S Paabo

..We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data...

..In combination with current mtDNA data, this excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution...

..Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues...

..We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering...

....

....

..Widely divergent topologies have been suggested based on various data sets and methods...

..However, it is often difficult to assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously...

..These concern the questions of where and when our species originated, what the genetic background for characters that differ between us and apes is, and how the phenotypic traits that vary among human groups have evolved...

....

....

..We also highlight some significant results and areas of promising future research...

....

..We identified species-specific gene expression patterns indicating that changes in protein and gene expression have been particularly pronounced in the human brain...

..Phylogenetic analyses show the sequences from the different chimpanzee subspecies to be intermixed and the distance between some chimpanzee sequences to be greater than the distance between them and the bonobo sequences...

..This suggests that careful attention should be paid to geographic sampling in studies of chimpanzee genetic variation...

..Furthermore, genetic data indicate that humans, but not the great apes, have experienced a period of dramatic growth in their early history...

..By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals...

..Here we show that human FOXP2 contains changes in amino-acid coding and a pattern of nucleotide polymorphism, which strongly suggest that this gene has been the target of selection during recent human evolution...

....

..These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases...

..Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed...

..For analyses of other fossil hominins, which may become possible in the future, we suggest a similar 'boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired...

..A possible exception is FMR2, which shows a higher number of nonsynonymous than synonymous substitutions on the human lineage, suggesting the action of positive selection...

..Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue...

..One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all...

..9-1.6 MYA and subsequent, primarily male-mediated gene flow until approximately 80,000-200,000 years ago. Furthermore, simulations revealed that more gene flow took place from eastern to western gorilla populations than vice versa...

..The time elapsed since the most recent common ancestor (MRCA) is 535,000+/-119,000 years. We expect this type of nuclear locus to provide more answers about the genetic origin and history of humans...

..The plants in the boluses further indicate that the climate 11 000 years BP was dryer than 20 000 and 28 500 years BP. However, the sloths seem to have visited water sources more frequently at 11 000 BP than at earlier times...

..However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages...

....

..Both striped and brown hyenas show low amounts of genetic diversity, with the latter ones displaying just a single haplotype...

..The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants...

..However, since the extent of divergence differs significantly among autosomes, additional unknown factors must also influence the accumulation of substitutions in the human genome...

..Consistent with this hypothesis, diversity levels no longer increase significantly with recombination rates after correction for divergence to chimpanzee...

..Thus, these results illustrate the usefulness of retrieving direct genetic information from ancient remains for understanding recent human evolution...

..The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general...

..The results suggest that reliable genome sequences can be obtained from Pleistocene organisms...

..Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes...

..The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans...

..The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms...

..Our findings reinforce the notion that tameness is correlated with differences in stress response and will facilitate future efforts to uncover the genetic basis for animal tameness...

..Since mice carrying one nonfunctional Foxp2 allele show opposite effects, this suggests that alterations in cortico-basal ganglia circuits might have been important for the evolution of speech and language in humans...

..Our results suggest that the mouse can be used to study at least some aspects of human-specific traits...

..We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia...

..In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms...

..Using this approach, we confirm that C/G base pairs observed as T/A base pairs in Neanderthal DNA sequences are due to a modification of the cytosine rather than guanine residues...

..Existing technology and fossil resources are now sufficient to initiate a Neanderthal genome-sequencing effort...

..These results show that ancient single-copy nuclear DNA can be recovered from warm, arid climates. Thus, nuclear DNA preservation is not restricted to cold climates...

..We also find no evidence that the morphology of the bears in the two caves changed to become more similar over time. We suggest that the two cave bear forms may have represented two reproductively isolated subspecies or species...

..Our findings suggest that the deterioration of the olfactory repertoire occurred concomitant with the acquisition of full trichromatic color vision in primates...

..These observations are likely due to differences in lifestyle, between humans and great apes, that have led to distinct sensory needs...

..Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans...

....

..Therefore, there is no reason to assume that major genetic discontinuities exist between different continents or "races."..

..However, in contrast to the olfactory receptor gene repertoire, where humans have a higher proportion of pseudogenes than apes, there is no evidence that the rate of loss of bitter taste receptor genes varies among humans and apes...

..Therefore, the recombination landscape has changed markedly between the two species...

....

..As a consequence, the fraction of OR pseudogenes in humans is almost twice as high as in the non-human primates, suggesting a human-specific process of OR gene disruption, likely due to a reduced chemosensory dependence relative to apes...

..Because there are indications that recombination rates may have changed rapidly during human evolution, we favor the latter explanation...

..This suggests that small size may have been an ancestral trait in cave bears and that large size evolved at least twice independently...

..Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts...

..There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small...

..The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length...

....

....

..Together, these results show that the QTL is probably not caused by a single selected site, but may instead represent the joint effects of several sites that were targets of polygenic selection...

..The male-to-female mutation rate ratio was estimated to be 2.5...

..The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete...

..We show that Sequential DEXAS yields high quality sequencing results directly from genomic DNA as well as directly from human blood without any prior isolation or purification of DNA...

..We conclude that a functional tRNA(Lys) encoded in the nuclear genome is imported into mitochondria in marsupials. Thus, tRNA import is not restricted to plant, yeast, and protozoan mitochondria but also occurs also in mammals...