The evolutionary history of Neanderthal and Denisovan Y chromosomes

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.Q.F. was supported by funding from the Chinese Academy of Sciences (XDB26000000) and the National Natural Science Foundation of China (91731303, 41925009, 41630102). A.R. was funded by Spanish government (MICINN/ FEDER) (grant number CGL2016-75109-P). The reassessment of the Spy collection by H.R., I.C., and P.S. was supported by the Belgian Science Policy Office (BELSPO 2004-2007, MO/36/0112). M.V.S., M.B.K., and A.P.D. were supported by the Russian Foundation for Basic Research (RFBR 17-29-04206). This study was funded by the Max Planck Society and the European Research Council (grant agreement number 694707)

The evolutionary history of Neandertal and Denisovan Y chromosomes

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.Q.F. was supported by funding from the Chinese Academy of Sciences (XDB26000000), and the National Natural Science Foundation of China (91731303, 41925009,41630102). A.R. was funded by Spanish government (MICINN/FEDER), grant number CGL2016-75109-P. The reassessment of the Spy collection by H.R., I.C. and P.S. was supported by the Belgian Science Policy Office (BELSPO 2004-2007, MO/36/0112). M.S., M.K. and A.D. were supported by the Russian Foundation for Basic Research (RFBR 17-29-04206). This study was funded by the Max Planck Society and the European Research Council (grant agreement number 694707).N

The complete genome sequence of a Neandertal from the Altai Mountains

We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans

Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them

Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260–210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast

Saradj-Chuko grotto.

Photo of the grotto, and plan of excavation showing the discovery points of artefacts typical of the Eastern Micoquian industry in Layer 6B. 1 –bifacial small handaxe; 2 –bifacial leaf point; 3, 4 –bifacial scraper-knives.</p

Weasel cave.

The retouched tools typical of the Zagros Mousterian industry. 1, 2 –elongated Mousterian points; 3 –Levallois retouched point; 4–6 –thick double scrapers; 7 –truncated-faceted scraper; 8, 9 –side-scrapers; 10, 11 –side-scrapers made on Levallois blades; 12 –déjeté scraper. Modified from [8: fig 10].</p

Mezmaiskaya cave.

The retouched tools typical for the Eastern Micoquian (1–13) and small obsidian flakes found in layers 3 and 2B4 (14–15). 1, 2 –bifacial small handaxes; 3, 4 –Mousterian points; 5–7 –déjeté scrapers; 8 –bifacial leaf point; 9–13 –bifacial scraper-knives.</p

Saradj-Chuko grotto.

2017 excavation. Layer 6B. Drawing and photo of refitting of a one-platform core and five flakes, three of which are laminar flake (1) and blades (3, 4). Numbers indicate the sequence of removals.</p

Tinit-1 open-air site.

The Zagros Mousterian assemblage. A. The Levallois products and retouched tools (2–5) typical of the Zagros Mousterian industry. 1 –Levallois flake; 2 –a tip fragment of Mousterian point (?); 3, 4 –side-scrapers; 5 –elongated Mousterian point with a broken tip; 6 –Levallois triangular flake (point); 7 –Levallois recurrent core. B–D. Drawings and photos of three refitting samples, representing volumetric parallel flaking (B) and Levallois recurrent flaking (C, D). Modified from [38: figs 6, 8, 9, 11].</p

Map showing distribution of the Eastern Micoquian industry in Eastern Europe and the west of North Caucasus and the Zagros Mousterian industry in the Zagros, Caucasus, and Armenian Highlands, including the east of North Caucasus.

Squares indicate open-air sites and triangles indicate cave sites. Various colors indicate: yellow–main Eastern Micoquian sites in the west of North Caucasus, red–Zagros Mousterian sites in the east of North Caucasus, green–main Zagros Mousterian sites in the Lesser Caucasus and Armenian Highlands, blue–main Zagros Mousterian sites in the Zagros. Data: Natural Earth (public domain at http://www.naturalearthdata.com). Figure produced using GRASS GIS 7.8 and Inkscape 0.97 software.</p