The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.

A sequencing study comparing ancient and contemporary genomes reveals that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, ancient north Eurasians (related to Upper Palaeolithic Siberians) and early European farmers of mainly Near Eastern origin. By sequencing and comparing the genomes of nine ancient Europeans that bridge the transition to agriculture in Europe between 8,000 and 7,000 years ago, David Reich and colleagues show that most present-day Europeans derive from at least three highly differentiated populations — west European hunter-gatherers, ancient north Eurasians (related to Upper Palaeolithic Siberians) and early European farmers of mainly Near Eastern origin. They further propose that early European farmers had about 44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages. These results raise interesting new questions, for instance that of where and when the Near Eastern farmers mixed with European hunter-gatherers to produce the early European farmers. We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ∼44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

War and Peace?: Modern behavior, including the development of advanced tools, musical instruments, and art, seems to have arisen in humans in stages. The earliest hints are seen in Africa about 70 to 90,000 years ago, but later in Europe about 45,000 years ago. An ongoing discussion centers on the origins and significance of human prosociality. During early human development, could the benefits of altruistic behavior have outweighed its costs (see the Perspective by Mace )? Bowles (p. 1293 ) constructed a model of conflict between groups of humans and extracted estimates of the critical parameters from archaeological and ethnographic data sets. Provocatively, it appears that warfare might have enhanced the emergence and persistence of altruistic behavior. Powell et al. (p. 1298 ) present a population model that shows that the development of modern behaviors may rely on the attainment of critical population densities and migratory patterns required for stable cultural transmission. The model is consistent with genetic inferences of population dynamics in Africa and Europe and suggests that these cultural changes may not solely reflect increased cognitive evolution.

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.