Gue de Constantine, Algiers Plastid E3 – 2x NCBI (FN997651)
europaea var. sylvestris “Oeiras 1” Portugal Plastid E3.1 – 2x NCBI (MG255763)
europaea var. sylvestris “Vallee du Fango 5” France Plastid E2.1 – 2x NCBI (MG255762)
maroccana “Immouzzer S1” Morocco (High Atlas) Plastid M – 6x NCBI (NC_015623)
guanchica “La Gomera 10” Spain Plastid M-g1 – 2x NCBI (MG255764)
laperrinei “Adjelella 10” Algeria Plastid E1-l1 – 2x NCBI (MG255765)
cuspidata - R Reunion island Nuclear, plastid, mitochondrial A – 2x This study
cuspidata “Almihwit 5.1” Yemen Plastid C2 – 2x NCBI (FN996943)
cuspidata “Guanghzou 1” China Plastid C1 – 2x NCBI (FN996944)
cuspidata “Maui 1” USA (Hawaii-Maui) Plastid A – 2x NCBI (NC_015604)
cuspidata “Menagesha Forest 14” Ethiopia Plastid C2 – 2x NCBI (MG255760)
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