We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

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85between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. 86 We show that the earliest populations of the Near East derived around half their 87 ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture 88 and that separated from other non-African lineages prior to their separation from each 89 other. The first farmers of the southern Levant (Israel and Jordan) and Zagros 90 Mountains (Iran) were strongly genetically differentiated, and each descended from 91 local hunter-gatherers. By the time of the Bronze Age, these two populations and 92 Anatolian-related farmers had mixed with each other and with the hunter-gatherers of 93 Europe to drastically reduce genetic differentiation. The impact of the Near Eastern 94 farmers extended beyond the Near East: farmers related to those of Anatolia spread 95 westward into Europe; farmers related to those of the Levant spread southward into 96 East Africa; farmers related to those from Iran spread northward into the Eurasian 97 steppe; and people related to both the early farmers of Iran and to the pastoralists of 98 the Eurasian steppe spread eastward into South Asia. 99 Between 10,000-9,000 BCE, humans began practicing agriculture in the Near East 1 . In the 100 ensuing five millennia, plants and animals domesticated in the Near East spread throughout 101 West Eurasia (a vast region that also includes Europe) and beyond. The relative homogeneity 102 of present-day West Eurasians in a world context 2 suggests the possibility of extensive 103 migration and admixture that homogenized geographically and genetically disparate sources 104 of ancestry. The spread of the world's first farmers from the Near East would have been a 105mechanism for such homogenization. To date, however, due to the poor preservation of DNA 106 in warm climates, it has been impossible to study the population structure and history of the 107 first farmers and to trace their contribution to later populations. 108In order to overcome the obstacle of poor DNA preservation, we took advantage of two 109 methodological developments. First, we sampled from the inner ear region of the petrous 110 bone 3,4 that can yield up to ~100 times more endogenous DNA than other skeletal elements 4 . 111Second, we used in-solution hybridization 5 to enrich extracted DNA for about 1.2 million 112 single nucleotide polymorphism (SNP) targets 6,7 , making efficient sequencing practical by 113 filtering out microbial and non-informative human DNA. We merged all sequences extracted 114 from each individual, and randomly sampled a single sequence to represent each SNP, 115 restricting to individuals with at least 9,000 SNPs covered at least once. We obtained 116 genome-wide data passing quality control for 45 individuals on whom we had a median 117 4 coverage of 172,819 SNPs (Methods). We assembled radiocarbon dates for 26 individuals

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P [18] [12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to nonequine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines. INTRODUCTIONEquine group A rotavirus (RVA) strains were first detected in diarrhoeic foals in England in 1975(Flewett et al., 1975 and are a major cause of dehydrating diarrhoea in young 3Present address: Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttelton, Centurion, 0140, South Africa.The GenBank/EMBL/DDBJ accession numbers for the equine rotavirus strains described in this study are JF712555-JF712565, JF712566-JF712576, JF712577-JF712587, JN872865-JN872875, JQ345489-JQ345499 and JN903507-JN903528. foals (Browning & Begg, 1996;Frederick et al., 2009; Imagawa et al., 1991;Saif et al., 1994). Serological data from Japan, the USA and France suggest that RVA is a ubiquitous pathogen in horse populations (Conner & Darlington, 1980;Imagawa et al., 1982;Pearson et al., 1982;Takahashi et al., 1979).RVA strains are icosahedral, non-enveloped viruses possessing a genome of 11 segments of dsRNA. The two outer capsid proteins, VP7 and VP4, elicit neutralizing antibodies independently and are used to differentiate RVA strains into G-types (glycoprotein) and P-types (proteasesensitive), respectively (Ciarlet & Estes, 2002 (Browning et al., 1991a). L338 was shown to possess the unique G13 and P[18] genotypes and a highly divergent NSP1 gene sequence, and to be distinct from other human and animal RVA strains by using RNA-RNA hybridization assays (Browning et al., 1991a; Iša & Snodgrass, 1994;Kojima et al., 1996;Taniguchi et al., 1994;Wu et al., 1993). In addition, a limited number of porcine-, bovineand feline-like RVA strains have been detected in horses. Examples include the G5P [7] RVA strain RVA/Horse-tc/ ...

Novel, intergenogroup reassortant G3 rotavirus strains are spreading in at least three continents: Asia, Australia, and Europe. The present study provides evidence that a closely related G3P[8] strain circulated in Hungary during 2015. Whole genome sequencing and phylogenetic analysis showed that the identified strain continues to evolve by reassortment. This observation demonstrates the genomic plasticity of the novel strain, which is thought to be a prerequisite of the success of emerging rotavirus genotypes.