Humans and Neanderthals interbred following the emergence of humans in Eurasia 60,000-

16 The time, extent, and genomic impact of the introgressions from archaic humans into 17 ancestors of extant human populations remain one of the most exciting venues of population 18 genetics research in the last decade. Several studies have shown population-specific 19 signatures of introgression events from Neanderthals, Denisovans, and potentially other 20 unknown hominin populations in different human groups. Moreover, it was shown that these 21 introgression events may have contributed to phenotypic variation in extant humans, with 22 biomedical and evolutionary consequences. In this study, we present a comprehensive 23 analysis of the unusually divergent haplotypes in the Eurasian genomes and showed that they 24 can be traced back to multiple introgression events. In parallel, we document hundreds of 25 deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such 26 shared deletion suggests the existence of a direct introgression event from the Altai 27 Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is 28 in agreement with the emergent notion that various Neanderthal populations contributed to 29 extant human genetic variation in a population-specific manner. 30