| archaic human ancestry in east asia. | recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of africa. at the same time, decreasing levels of human genetic diversity have been found at increasing distance from africa as a consequence of human expansion out of africa. we analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of huma ... | 2011 | 22042846 |
| contrasted patterns of variation and evolutionary convergence at the antiviral oas1 gene in old world primates. | the oligoadenylate synthetase 1 (oas1) enzyme acts as an innate sensor of viral infection and plays a major role in the defense against a wide diversity of viruses. polymorphisms at oas1 have been shown to correlate with differential susceptibility to several infections of great public health significance, including hepatitis c virus, sars coronavirus, and west nile virus. population genetics analyses in hominoids have revealed interesting evolutionary patterns. in central african chimpanzee, oa ... | 2015 | 26156123 |
| linking dopamine neurotransmission and neurogenesis: the evolutionary history of the ntad (ncam1-ttc12-ankk1-drd2) gene cluster. | genetic studies have long suggested the important role of the drd2 gene in psychiatric disorders and behavior. further research has shown a conjoined effect of genes in the chr11q22-23 region, which includes the ncam1, ttc12, ankk1 and drd2 genes, or ntad cluster. despite a growing need to unravel the role of this cluster, few studies have taken into account interspecies and evolutionary approaches. this study shows that behaviorally relevant snps from the ntad cluster, such as rs1800497 (taq1a) ... | 2012 | 23412349 |
| genetic evidence of human adaptation to a cooked diet. | humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not ... | 2016 | 26979798 |
| molecular evolution of wdr62, a gene that regulates neocorticogenesis. | human brain evolution is characterized by dramatic expansion in cerebral cortex size. wdr62 (wd repeat domain 62) is one of the important gene in controlling human cortical development. mutations in wdr62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. this study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of wdr62 and hence pinpoin ... | 2016 | 27114917 |
| Learning about human population history from ancient and modern genomes. | Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of mode ... | 2011 | 21850041 |
| genetic and phenotypic consequences of introgression between humans and neanderthals. | strong evidence for introgression of neanderthal genes into parts of the modern human gene pool has recently emerged. the evidence indicates that some populations of modern humans have received infusions of genes from two different groups of neanderthals. one of these neanderthal groups lived in the middle east and central europe and the other group (the denisovans) is known to have lived in central asia and was probably more widespread. this review examines two questions. first, how were these ... | 2011 | 22099691 |
| denisova admixture and the first modern human dispersals into southeast asia and oceania. | it has recently been shown that ancestors of new guineans and bougainville islanders have inherited a proportion of their ancestry from denisovans, an archaic hominin group from siberia. however, only a sparse sampling of populations from southeast asia and oceania were analyzed. here, we quantify denisova admixture in 33 additional populations from asia and oceania. aboriginal australians, near oceanians, polynesians, fijians, east indonesians, and mamanwa (a "negrito" group from the philippine ... | 2011 | 21944045 |
| paleogenomics of archaic hominins. | in order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. with the advent of ancient dna study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. our closest known r ... | 2011 | 22192823 |
| the shaping of modern human immune systems by multiregional admixture with archaic humans. | whole genome comparisons identified introgression from archaic to modern humans. our analysis of highly polymorphic human leukocyte antigen (hla) class i, vital immune system components subject to strong balancing selection, shows how modern humans acquired the hla-b*73 allele in west asia through admixture with archaic humans called denisovans, a likely sister group to the neandertals. virtual genotyping of denisovan and neandertal genomes identified archaic hla haplotypes carrying functionally ... | 2011 | 21868630 |
| ancient origin of a deletion in human bst2/tetherin that confers protection against viral zoonoses. | bst2/tetherin is an antiviral factor that blocks the release of enveloped virions from infected cells. recent data suggest that efficient bst2 antagonism was a prerequisite for the global spread of hiv/aids. most simian immunodeficiency viruses (sivs), including the direct precursors of hiv, use their nef protein to antagonize bst2 of their respective host species. human bst2, however, contains a five amino acid deletion in its cytoplasmic domain that confers resistance to nef. thus, this antivi ... | 2011 | 21796732 |
| the complete mitochondrial dna genome of an unknown hominin from southern siberia. | with the exception of neanderthals, from which dna sequences of numerous individuals have now been determined, the number and genetic relationships of other hominin lineages are largely unknown. here we report a complete mitochondrial (mt) dna sequence retrieved from a bone excavated in 2008 in denisova cave in the altai mountains in southern siberia. it represents a hitherto unknown type of hominin mtdna that shares a common ancestor with anatomically modern human and neanderthal mtdnas about 1 ... | 2010 | 20336068 |
| early history of neanderthals and denisovans. | extensive dna sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. we introduce a method to study the past several hundred thousand years. our results show that (i) the neanderthal-denisovan lineage declined to a small size just after separating from the modern lineage, (ii) neanderthals and denisovans separated soon thereafter, and (iii) the subsequent neanderthal population was large and deeply subdivided. they also (iv) support previous estima ... | 2017 | 28784789 |
| or2m3: a highly specific and narrowly tuned human odorant receptor for the sensitive detection of onion key food odorant 3-mercapto-2-methylpentan-1-ol. | the detection of key food odorants appears to be an important capability of odorant receptors. here, thiols occupy an outstanding position among the 230 known key food odorants because of their very low odor thresholds. members of the homologous series of 3-mercapto-2-methylalkan-1-ols have been described as onion key food odorants or food constituents and are detected at logarithmically different thresholds. 3-mercapto-2-methylpentan-1-ol being the only key food odorant within this series also ... | 2017 | 27916748 |
| detecting ancient positive selection in humans using extended lineage sorting. | natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. the ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, neandertals and ... | 2017 | 28784836 |
| the mitonuclear dimension of neanderthal and denisovan ancestry in modern human genomes. | some human populations interbred with neanderthals and denisovans, resulting in substantial contributions to modern-human genomes. therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. more generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. there is no evidence of mtdna introgression into modern human popul ... | 2017 | 28854627 |
| the mobile element locator tool (melt): population-scale mobile element discovery and biology. | mobile element insertions (meis) represent ~25% of all structural variants in human genomes. moreover, when they disrupt genes, meis can influence human traits and diseases. therefore, meis should be fully discovered along with other forms of genetic variation in whole genome sequencing (wgs) projects involving population genetics, human diseases, and clinical genomics. here, we describe the mobile element locator tool (melt), which was developed as part of the 1000 genomes project to perform me ... | 2017 | 28855259 |
| neanderthals and denisovans as biological invaders. | | 2017 | 28860198 |
| the status of homo heidelbergensis (schoetensack 1908). | the species homo heidelbergensis is central to many discussions about recent human evolution. for some workers, it was the last common ancestor for the subsequent species homo sapiens and homo neanderthalensis; others regard it as only a european form, giving rise to the neanderthals. following the impact of recent genomic studies indicating hybridization between modern humans and both neanderthals and "denisovans", the status of these as separate taxa is now under discussion. accordingly, clari ... | 2012 | 22718477 |
| a mitochondrial genome sequence of a hominin from sima de los huesos. | excavations of a complex of caves in the sierra de atapuerca in northern spain have unearthed hominin fossils that range in age from the early pleistocene to the holocene. one of these sites, the 'sima de los huesos' ('pit of bones'), has yielded the world's largest assemblage of middle pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. the skeletal remains share a number of morphological features with fossils classified as homo heidelbergensis an ... | 2014 | 24305051 |
| hominin interbreeding and the evolution of human variation. | mitochondrial eve confirms the "out of africa" theory, but the evidence also supports interbreeding between homo sapiens and other hominins: neanderthals, denisovans, and homo heidelbergensis. this article explains how interbreeding between early h. sapiens and archaic hominins occurred. the availability of edible insects in east asia aided the spread of the unaggressive, highly cooperative neanderthals, who interbred with h. sapiens in asia, resulting in a higher admixture of neanderthal dna in ... | 2016 | 27429943 |
| denisovans, melanesians, europeans, and neandertals: the confusion of dna assumptions and the biological species concept. | a number of recent articles have appeared on the denisova fossil remains and attempts to produce dna sequences from them. one of these recently appeared in science by vernot et al. (science 352:235-239, 2016). we would like to advance an alternative interpretation of the data presented. one concerns the problem of contamination/degradation of the determined dna sequenced. just as the publication of the first neandertal sequence included an interpretation that argued that neandertals had not cont ... | 2016 | 27517578 |
| one pedigree we all may have come from - did adam and eve have the chromosome 2 fusion? | in contrast to great apes, who have 48 chromosomes, modern humans and likely neandertals and denisovans have and had, respectively, 46 chromosomes. the reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (hsa2) and may have contributed to the reproductive barrier with great apes. | 2016 | 27708712 |
| the osteoarthritis and height gdf5 locus yields its secrets. | a new study reports molecular characterization of the gdf5 locus, which is associated with osteoarthritis risk and adult height in humans. this study provides evidence of positive selection for short stature at gdf5 in modern humans, as well as in archaic neandertals and denisovans. | 2017 | 28747750 |
| cross-comparison of the genome sequences from human, chimpanzee, neanderthal and a denisovan hominin identifies novel potentially compensated mutations. | the recent publication of the draft genome sequences of the neanderthal and a ~50,000-year-old archaic hominin from denisova cave in southern siberia has ushered in a new age in molecular archaeology. we previously cross-compared the human, chimpanzee and neanderthal genome sequences with respect to a set of disease-causing/disease-associated missense and regulatory mutations (human gene mutation database) and succeeded in identifying genetic variants which, although apparently pathogenic in hum ... | 2011 | 21807602 |
| on characterizing adaptive events unique to modern humans. | ever since the first draft of the human genome was completed in 2001 there has been increased interest in identifying genetic changes that are uniquely human, which could account for our distinct morphological and cognitive capabilities with respect to other apes. recently, draft sequences of two extinct hominin genomes, a neanderthal and denisovan, have been released. these two genomes provide a much greater resolution to identify human-specific genetic differences than the chimpanzee, our clos ... | 2011 | 21803765 |
| [adaptive evolution of the homo mitochondrial genome]. | adaptive evolution of 12 protein-coding mitochondrial genes in members of genus homo (denisova hominin (h. sp. altai), neandertals (h. neanderthalensis) and modern humans (h. sapiens)) has been evaluated by assessing the pattern of changes in the physicochemical properties of amino acid replacements during the primate evolution. it has been found that in the homo molecular adaptation (positive destabilizing selection) become apparent in the form of 12 radical amino acid replacements accompanied ... | 2012 | 22393781 |
| pseudogenization of testis-specific lfg5 predates human/neanderthal divergence. | recent reviews discussed the critical roles of apoptosis in human spermatogenesis and infertility. these reviews highlight the fasl-induced caspase cascade in apoptosis lending importance to our discovery of the pseudogene status of the lfg5 gene in modern humans, neanderthal and the denisovan. this gene is a member of the ancient and highly conserved apoptosis lifeguard family. this pseudogenization is the result of a premature stop codon at the 3'-end of exon 8 not found in any other ortholog. ... | 2014 | 24599118 |
| human occupation of northern australia by 65,000 years ago. | the time of arrival of people in australia is an unresolved question. it is relevant to debates about when modern humans first dispersed out of africa and when their descendants incorporated genetic material from neanderthals, denisovans and possibly other hominins. humans have also been implicated in the extinction of australia's megafauna. here we report the results of new excavations conducted at madjedbebe, a rock shelter in northern australia. artefacts in primary depositional context are c ... | 2017 | 28726833 |
| detecting ancient positive selection in humans using extended lineage sorting. | natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. the ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, neandertals and ... | 2017 | 28720580 |
| a fourth denisovan individual. | the presence of neandertals in europe and western eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. in contrast, fossil evidence for denisovans, a sister group of neandertals recently identified on the basis of dna sequences, is limited to three specimens, all of which originate from denisova cave in the altai mountains (siberia, russia). we report the retrieval of dna from a deciduous lower second molar (denisova 2), discovere ... | 2017 | 28695206 |
| deeply divergent archaic mitochondrial genome provides lower time boundary for african gene flow into neanderthals. | ancient dna is revealing new insights into the genetic relationship between pleistocene hominins and modern humans. nuclear dna indicated neanderthals as a sister group of denisovans after diverging from modern humans. however, the closer affinity of the neanderthal mitochondrial dna (mtdna) to modern humans than denisovans has recently been suggested as the result of gene flow from an african source into neanderthals before 100,000 years ago. here we report the complete mtdna of an archaic femu ... | 2017 | 28675384 |
| ancient selection for derived alleles at a gdf5 enhancer influencing human growth and osteoarthritis risk. | variants in gdf5 are associated with human arthritis and decreased height, but the causal mutations are still unknown. we surveyed the gdf5 locus for regulatory regions in transgenic mice and fine-mapped separate enhancers controlling expression in joints versus growing ends of long bones. a large downstream regulatory region contains a novel growth enhancer (grow1), which is required for normal gdf5 expression at ends of developing bones and for normal bone lengths in vivo. human grow1 contains ... | 2017 | 28671685 |
| a tale of agriculturalists and hunter-gatherers: exploring the thrifty genotype hypothesis in native south americans. | to determine genetic differences between agriculturalist and hunter-gatherer southern native american populations for selected metabolism-related markers and to test whether neel's thrifty genotype hypothesis (tgh) could explain the genetic patterns observed in these populations. | 2017 | 28464262 |
| the psoriasis-associated deletion of late cornified envelope genes lce3b and lce3c has been maintained under balancing selection since human denisovan divergence. | a common, 32kb deletion of lce3b and lce3c genes is strongly associated with psoriasis. we recently found that this deletion is ancient, predating human-denisovan divergence. however, it was not clear why negative selection has not removed this deletion from the population. | 2016 | 27919236 |
| archaic hominin admixture facilitated adaptation to out-of-africa environments. | as modern humans dispersed from africa throughout the world, they encountered and interbred with archaic hominins, including neanderthals and denisovans [1, 2]. although genome-scale maps of introgressed sequences have been constructed [3-6], considerable gaps in knowledge remain about the functional, phenotypic, and evolutionary significance of archaic hominin dna that persists in present-day individuals. here, we describe a comprehensive set of analyses that identified 126 high-frequency archa ... | 2016 | 27839976 |
| the impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. | over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the out-of-africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. the confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. we argue, however, that when statistics more directly related to load are used, the results of different studies and data s ... | 2016 | 27744216 |
| elucidating the origin of hla-b*73 allelic lineage: did modern humans benefit by archaic introgression? | a previous study reported that some of the human leukocyte antigen (hla) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged hla-b*73 allele was proposed to be transmitted from denisovans, although the dna sequence of hla-b*73 has not been detected in the denisovan genome. here, we argue against the hypothesis that hla-b*73 introgressed from denisovans into early modern humans. a phylogenetic analysis revealed that ... | 2017 | 27695917 |
| archaic admixture in human history. | modern humans evolved in southern or eastern africa, and spread from there across the rest of the world. as they expanded across africa and eurasia, they encountered other hominin groups. the extent to which modern and 'archaic' human groups interbred is an area of active research, and while we know that modern humans interbred with neanderthals and denisovans, there is not yet agreement on how many admixture events there were or on how much neanderthal or denisovan dna can be found in contempor ... | 2016 | 27662059 |
| tlrs of our fathers. | two new studies published in the american journal of human genetics (dannemann et al., 2016; deschamps et al., 2016) show that introgression of innate immune genes from neandertals and denisovans contributed to the modern genome of european and asian, but not african, populations, and this might partly explain differences in susceptibility to immune-mediated diseases. | 2016 | 26885854 |
| fire usage and ancient hominin detoxification genes: protective ancestral variants dominate while additional derived risk variants appear in modern humans. | studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. to investigate whether such genetic selection occurred, we investigated the alleles in neanderthals, denisovans and ... | 2017 | 27655273 |
| statistical methods for analyzing ancient dna from hominins. | in the past few years, the number of autosomal dna sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, neanderthal and denisovans. i review commonly used statistical methods applied to these sequences. these methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. the latter two classes are largely methods developed ... | 2016 | 27606907 |
| ancestral origins and genetic history of tibetan highlanders. | the origin of tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. analyses of deeply sequenced (30×-60×) genomes of 38 tibetan highlanders and 39 han chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of tibetans and uncover their origins. non-modern human sequences compose ∼6% of the tibetan gene pool and form unique haplotypes in some genomic regions, where denisov ... | 2016 | 27569548 |
| divergent ah receptor ligand selectivity during hominin evolution. | we have identified a fixed nonsynonymous sequence difference between humans (val381; derived variant) and neandertals (ala381; ancestral variant) in the ligand-binding domain of the aryl hydrocarbon receptor (ahr) gene. in an exome sequence analysis of four neandertal and denisovan individuals compared with nine modern humans, there are only 90 total nucleotide sites genome-wide for which archaic hominins are fixed for the ancestral nonsynonymous variant and the modern humans are fixed for the d ... | 2016 | 27486223 |
| opsin gene repertoires in northern archaic hominids. | the neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. we surveyed visual opsin genes from four neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. this analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vis ... | 2016 | 27463216 |
| chromosome-specific centromere sequences provide an estimate of the ancestral chromosome 2 fusion event in hominin genomes. | human chromosome 2 is a product of a telomere fusion of two ancestral chromosomes and loss/degeneration of one of the two original centromeres. genomic signatures of this event are limited to inverted telomeric repeats at the precise site of chromosomal fusion and to the small amount of relic centromeric sequences that remain on 2q21.2. unlike the site of fusion, which is enriched for sequences that are shared elsewhere in the human genome, the region of the nonfunctioning and degenerate ancestr ... | 2017 | 27423248 |
| the origin and evolution of homo sapiens. | if we restrict the use of homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant h. sapiens, the origin of our species would be placed in the african late middle pleistocene, based on fossils such as omo kibish 1, herto 1 and 2, and the levantine material from skhul and qafzeh. however, genetic data suggest that we and our sister species homo neanderthalensis shared a last common ancestor in the middle pleistocene approxima ... | 2016 | 27298468 |
| ancient dna and human history. | we review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient dna (adna) can provide about the demographic history of humans and our closest relatives. we concentrate on nuclear genomic sequences that have been published in the past few years. in many cases, particularly in the arctic, the americas, and europe, adna has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day g ... | 2016 | 27274045 |
| neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. | high quality altai neanderthal and denisovan genomes are revealing which regions of archaic hominin dna have persisted in the modern human genome. a number of these regions are associated with response to infection and immunity, with a suggestion that derived neanderthal alleles found in modern europeans and east asians may be associated with autoimmunity. as such neanderthal genomes are an independent line of evidence of which infectious diseases neanderthals were genetically adapted to. sympat ... | 2016 | 27063929 |
| why are there no persisting hybrids of humans with denisovans, neanderthals, or anyone else? | | 2016 | 27044111 |
| the combined landscape of denisovan and neanderthal ancestry in present-day humans. | some present-day humans derive up to ∼5% [1] of their ancestry from archaic denisovans, an even larger proportion than the ∼2% from neanderthals [2]. we developed methods that can disambiguate the locations of segments of denisovan and neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual oceanians with high denisovan ancestry [3]. in oceanians, the average size of denisovan fragments is larger than n ... | 2016 | 27032491 |
| the out of africa hypothesis and the ancestry of recent humans: cherchez la femme (et l'homme). | the out of africa hypothesis (ooah) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. however, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. the palaeontological progress relates to early homo finds in the caucasus, denisova finds in the altai mountains and neanderthal finds in a wide range of localities from the altai mountains, t ... | 2016 | 26995655 |
| excavating neandertal and denisovan dna from the genomes of melanesian individuals. | although neandertal sequences that persist in the genomes of modern humans have been identified in eurasians, comparable studies in people whose ancestors hybridized with both neandertals and denisovans are lacking. we developed an approach to identify dna inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown island melanesian genomes. in aggregate, we recovered 1.34 gigabases and 3 ... | 2016 | 26989198 |
| nuclear dna sequences from the middle pleistocene sima de los huesos hominins. | a unique assemblage of 28 hominin individuals, found in sima de los huesos in the sierra de atapuerca in spain, has recently been dated to approximately 430,000 years ago. an interesting question is how these middle pleistocene hominins were related to those who lived in the late pleistocene epoch, in particular to neanderthals in western eurasia and to denisovans, a sister group of neanderthals so far known only from southern siberia. while the sima de los huesos hominins share some derived mor ... | 2016 | 26976447 |
| the uromodulin gene locus shows evidence of pathogen adaptation through human evolution. | common variants in the umod gene encoding uromodulin, associated with risk of hypertension and ckd in the general population, increase umod expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. to determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead umod variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. the t allele of rs4293393, associa ... | 2016 | 26966016 |
| neandertal and denisovan dna from pleistocene sediments. | although a rich record of pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. using targeted enrichment of mitochondrial dna, we show that cave sediments represent a rich source of ancient mammalian dna that often includes traces of hominin dna, even at sites and in layers where no hominin remains have been discovered. by automation-assisted screening of numerous sediment samples, we de ... | 2017 | 28450384 |
| meiotic genes are enriched in regions of reduced archaic ancestry. | about 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. it has recently been shown that autosomal genomic regions with a reduced proportion of neanderthal and denisovan ancestries are significantly enriched in genes that are more expressed in testis than in other tissues. to determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the ... | 2017 | 28444387 |
| an updated age for the xujiayao hominin from the nihewan basin, north china: implications for middle pleistocene human evolution in east asia. | the xujiayao site in the nihewan basin (north china) is one of the most important paleolithic sites in east asia. twenty homo fossils, which were previously assigned to an archaic homo sapiens group, have been excavated along with more than 30,000 lithic artifacts and ∼5000 mammalian fossil specimens. dating of the xujiayao hominin has been pursued since its excavation in the 1970s, but its age has remained controversial because of limitations of the dating techniques that have been applied to a ... | 2017 | 28434540 |
| ibd sharing between africans, neandertals, and denisovans. | interbreeding between ancestors of humans and other hominins outside of africa has been studied intensively, while their common history within africa still lacks proper attention. however, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of africa. we investigate the genetic relationships of humans, neandertals, and denisovans by identifying very short dna segments in the 1000 genomes phase 3 data that the ... | 2016 | 28158547 |
| the evolutionary history of genes involved in spoken and written language: beyond foxp2. | humans possess a communication system based on spoken and written language. other animals can learn vocalization by imitation, but this is not equivalent to human language. many genes were described to be implicated in language impairment (li) and developmental dyslexia (dd), but their evolutionary history has not been thoroughly analyzed. herein we analyzed the evolution of ten genes involved in dd and li. results show that the evolutionary history of li genes for mammals and aves was comparabl ... | 2016 | 26912479 |
| paleogenetics and past infections: the two faces of the coin of human immune evolution. | with the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. these paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with neanderthals having contributed to 1.5% to 2.1% of modern eurasian genomes, and denisovans to 3% to 6% of modern melanesian genomes and to approximately 0.2% of ... | 2016 | 27337483 |
| transmission between archaic and modern human ancestors during the evolution of the oncogenic human papillomavirus 16. | every human suffers through life a number of papillomaviruses (pvs) infections, most of them asymptomatic. a notable exception are persistent infections by human papillomavirus 16 (hpv16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. oncogenic potential is not homogeneous among hpv16 lineages, and genetic variation within hpv16 exhibits some geographic structure. however, an in-depth analysis of the hpv16 evolutionary history was st ... | 2017 | 28025273 |
| neandertals revised. | the last decade has seen a significant growth of our knowledge of the neandertals, a population of pleistocene hunter-gatherers who lived in (western) eurasia between ∼400,000 and 40,000 y ago. starting from a source population deep in the middle pleistocene, the hundreds of thousands of years of relative separation between african and eurasian groups led to the emergence of different phenotypes in late pleistocene europe and africa. both recently obtained genetic evidence and archeological data ... | 2016 | 27274044 |
| epigenetics: it's getting old. past meets future in paleoepigenetics. | recent years have witnessed the rise of ancient dna (adna) technology, allowing comparative genomics to be carried out at unprecedented time resolution. while it is relatively straightforward to use adna to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. here we review recent works demonstrating that highly degraded adna still contains sufficient information to allow reconstruction of epigenetic signals, including dna methylatio ... | 2016 | 26898827 |
| model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in central african pygmies. | comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-africans and now extinct hominids such as neanderthals and denisovans. one implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in eurasia. within africa, fossil evidence suggests that anatomically modern humans (am ... | 2016 | 26888264 |
| ancient gene flow from early modern humans into eastern neanderthals. | it has been shown that neanderthals contributed genetically to modern humans outside africa 47,000-65,000 years ago. here we analyse the genomes of a neanderthal and a denisovan from the altai mountains in siberia together with the sequences of chromosome 21 of two neanderthals from spain and croatia. we find that a population that diverged early from other modern humans in africa contributed genetically to the ancestors of neanderthals from the altai mountains roughly 100,000 years ago. by cont ... | 2016 | 26886800 |
| analysis of ancient dna in microbial ecology. | the development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as neandertals and denisovans. moreover, it has also yielded novel insights into the evolution of ancient pathogens. the ana ... | 2016 | 26791510 |
| introgression of neandertal- and denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. | pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. archaic humans, who lived in europe and western asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. it is therefore conceivable that modern humans entering europe and western as ... | 2016 | 26748514 |
| the "globularization hypothesis" of the language-ready brain as a developmental frame for prosodic bootstrapping theories of language acquisition. | in recent research (boeckx and benítez-burraco, 2014a,b) have advanced the hypothesis that our species-specific language-ready brain should be understood as the outcome of developmental changes that occurred in our species after the split from neanderthals-denisovans, which resulted in a more globular braincase configuration in comparison to our closest relatives, who had elongated endocasts. according to these authors, the development of a globular brain is an essential ingredient for the langu ... | 2015 | 26696916 |
| the evolution of homo sapiens denisova and homo sapiens neanderthalensis mirna targeting genes in the prenatal and postnatal brain. | as the evolution of mirna genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of mirna genes in two archaic hominines, homo sapiens neanderthalensis and homo sapiens denisova, and elucidated the expression of their target mrnas in bain. | 2015 | 26693966 |
| nuclear and mitochondrial dna sequences from two denisovan individuals. | denisovans, a sister group of neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (denisova 3) found in denisova cave in the altai mountains. the only other denisovan specimen described to date is a molar (denisova 4) found at the same site. this tooth carries a mtdna sequence similar to that of denisova 3. here we present nuclear dna sequences from denisova 4 and a morphological description, as well as mitochondrial and nuclear dna sequence data, fro ... | 2015 | 26630009 |
| bayesian analyses of yemeni mitochondrial genomes suggest multiple migration events with africa and western eurasia. | anatomically, modern humans are thought to have migrated out of africa ∼60,000 years ago in the first successful global dispersal. this initial migration may have passed through yemen, a region that has experienced multiple migrations events with africa and eurasia throughout human history. we use bayesian phylogenetics to determine how ancient and recent migrations have shaped yemeni mitogenomic variation. | 2016 | 26567083 |
| functional analyses of transcription factor binding sites that differ between present-day and archaic humans. | we analyze 25 previously identified transcription factor binding sites that carry dna sequence changes that are present in all or nearly all present-day humans, yet occur in the ancestral state in neandertals and denisovans, the closest evolutionary relatives of humans. when the ancestral and derived forms of the transcription factor binding sites are tested using reporter constructs in 3 neuronal cell lines, the activity of 12 of the derived versions of transcription factor binding sites differ ... | 2016 | 26454764 |
| small amounts of archaic admixture provide big insights into human history. | modern humans overlapped in time and space with other hominins, such as neanderthals and denisovans, and limited amounts of hybridization occurred. here, we review recent work that has identified archaic hominin sequence that survives in modern human genomes and what these genomic excavations reveal about human evolutionary history. | 2015 | 26451479 |
| brain asymmetry in the white matter making and globularity. | recent studies from the field of language genetics and evolutionary anthropology have put forward the hypothesis that the emergence of our species-specific brain is to be understood not in terms of size, but in light of developmental changes that gave rise to a more globular braincase configuration after the split from neanderthals-denisovans. on the grounds that (i) white matter myelination is delayed relative to other brain structures and, in humans, is protracted compared with other primates ... | 2015 | 26441731 |
| chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans. | chromosomal rearrangements, which shuffle dna throughout the genome, are an important source of divergence across taxa. using a paired-end read approach with illumina sequence data for archaic humans, i identify changes in genome structure that occurred recently in human evolution. hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. additionally, genes adjacent to genome structure changes in neanderth ... | 2015 | 26399483 |
| all-or-(n)one - an epistemological characterization of the human tumorigenic neuronal paralogous fam72 gene loci. | fam72 is a novel neuronal progenitor cell (npc) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. accumulating data indicate the potential pivotal tumourigenic effects of fam72. our in silico human genome-wide analysis (gwa) revealed that the fam72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. unique asymmetric fam72 segmental gene duplications are most likely to have occurred ... | 2015 | 26206078 |
| distribution of hla haplotypes across japanese archipelago: similarity, difference and admixture. | the human leukocyte antigen (hla) region is the most polymorphic region in the human genome. the polymorphic nature of the hla region is thought to have been shaped from balancing selection. the complex migration events during the out-of-africa expansion have influenced geographic patterns of hla allele frequencies and diversities across present-day human populations. differences in the hla allele frequency may contribute geographic differences in the susceptibility to many diseases, such as inf ... | 2015 | 26202576 |
| possible functional links among brain- and skull-related genes selected in modern humans. | the sequencing of the genomes from extinct hominins has revealed that changes in some brain-related genes have been selected after the split between anatomically-modern humans and neanderthals/denisovans. to date, no coherent view of these changes has been provided. following a line of research we initiated in boeckx and benítez-burraco (2014a), we hypothesize functional links among most of these genes and their products, based on the existing literature for each of the gene discussed. the genes ... | 2015 | 26136701 |
| denisovan ancestry in east eurasian and native american populations. | although initial studies suggested that denisovan ancestry was found only in modern human populations from island southeast asia and oceania, more recent studies have suggested that denisovan ancestry may be more widespread. however, the geographic extent of denisovan ancestry has not been determined, and moreover the relationship between the denisovan ancestry in oceania and that elsewhere has not been studied. here we analyze genome-wide single nucleotide polymorphism data from 2,493 individua ... | 2015 | 26104010 |
| global survey of variation in a human olfactory receptor gene reveals signatures of non-neutral evolution. | allelic variation at 4 loci in the human olfactory receptor gene or7d4 is associated with perceptual variation in the sex steroid-derived odorants, androstenone, and androstadienone. androstadienone has been linked with chemosensory identification whereas androstenone makes pork from uncastrated pigs distasteful ("boar taint"). in a sample of 2224 individuals from 43 populations, we identified 45 or7d4 single nucleotide polymorphisms. coalescent modeling of frequency-site-spectrum-based statisti ... | 2015 | 26072518 |
| mapping the space of genomic signatures. | we propose a computational method to measure and visualize interrelationships among any number of dna sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. an "image distance" is computed for each pair of graphical representations of dna sequences, and the distances are visualized as a molecular distance map: each point on the map represents a dna sequence, and the spatial proximity between any two points reflects the degree of structural si ... | 2015 | 26000734 |
| erratum for the report "ancient ethiopian genome reveals extensive eurasian admixture in eastern africa" (previously titled "ancient ethiopian genome reveals extensive eurasian admixture throughout the african continent") by m. gallego llorente, e. r. jones, a. eriksson, v. siska, k. w. arthur, j. w. arthur, m. c. curtis, j. t. stock, m. coltorti, p. pieruccini, s. stretton, f. brock, t. higham, y. park, m. hofreiter, d. g. bradley, j. bhak, r. pinhasi, a. manica. | in the report “ancient ethiopian genome reveals extensive eurasian admixture in eastern africa,” the results were affected by a bioinformatics error. a script necessary to convert the input produced by samtools v0.1.19 to be compatible with plink was not run when merging the ancient genome, mota, with the contemporary populations snp panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with neandertals and denisovans was no ... | 2016 | 26912899 |
| the diverse origins of the human gene pool. | analyses of the genomes of neanderthals and denisovans, the closest evolutionary relatives of present-day humans, suggest that our ancestors were part of a web of now-extinct populations linked by limited, but intermittent or sometimes perhaps even persistent, gene flow. | 2015 | 25982166 |
| the evolution and functional impact of human deletion variants shared with archaic hominin genomes. | allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-african introgression from archaic hominins. however, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. we identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the human-neandertal divergence (ancient) an ... | 2015 | 25556237 |
| [mutation process in the protein-coding genes of human mitochondrial genome in context of evolution of the genus]. | the human mitochondrial genome, although it has a small size, is characterized by high level of variation, non-uniformly distributed in groups of nucleotide positions that differ in the degree of variability. considering the mutation process in human mtdna relative to the mitochondrial genomes of the genus homo-neandertals, denisova hominin and other primate species, it appears that more than half (56.5%) variable positions in the human mtdna protein-coding genes are characterized by back (rever ... | 2014 | 25509854 |
| almost 20 years of neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction. | nearly two decades since the first retrieval of neanderthal dna, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a neanderthal and a denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the neanderthal lineage. this genomic information, coupled with diversity exome data from several neanderthal specimens is shedding new light on evolutionary processes ... | 2015 | 25487326 |
| leukotriene signaling in the extinct human subspecies homo denisovan and homo neanderthalensis. structural and functional comparison with homo sapiens. | mammalian lipoxygenases (loxs) have been implicated in cell differentiation and in the biosynthesis of pro- and anti-inflammatory lipid mediators. the initial draft sequence of the homo neanderthalensis genome (coverage of 1.3-fold) suggested defective leukotriene signaling in this archaic human subspecies since expression of essential proteins appeared to be corrupted. meanwhile high quality genomic sequence data became available for two extinct human subspecies (h. neanderthalensis, homo denis ... | 2015 | 25447821 |
| ancient humans and the origin of modern humans. | recent advances in sequencing technologies and molecular methods have facilitated the sequencing of dna from ancient human remains which has, in turn, provided unprecedented insight into human history. within the past 4 years the genomes of neandertals and denisovans, as well as the genomes of at least two early modern humans, have been sequenced. these sequences showed that there have been several episodes of admixture between modern and archaic groups; including admixture from neandertals into ... | 2014 | 25286439 |
| epigenetic information from ancient dna provides new insights into human evolution. commentary on gokhman d et al. (2014): reconstructing the dna methylation maps of the neanderthal and the denisovan. science 344:523-527. | | 2014 | 25277105 |
| the evolution of cancer-related genes in hominoids. | the evolution of cancer suppression is essential for the maintenance of multicellularity. the lack of correlation between body size and cancer risk across species, known as peto's paradox, suggests that genetic variation in cancer resistance is sufficient to compensate for increases of cell numbers in bigger animals. to assess evolutionary dynamics of cancer-related genes, we analyzed ka, ks,and ka/ks values in 120 oncogenes and tumor suppressor genes (tsg) among seven hominoid species, includin ... | 2015 | 25249249 |
| preserving immune diversity through ancient inheritance and admixture. | the progress of genomic technologies is allowing researchers to scan the genomes of different species for the occurrence of natural selection at an unprecedented level of resolution. these studies show that genes involved in immune processes are preferential targets of different forms of selection, some of which act to preserve immune diversity over time. recent work in humans shows that this can be achieved either by inheriting advantageous immune variation from distant ancestral species, throu ... | 2014 | 25190608 |
| a test for ancient selective sweeps and an application to candidate sites in modern humans. | we introduce a new method to detect ancient selective sweeps centered on a candidate site. we explored different patterns produced by sweeps around a fixed beneficial mutation, and found that a particularly informative statistic measures the consistency between majority haplotypes near the mutation and genotypic data from a closely related population. we incorporated this statistic into an approximate bayesian computation (abc) method that tests for sweeps at a candidate site. we applied this me ... | 2014 | 25172957 |
| novel denisovan and neanderthal retroviruses. | following the recent availability of high-coverage genomes for denisovan and neanderthal hominids, we conducted a screen for endogenized retroviruses, identifying six novel, previously unreported herv-k(hml2) elements (herv-k is human endogenous retrovirus k). these elements are absent from the human genome (hg38) and appear to be unique to archaic hominids. these findings provide further evidence supporting the recent activity of the herv-k(hml2) group, which has been implicated in human diseas ... | 2014 | 25142605 |
| primate evolution of the recombination regulator prdm9. | the prdm9 gene encodes a protein with a highly variable tandem-repeat zinc finger (zf) dna-binding domain that plays a key role in determining sequence-specific hotspots of meiotic recombination genome wide. here we survey the diversity of the prdm9 zf domain by sequencing this region in 64 primates from 18 species, revealing 68 unique alleles across all groups. we report ubiquitous positive selection at nucleotide positions corresponding to dna contact residues and the expansion of zfs within c ... | 2014 | 25001002 |
| did neanderthals and denisovans have our de novo genes? | | 2014 | 24952670 |
| insights into the genetic structure and diversity of 38 south asian indians from deep whole-genome sequencing. | south asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. there have been numerous reports on the genetic structure of asian indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and y chromosomes. asian indians in singapore are primarily descendants of immigrants from dravidian-language-speaking states in south india, and 38 individuals from the general population u ... | 2014 | 24832686 |
| reconstructing the dna methylation maps of the neandertal and the denisovan. | ancient dna sequencing has recently provided high-coverage archaic human genomes. however, the evolution of epigenetic regulation along the human lineage remains largely unexplored. we reconstructed the full dna methylation maps of the neandertal and the denisovan by harnessing the natural degradation processes of methylated and unmethylated cytosines. comparing these ancient methylation maps to those of present-day humans, we identified ~2000 differentially methylated regions (dmrs). particular ... | 2014 | 24786081 |
| the shape of the human language-ready brain. | our core hypothesis is that the emergence of our species-specific language-ready brain ought to be understood in light of the developmental changes expressed at the levels of brain morphology and neural connectivity that occurred in our species after the split from neanderthals-denisovans and that gave us a more globular braincase configuration. in addition to changes at the cortical level, we hypothesize that the anatomical shift that led to globularity also entailed significant changes at the ... | 2014 | 24772099 |
| a 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered. | by combining state-of-the-art approaches in ancient genomics, meyer and co-workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at sierra de atapuerca, spain about 400,000 years ago. this achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as neanderthals and denisovans. molecular phylogenetic reconstructions placed the atapuercan as a sister group to denisovans, although its morpholo ... | 2014 | 24706482 |