| 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 |
| neanderthal and denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms. | analyses of the genetic relationships among modern humans, neanderthals and denisovans have suggested that 1-4% of the non-sub-saharan african gene pool may be neanderthal derived, while 6-8% of the melanesian gene pool may be the product of admixture between the denisovans and the direct ancestors of melanesians. in the present study, we analyzed single nucleotide polymorphism (snp) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution ... | 2013 | 23872234 |
| loss of olfactory receptor function in hominin evolution. | the mammalian sense of smell is governed by the largest gene family, which encodes the olfactory receptors (ors). the gain and loss of or genes is typically correlated with adaptations to various ecological niches. modern humans have 853 or genes but 55% of these have lost their function. here we show evidence of additional or loss of function in the neanderthal and denisovan hominin genomes using comparative genomic methodologies. ten neanderthal and 8 denisovan ors show evidence of loss of fun ... | 2014 | 24392153 |
| a penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. | previous studies show that humans have a large genomic deletion downstream of the androgen receptor gene that eliminates an ancestral mammalian regulatory enhancer that drives expression in developing penile spines and sensory vibrissae. here we use a combination of large-scale sequence analysis and pcr amplification to demonstrate that the penile spine/vibrissa enhancer is missing in all humans surveyed and in the neandertal and denisovan genomes, but is present in dna samples of chimpanzees an ... | 2013 | 24367647 |
| hiv infection reveals widespread expansion of novel centromeric human endogenous retroviruses. | human endogenous retroviruses (hervs) make up 8% of the human genome. the herv-k (hml-2) family is the most recent group of these viruses to have inserted into the genome, and we have detected the activation of herv-k (hml-2) proviruses in the blood of patients with hiv-1 infection. we report that hiv-1 infection activates expression of a novel herv-k (hml-2) provirus, termed k111, present in multiple copies in the centromeres of chromosomes throughout the human genome yet not annotated in the m ... | 2013 | 23657884 |
| human brain evolution: transcripts, metabolites and their regulators. | what evolutionary events led to the emergence of human cognition? although the genetic differences separating modern humans from both non-human primates (for example, chimpanzees) and archaic hominins (neanderthals and denisovans) are known, linking human-specific mutations to the cognitive phenotype remains a challenge. one strategy is to focus on human-specific changes at the level of intermediate phenotypes, such as gene expression and metabolism, in conjunction with evolutionary changes in g ... | 2013 | 23324662 |
| the cognitive ability of extinct hominins: bringing down the hierarchy using genomic evidences. | the availability of the full genomes of homo sapiens, homo neanderthalensis, and denisovans, as well as modern bioinformatic tools, are opening new possibilities for the understanding of the differences and similarities present in these taxa. | 2013 | 23907779 |
| cognitive functions: human vs. animal - 4:1 advantage |-fam72-srgap2-|. | with the advent of computational genomics, an intensive search is underway for unique biomarkers for homo sapiens that could be used to differentiate taxa within the hominoidea, in particular to distinguish homo from the apes (pan, gorilla, pongo, and hylobates) and species or subspecies within the genus homo (h. sapiens, h. heidelbergensis, h. neanderthalensis, h. erectus, and the denisovans). here, we suggest that the |-fam72-srgap2-| (family with sequence similarity 72/slit-robo rho gtpase ac ... | 2017 | 28255958 |
| proteogenomic review of the changes in primate apoc-i during evolution. | apolipoprotein c-i has evolved more rapidly than any of the other soluble apolipoproteins. during the course of primate evolution, the gene for this apolipoprotein was duplicated. prompted by our observation that the two resulting genes encode two distinct forms of apoc-i in great apes, we have reviewed both the genomic and proteomic data to examine what changes have occurred during the course of primate evolution. we have found data showing that one of the duplicated genes, known to be a pseudo ... | 2013 | 28757862 |
| archaic human genomics. | for much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. homo erectus was seen arising in africa from an earlier member of the genus and then spreading throughout the old world and into the oceania. a regional continuity model of anagenetic change from h. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by h. erectus was labeled the multiregional model of human evolution (mre). a c ... | 2012 | 23124308 |
| 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 |
| unexpectedly many extinct hominins. | recent studies indicate that neanderthal and denisova hominins may have been separate species, while debate continues on the status of homo floresiensis. the decade-long debate between "splitters," who recognize over 20 hominin species, and "lumpers," who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. here, we present probability distributions for the number of speciation events and the number of contempo ... | 2012 | 22946817 |
| wide distribution and altitude correlation of an archaic high-altitude-adaptive epas1 haplotype in the himalayas. | high-altitude adaptation in tibetans is influenced by introgression of a 32.7-kb haplotype from the denisovans, an extinct branch of archaic humans, lying within the endothelial pas domain protein 1 (epas1), and has also been reported in sherpa. we genotyped 19 variants in this genomic region in 1507 eurasian individuals, including 1188 from bhutan and nepal residing at altitudes between 86 and 4550 m above sea level. derived alleles for five snps characterizing the core denisovan haplotype (agg ... | 2016 | 26883865 |
| a high-coverage genome sequence from an archaic denisovan individual. | we present a dna library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a denisovan, an extinct relative of neandertals. the quality of this genome allows a direct estimation of denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. it also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of denisovan and neandertal admixture into presen ... | 2012 | 22936568 |
| neandertal and denisovan retroviruses. | | 2012 | 22677281 |
| human evolution. cave was lasting home to denisovans. | | 2015 | 26383930 |
| archaic inheritance: supporting high-altitude life in tibet. | the tibetan plateau, often called the roof of the world, sits at an average altitude exceeding 4,500 m. because of its extreme altitude, the plateau is one of the harshest human-inhabited environments in the world. this, however, did not impede human colonization, and the tibetan people have made the tibetan plateau their home for many generations. many studies have quantified their markedly different physiological response to altitude and proposed that tibetans were genetically adapted. recentl ... | 2015 | 26294746 |
| specific inactivation of two immunomodulatory siglec genes during human evolution. | sialic acid-recognizing ig-like lectins (siglecs) are signaling receptors that modulate immune responses, and are targeted for interactions by certain pathogens. we describe two primate siglecs that were rendered nonfunctional by single genetic events during hominin evolution after our common ancestor with the chimpanzee. siglec13 was deleted by an alu-mediated recombination event, and a single base pair deletion disrupted the orf of siglec17. siglec-13 is expressed on chimpanzee monocytes, inna ... | 2012 | 22665810 |
| searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes. | adaptation to low temperatures has been reasonably developed in the human species during the colonization of the eurasian landmass subsequent to out of africa migrations of anatomically modern humans. in addition to morphological and cultural changes, also metabolic ones are supposed to have favored human isolation from cold and body heat production and this can be hypothesized also for most neandertal and at least for some denisovan populations, which lived in geographical areas that strongly e ... | 2014 | 24667833 |
| [mitochondrial dna polymorphisms shared between modern humans and neanderthals: adaptive convergence or evidence for interspecific hybridization?]. | an analysis of the variability of the nucleotide sequences in the mitochondrial genome of modern humans, neanderthals, denisovans, and other primates has shown that there are shared polymorphisms at positions 2758 and 7146 between modern homo sapiens (in phylogenetic cluster l2'3'4'5'6) and homo neanderthalensis (in the group of european neanderthals younger than 48000 years). it is suggested that the convergence may be due to adaptive changes in the mitochondrial genomes of modern humans and ne ... | 2013 | 25486780 |
| human evolution out of africa: the role of refugia and climate change. | although an african origin of the modern human species is generally accepted, the evolutionary processes involved in the speciation, geographical spread, and eventual extinction of archaic humans outside of africa are much debated. an additional complexity has been the recent evidence of limited interbreeding between modern humans and the neandertals and denisovans. modern human migrations and interactions began during the buildup to the last glacial maximum, starting about 100,000 years ago. by ... | 2012 | 22422974 |
| genetic history of an archaic hominin group from denisova cave in siberia. | using dna extracted from a finger bone found in denisova cave in southern siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. this individual is from a group that shares a common origin with neanderthals. this population was not involved in the putative gene flow from neanderthals into eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day melanesians. we designate this hominin population 'denisovans ... | 2010 | 21179161 |
| the complete genome sequence of a neanderthal from the altai mountains. | we present a high-quality genome sequence of a neanderthal 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 neanderthal 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 neanderthals, denisovans a ... | 2014 | 24352235 |
| identification of putative target genes of the transcription factor runx2. | comparisons of the genomes of neandertals and denisovans with present-day human genomes have suggested that the gene runx2, which encodes a transcription factor, may have been positively selected during early human evolution. here, we overexpress runx2 in ten human cell lines and identify genes that are directly or indirectly affected by runx2 expression. we find a number of genes not previously known to be affected by runx2 expression, in particular birc3, genes encoded on the mitochondrial gen ... | 2013 | 24349465 |
| hominin evolution and gene flow in the pleistocene africa. | africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. recently, hammer et al. (2011) and harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in africa as recently as 35,000 years ago. however, a genetic evidence of hybridization between hominin lineages during the lower and middle pleis ... | 2013 | 23980394 |
| neanderthal introgression at chromosome 3p21.31 was under positive natural selection in east asians. | studies of the neanderthal and denisovan genomes demonstrate archaic hominin introgression in eurasians. here, we present evidence of neanderthal introgression within the chromosome 3p21.31 region, occurring with a high frequency in east asians (ranging from 49.4% to 66.5%) and at a low frequency in europeans. we also detected a signal of strong positive selection in this region only in east asians. our data indicate that likely candidate targets of selection include rs12488302-t and its associa ... | 2014 | 24336922 |
| neanderthal and denisovan retroviruses in modern humans. | | 2013 | 24262833 |
| the genochip: a new tool for genetic anthropology. | the genographic project is an international effort aimed at charting human migratory history. the project is nonprofit and nonmedical, and, through its legacy fund, supports locally led efforts to preserve indigenous and traditional cultures. although the first phase of the project was focused on uniparentally inherited markers on the y-chromosome and mitochondrial dna (mtdna), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human gen ... | 2013 | 23666864 |
| the denisova hominin need not be an out of africa story. | | 2011 | 21129766 |
| 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 |
| using the neanderthal and denisova genetic data to understand the common mapt 17q21 inversion in modern humans. | the polymorphic inversion on 17q21, that includes the mapt gene, represents a unique locus in the human genome characterized by a large region with strong linkage disequilibrium. two distinct haplotypes, h1 and h2, exist in modern humans, and h1 has been unequivocally related to several neurodegenerative disorders. recent data indicate that recurrent inversions of this genomic region have occurred through primate evolution, with the h2 haplotype being the ancestral state. neandertals harbored th ... | 2012 | 23959642 |
| discerning the origins of the negritos, first sundaland people: deep divergence and archaic admixture. | human presence in southeast asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called sundaland. in the philippine islands, peninsular malaysia, and andaman islands, there exist indigenous groups collectively called negritos whose ancestry can be traced to the "first sundaland people." to understand the relationship between these negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the phili ... | 2017 | 28854687 |
| evolutionary history of tibetans inferred from whole-genome sequencing. | the indigenous people of the tibetan plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. recent studies have demonstrated that the tibetan epas1 haplotype is involved in high altitude-adaptation and originated in an archaic denisovan-related population. we sequenced the whole-genomes of 27 tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. we detected evidence of popul ... | 2017 | 28448578 |
| adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. | adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. here, the various attributes of these three potential sources of adaptive variation are compared. for example, the rate of adaptive change is generally thought to be faster from standing variation, slower fr ... | 2013 | 23906376 |
| [mitochondrial dna polymorphisms shared between modern humans and neanderthals: adaptive convergence or evidence for interspecific hybridization?]. | an analysis of the variability of the nucleotide sequences in the mitochondrial genome of modern humans, neanderthals, denisovans, and other primates has shown that there are shared polymorphisms at positions 2758 and 7146 between modern homo sapiens (in phylogenetic cluster l2'3'4'5'6) and homo neanderthalensis (in the group of european neanderthals younger than 48000 years). it is suggested that the convergence may be due to adaptive changes in the mitochondrial genomes of modern humans and ne ... | 2013 | 25508911 |
| archaic adaptive introgression in tbx15/wars2. | a recent study conducted the first genome-wide scan for selection in inuit from greenland using single nucleotide polymorphism chip data. here, we report that selection in the region with the second most extreme signal of positive selection in greenlandic inuit favored a deeply divergent haplotype that is closely related to the sequence in the denisovan genome, and was likely introgressed from an archaic population. the region contains two genes, wars2 and tbx15, and has previously been associat ... | 2017 | 28007980 |
| revised stratigraphy and chronology for homo floresiensis at liang bua in indonesia. | homo floresiensis, a primitive hominin species discovered in late pleistocene sediments at liang bua (flores, indonesia), has generated wide interest and scientific debate. a major reason this taxon is controversial is because the h. floresiensis-bearing deposits, which include associated stone artefacts and remains of other extinct endemic fauna, were dated to between about 95 and 12 thousand calendar years (kyr) ago. these ages suggested that h. floresiensis survived until long after modern hu ... | 2016 | 27027286 |
| genes regulated by vitamin d in bone cells are positively selected in east asians. | vitamin d and folate are activated and degraded by sunlight, respectively, and the physiological processes they control are likely to have been targets of selection as humans expanded from africa into eurasia. we investigated signals of positive selection in gene sets involved in the metabolism, regulation and action of these two vitamins in worldwide populations sequenced by phase i of the 1000 genomes project. comparing allele frequency-spectrum-based summary statistics between these gene sets ... | 2015 | 26719974 |
| deciphering the denisovans. | | 2015 | 26668361 |
| a 3.4-kb copy-number deletion near epas1 is significantly enriched in high-altitude tibetans but absent from the denisovan sequence. | tibetan high-altitude adaptation (haa) has been studied extensively, and many candidate genes have been reported. subsequent efforts targeting haa functional variants, however, have not been that successful (e.g., no functional variant has been suggested for the top candidate haa gene, epas1). with winxpcnver, a method developed in this study, we detected in microarray data a tibetan-enriched deletion (ted) carried by 90% of tibetans; 50% were homozygous for the deletion, whereas only 3% carried ... | 2015 | 26073780 |
| the red queen model of recombination hotspots evolution in the light of archaic and modern human genomes. | recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. in the human genome, recombination events are clustered in hotspots, whose location is determined by the prdm9 protein. there is evidence that the location of hotspots evolves rapidly, as a consequence of changes in prdm9 dna-binding domain. however, the reasons for these changes and the rate at which they occu ... | 2014 | 25393762 |
| altitude adaptation in tibetans caused by introgression of denisovan-like dna. | as modern humans migrated out of africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. these diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. one of the most celebrated examples in humans is the adaptation of tibetans to the hypoxic environment of the high-altitude tibetan plateau. a hypoxia pathway gene, epas1, was previously identified as hav ... | 2014 | 25043035 |
| human evolution. elusive denisovans sighted in oldest human dna. | | 2013 | 24311652 |
| hunter-gatherers in southeast asia: from prehistory to the present. | anatomically modern hunter-gatherers expanded from africa into southeast asia at least 50,000 years ago, where they probably encountered and interacted with populations of homo erectus and homo floresiensis and the recently discovered denisovans. simulation studies suggest that these hunter-gatherers may well have followed a coastal route that ultimately led to the settlement of sahul, while archaeology confirms that they also crossed significant seas and explored well into the interior. they al ... | 2013 | 24297219 |
| introduction: revisiting the "negrito" hypothesis: a transdisciplinary approach to human prehistory in southeast asia. | the "negrito" hypothesis predicts that a shared phenotype among various contemporary groups of hunter-gatherers in southeast asia--dark skin, short stature, tight curly hair--is due to common descent from a region-wide, pre-neolithic substrate of humanity. the alternative is that their distinctive phenotype results from convergent evolution. the core issues of the negrito hypothesis are today more relevant than ever to studies of human evolution, including the out-of-africa migration, admixture ... | 2013 | 24297218 |
| paleontology. did the denisovans cross wallace's line? | | 2013 | 24136958 |
| the apolipoprotein e (apoe) gene appears functionally monomorphic in chimpanzees (pan troglodytes). | the human apolipoprotein e (apoe) gene is polymorphic, with three primary alleles (e2, e3, e4) that differ at two key non-synonymous sites. these alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, alzheimer's disease risk, and longevity. the relative frequencies of these alleles vary across human populations, and the evolution and m ... | 2012 | 23112842 |
| evolution of siglec-11 and siglec-16 genes in hominins. | we previously reported a human-specific gene conversion of siglec11 by an adjacent paralogous pseudogene (siglec16p), generating a uniquely human form of the siglec-11 protein, which is expressed in the human brain. here, we show that siglec-11 is expressed exclusively in microglia in all human brains studied-a finding of potential relevance to brain evolution, as microglia modulate neuronal survival, and siglec-11 recruits shp-1, a tyrosine phosphatase that modulates microglial biology. followi ... | 2012 | 22383531 |
| paleoanthropology. a denisovan legacy in the immune system? | | 2011 | 21868647 |
| paleoanthropology. who were the denisovans? | | 2011 | 21868646 |
| gain-of-function egln1 prolyl hydroxylase (phd2 d4e:c127s) in combination with epas1 (hif-2α) polymorphism lowers hemoglobin concentration in tibetan highlanders. | tibetans have lived at high altitude for generations and are thought to be genetically adapted to hypoxic environments. most are protected from hypoxia-induced polycythemia, and a haplotype of epas1, encoding hypoxia-inducible factor (hif-2α), has been associated with lower hemoglobin levels. we earlier reported a tibetan-specific egln1 haplotype encoding phd2 which abrogates hif augmentation in hypoxia. we genotyped 347 tibetan individuals from varying altitudes for both the tibetan-specific eg ... | 2017 | 28233034 |
| evolutionary selected tibetan variants of hif pathway and risk of lung cancer. | tibetans existed in high altitude for ~25 thousand years and have evolutionary selected unique haplotypes assumed to be beneficial to hypoxic adaptation. egln1/phd2 and epas1/hif-2α, both crucial components of hypoxia sensing, are the two best-established loci contributing to high altitude adaptation. the co-adapted tibetan-specific haplotype encoding for phd2:p.[d4e/c127s] promotes increased hif degradation under hypoxic conditions. the tibetan-specific 200 kb epas1 haplotype introgressed from ... | 2017 | 28036300 |