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Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.

The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population.

Summary The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics., Graphical Abstract, Highlights • Yersinia pestis was common across Eurasia in the Bronze Age • The most recent common ancestor of all Y. pestis was 5,783 years ago • The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas • Bronze Age Y. pestis was not capable of causing bubonic plague, The plague-causing bacteria Yersinia pestis infected humans in Bronze Age Eurasia, three millennia earlier than any historical records of plague, but only acquired the genetic changes making it a highly virulent, flea-borne bubonic strain ∼3,000 years ago.

Humans have had a major impact on the environment. This has been particularly intense in the last millennium but has been noticeable since the development of food production and the associated higher population densities in the last 10,000 years. The use of fire and over-exploitation of large mammals has also been recognized as having an effect on the world's ecology, going back perhaps 100,000 years or more. Here we report on an earlier anthropogenic environmental change. The use of stone tools, which dates back over 2.5 million years, and the subsequent evolution of a technologically-dependent lineage required the exploitation of very large quantities of rock. However, measures of the impact of hominin stone exploitation are rare and inherently difficult. The Messak Settafet, a sandstone massif in the Central Sahara (Libya), is littered with Pleistocene stone tools on an unprecedented scale and is, in effect, a man-made landscape. Surveys showed that parts of the Messak Settafet have as much as 75 lithics per square metre and that this fractured debris is a dominant element of the environment. The type of stone tools--Acheulean and Middle Stone Age--indicates that extensive stone tool manufacture occurred over the last half million years or more. The lithic-strewn pavement created by this ancient stone tool manufacture possibly represents the earliest human environmental impact at a landscape scale and is an example of anthropogenic change. The nature of the lithics and inferred age may suggest that hominins other than modern humans were capable of unintentionally modifying their environment. The scale of debris also indicates the significance of stone as a critical resource for hominins and so provides insights into a novel evolutionary ecology.

The evolution of modern humans was a complex process, involving major changes in levels of diversity through time. The fossils and stone tools that record the spatial distribution of our species in the past form the backbone of our evolutionary history, and one that allows us to explore the different processes—cultural and biological—that acted to shape the evolution of different populations in the face of major climate change. Those processes created a complex palimpsest of similarities and differences, with outcomes that were at times accelerated by sharp demographic and geographical fluctuations. The result is that the population ancestral to all modern humans did not look or behave like people alive today. This has generated questions regarding the evolution of human universal characters, as well as the nature and timing of major evolutionary events in the history of Homo sapiens . The paucity of African fossils remains a serious stumbling block for exploring some of these issues. However, fossil and archaeological discoveries increasingly clarify important aspects of our past, while breakthroughs from genomics and palaeogenomics have revealed aspects of the demography of Late Quaternary Eurasian hominin groups and their interactions, as well as those between foragers and farmers. This paper explores the nature and timing of key moments in the evolution of human diversity, moments in which population collapse followed by differential expansion of groups set the conditions for transitional periods. Five transitions are identified (i) at the origins of the species, 240–200 ka; (ii) at the time of the first major expansions , 130–100 ka; (iii) during a period of dispersals , 70–50 ka; (iv) across a phase of local/regional structuring of diversity, 45–25 ka; and (v) during a phase of significant extinction of hunter–gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter ), 15–0 ka. This article is part of the themed issue ‘Major transitions in human evolution’.