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.

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently.

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

One Sentence Summary: 40The passenger pigeon's abundance and recombination landscape led to natural selection 41 dominating genome-wide neutral site evolution. 42 43 44 3 Abstract: 45The extinct passenger pigeon was once the most abundant bird in North America, and 46 possibly the world. While theory predicts that large populations will be more genetically 47 diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this, we 48 analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes 49 from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger 50pigeons' large population size appears to have allowed for faster adaptive evolution and 51 removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These 52 results demonstrate the impact selection can have on a vertebrate genome, and contradict 53 results that suggested population instability contributed to this species' surprisingly rapid 54 extinction. 55 56 Main text: 57The passenger pigeon (Ectopistes migratorius) numbered between 3 and 5 billion individuals 58 prior to its 19th century decline and eventual extinction (1). Passenger pigeons were highly 59 mobile, bred in large social colonies, and their population lacked clear geographic structure 60 (2). Few vertebrates have populations this large and cohesive and, according to the neutral 61 model of molecular evolution, this should lead to a large effective population size (N e ) and 62 high genetic diversity (3). Preliminary analyses of passenger pigeon genomes have, 63 however, revealed surprisingly low genetic diversity (4). This has been interpreted within the 64 framework of the neutral theory of molecular evolution as the result of a history of dramatic 65 demographic fluctuations (4). However, in large populations, natural selection may be 66 particularly important in shaping genetic diversity: population genetic theory predicts that 67 selection will be more effective in large populations (3), and selection on one locus can 68 cause a loss of diversity at other loci, particularly those that are closely linked (5-8). It has 69 4 been suggested that this could explain why the genetic diversity of a species is poorly 70 predicted by its population size (9-11). 71 72We investigated the impact of natural selection on passenger pigeon genomes through 73 comparative genomic analyses of both passenger pigeons and band-tailed pigeons 74 (Patagioenas fasciata). While ecologically and physiologically similar to passenger pigeons, 75 band-tailed pigeons have a present-day population size three orders of magnitude smaller 76 than their close relative the passenger pigeon (2, 12, 13). 77 78We applied a Bayesian skyline model of ancestral population dynamics to the mitochondrial 79 genomes of 41 passenger pigeons from across their former breeding range ( Fig. 1A and 80 table S1) (14). This returned a most recent effective population size (N e ) of 13 million (95% 81 HPD: 2-58 million) and similar, stable N e...

Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely. We present a powerful computational approach for determining the constituent haplotypes in massively parallel sequencing data from potentially mixed samples. At the heart of our approach is an expectation maximization based algorithm that co-estimates the overall mixture proportions and the source haplogroup for each read individually. This approach, implemented in the software package mixemt, correctly identifies haplogroups from mixed samples across a range of mixture proportions. Furthermore, our method can separate fragments in a mixed sample by the most likely originating contributor and generate reconstructions of the constituent haplotypes based on known patterns of mtDNA diversity.