19 Domestication of the watermelon (Citrullus lanatus) has alternatively been placed in South 20 Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence 21 coming from Libya and Egypt. The geographic origin and domestication of watermelons has 22 therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-23 year-old Citrullus leaf from a mummy's sarcophagus and skimmed genomes for 24 representatives of the seven extant species of Citrullus, we show that modern cultivars and the 25 ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp 26 color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This 27 implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom 28 Egyptians were cultivating domesticated watermelons. The genomic data also identify extant 29 Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated 30 watermelons. 31 32 Archaeogenomics | plant domestication | ancient plant genome | Africa | New Kingdom Egypt 33 | Pharaonic tomb 34 35 Significance statement [120 words] 36 With some 197.8 million tons in 2017, watermelon, Citrullus lanatus, is among the World's 37 most important crops, yet its area of origin and domestication have remained unclear, with 38 competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. 39 We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a 40 Pharaonic sarcophagus and performed genome skimming for representatives of all other 41 Citrullus species to compare key genes involved in fruit bitterness and color. White-fleshed, 42 non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, 43 and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form 44 (but no wild forms), implying that 18 th Dynasty Egyptians were cultivating domesticated 45 watermelon by 3500 years ago. 46

[190 words] 33not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/106302 doi: bioRxiv preprint first posted online Feb. 6, 2017; 2• The Andean mountains of South America are the most species-rich 34 biodiversity hotspot worldwide with about 15% of the world's plant species, in 35 only 1% of the world's land surface. Orchids are a key element of the Andean 36 flora, and one of the most prominent components of the Neotropical epiphyte 37diversity, yet very little is known about their origin and diversification. 38• We address this knowledge gap by inferring the biogeographical history and 39 evolutionary dynamics of the two largest Neotropical orchid groups 40 (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled 41 orchid phylogenies (including 400+ newly generated DNA sequences), 42 comparative phylogenetic methods, geological and biological datasets.

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical organisms. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models with and without founder-event speciation, we infer that the most recent common ancestor of Cycnoches may have originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, such biological exchange occurred well after major mountain building periods. The Andes have not acted as an impassable barrier for epiphytic lowland lineages such as orchids having a great potential for effortless dispersal because of the very light, anemochorous seeds.

The date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies.We addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species.The ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris.Our study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species.