The complete genome sequence of a Neanderthal from the Altai Mountains
Open accessAbstract
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 and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Present-day non-African human populations inherit 1-4% of their genetic ancestry from introgression with Neanderthals.
“Genomic analyses have revealed that present-day non-African human populations inherit 1–4% of their genetic ancestry from introgression with Neanderthals (Green et al., 2010; Prüfer et al., 2014).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Prüfer et al., 2014
The “Neandertal gene flow into modern humans” section supports Neanderthal ancestry in present-day populations outside Africa, but estimates its proportion at 1.5–2.1%, not the cited 1–4% range. The Discussion also attributes the allele sharing to recent admixture. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe introgressing Neanderthals were probably from populations separated in time and space from the three high-coverage archaic individuals (DAV).
“Moreover, the introgressing Neanderthals were probably from populations that were separated both in time and space from the three archaic individuals who have so far been sequenced to high coverage-hereafter referred to as DAV (Denisovan, Altai Neanderthal and Vindija Neanderthal) 1,17,18 .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [18]
The Archaic population differentiation section estimates that the introgressing Neanderthal population split from the Altai Neanderthal population 77,000–114,000 years ago. The Discussion also says Neanderthal populations had separated by the time of gene flow and compares the introgressed DNA with individuals from the Altai, Croatia and the Caucasus. Our copy does not establish that the introgressing population was geographically separated from all three named individuals; it also refers to two, not three, high-coverage archaic genomes. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIntrogression from extinct Neanderthal and Denisovan human species contributes to the genetic pool of modern human populations and their phenotypic spectrum.
“Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum.”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [14]
The sections ‘Neandertal gene flow into modern humans’ and ‘Denisovan gene flow in mainland Asia’ report contributions from both groups to present-day human genomes. The section ‘Neandertal gene flow into Denisovans’ says archaic HLA alleles have been suggested to have functional relevance in modern humans, but the paper does not establish a contribution to the broader phenotypic spectrum claimed. Page numbers are unavailable in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredNon-African populations show 1% to 2% Neanderthal ancestry; Melanesians and East Asians display 3% and 0.2% Denisovan ancestry, respectively.
“In particular, non-African populations show 1% to 2% of Neanderthal ancestry in their genomes (Green et al. 2010; Prüfer et al. 2014) and Melanesians and East Asians display 3% and 0.2%, respectively, from Denisovans ancestry (Green et al. 2010; Meyer et al. 2012; Prüfer et al. 2014).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Prüfer et al. 2014
The 'Neandertal gene flow into modern humans' section estimates 1.5–2.1% Neandertal-derived DNA in people outside Africa. 'Denisovan gene flow in mainland Asia' estimates about 0.2% Denisovan contribution in mainland Asians, but does not give the claimed 3% figure for Melanesians; its comparison implies about 5% for populations in Papua New Guinea and Australia. Page numbers are unavailable in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredWest Eurasians harbour significantly less Neanderthal ancestry than East Asians.
“West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
In “Denisovan gene flow in mainland Asia” (page unavailable), the paper says populations in Asia and America appear to have more regions of Neandertal origin than populations in Europe. This supports the direction of the comparison, but the passage does not establish statistical significance for Neandertal ancestry or address West Eurasians as a whole. The reported Z-score concerns Denisovan, not Neandertal, ancestry. (LLM, conf=0.84)
Experimental — accuracy not yet measured
There is a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals.
“Supporting this theory, we observe a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals19 (Supplementary Information, section 5; Fig. 2).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
The paper’s ‘Neandertal gene flow into modern humans’ section reports Neanderthal-derived DNA in people outside Africa, and its Discussion describes allele sharing between Neanderthals and non-African populations (page not supplied). It does not report a correlation with Basal Eurasian ancestry. The citing sentence presents that correlation as the citing authors’ own observation (‘we observe’), rather than a finding of this source. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe mapping approaches employed in this study are consistent with those used in previous research.
“The mapping approaches employed in this study are consistent with those used in previous research [2, 6].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [2]
Evidence for super-archaic introgression into the ancestors of the Altai Denisovans and, possibly, Andamanese populations suggests that viable reproduction between super-archaic hominins and more derived hominins may have been possible.
“Evidence for super-archaic introgression into the ancestors of the Altai Denisovans 30 and, possibly, Andamanese populations 31-33 , suggests that viable reproduction may actually have been possible, though further evaluation of these hypotheses at present is not possible given the available data.”
From Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture (2021) · cites this paper as [30]
Analyses of the genomes of Neandertals and modern humans show that they encountered each other outside Africa and interbred.
“Analyses of the genomes of Neandertals and modern humans show that they encountered each other outside Africa and interbred [6, 15, 16].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [15]
After modern humans left Africa more than 60,000 years ago, multiple admixture events around 55,000 years ago occurred between modern humans and now extinct archaic humans including Neandertals and Denisovans.
“After modern humans left Africa more than 60,000 years ago, genetic evidence suggests multiple admixture events ~55,000 years [9] between modern humans and now extinct archaic humans including Neandertals [10–12] and Denisovans [13, 14].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [10]
The lower efficacy of selection in Neanderthals allowed the accumulation of weakly deleterious alleles in Neanderthal populations.
“The resulting lower efficacy of selection allowed the accumulation of weakly deleterious alleles in Neanderthal populations31.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [31]
The ‘Heterozygosity and population size’ section reports low Neandertal genetic diversity and a decline in ancestral population size. Searches for weakly deleterious alleles, purifying selection, and their accumulation found no passage in our copy linking reduced selection efficacy to an accumulation of such alleles. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe highest estimates of Basal Eurasian ancestry are from the Near East.
“It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East, given the hypothesis that it was there that most admixture between Neanderthals and modern humans occurred19,23.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
The 'Neandertal gene flow into modern humans' section estimates Neandertal-derived DNA in people outside Africa, but does not estimate Basal Eurasian ancestry. Searches for Basal Eurasian ancestry and Near Eastern estimates found no passage supporting the claim that the highest estimates are from the Near East. (LLM, conf=0.75)
Experimental — accuracy not yet measuredNeanderthal ancestry in all present-day non-Africans is estimated to be 1.5-2.1 %.
“Neanderthal ancestry in all present-day non-Africans is estimated to be 1.5–2.1 % [14].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
Neanderthal-derived DNA in all non-Africans is more closely related to a Neanderthal from the Caucasus than to either the Neanderthal from Siberia or the Neanderthal from Croatia.
“the Neanderthal-derived DNA in all non-Africans is more closely related to a Neanderthal from the Caucasus than it is to either the Neanderthal from Siberia or the Neanderthal from Croatia [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
A low level (~0.2 %) of Denisovan ancestry is found across Eastern Eurasia and in Native American populations.
“A low level (~0.2 %) of Denisovan ancestry is also found across Eastern Eurasia and in Native American populations [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
Archaic admixture occurred in West Asia early during modern humans' exit from Africa.
“providing more evidence that archaic admixture occurred in West Asia early during modern humans’ exit from Africa.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
Denisovans themselves appear to have received gene flow from other archaic humans.
“Denisovans themselves appear to have received gene flow from other archaic humans.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
At least 0.5 % of the Denisovan genome was contributed by Neanderthals.
“It has been estimated that at least 0.5 % of the Denisovan genome was contributed by Neanderthals”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
0.5-8 % of the Denisovan genome comes from an unknown hominin who split from other hominins between 1.1 and 4 million ya.
“and that 0.5–8 % comes from an unknown hominin who split from other hominins between 1.1 and 4 million ya [14].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
Modern human ancestors and archaic hominins evolved separately for 550,000-765,000 years.
“This conclusion is surprising because modern human ancestors and archaic hominins evolved separately for 550,000–765,000 years [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
CASC5, KIF18A, and SPAG5 carry modern human-specific amino-acid substitutions and localize to the mitotic spindle or kinetochore.
“The centrosome-associated cell division machinery contains at least three more proteins that carry modern human-specific amino-acid substitutions. CASC5 (cancer susceptibility candidate 5), KIF18A (kinesin family member 18A), and SPAG5 (sperm-associated antigen 5) localize to the mitotic spindle, which is organized by the centrosome, or to the kinetochore, which attaches chromosomes to the spindle”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Prufer et al., 2014
Prüfer et al. used a similar technique to quantify divergence between archaic and modern genomes and found that branch length differences between sequencing batches often exceeded branch length differences between populations.
“Prüfer et al. (22) used a similar technique to quantify divergence between archaic and modern genomes and found that branch length differences between sequencing batches often exceeded branch length differences between populations.”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [22]
A significant intersection was found with the data from Prüfer et al. [44] (p < 0.05) and with the combined data from Prüfer et al. [44] and Racimo [48] (p < 0.05).
“A significant intersection was found with the data from Prüfer et al. [44] (p < 0.05) and with the combined data from Prüfer et al. [44] and Racimo [48] (p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
CBL is located in a region showing signals of a strong selective sweep in AMH compared to Altai Neanderthals.
“CBL is located in a region showing signals of a strong selective sweep in AMH compared to Altai Neanderthals [44]”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
ERBB4 is one of many neural crest-related genes associated with selective signals in AMH, some of which show fixed or nearly fixed amino acid changes compared to Neanderthals.
“ERBB4 is one of many neural crest-related genes associated with selective signals in AMH (e.g., SNAI2 [44], CITED2 [44], PRDM10 [46, 78], and others [38]), some of which show fixed or nearly fixed amino acid changes compared to Neanderthals.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05).
“A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
Others, like RB1CC1 or PRDM10 and NCOA6, have been found in selective sweep screens, suggesting contributions of individual transcription factors rather than the whole class of proteins.
“Others, like RB1CC120 or PRDM10 and NCOA633 have been found in selective sweep screens, suggesting contributions of individual transcription factors, rather than the whole class of proteins.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
These genotype calls are absent from the files provided for the three archaic genomes due to different genotype calling and filtering procedures compared to the original publication of the Altai Neanderthal genome.
“These genotype calls are absent from the files provided for the three archaic genomes due to different genotype calling and filtering procedures compared to the original publication of the Altai Neanderthal genome20,21.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
Among the 15 fixed protein-coding changes identified here but absent from previous analyses, some might have contributed to complex modifications of pathways in cell division, like AHR or DNHD1, as well as other genes with HHMCs, like CHEK1 or TOP2A.
“Among the 15 fixed protein-coding changes identified here but absent from previous analyses1,20, some might have also contributed to complex modifications of pathways in cell division, like AHR65 or DNHD166 (Supplementary Information 1), as well as other genes with HHMCs, like CHEK167 or the gene encoding for the protein TOP2A68, which shows the largest number of interactions with other HHMC-carry”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
Genes with fixed non-synonymous changes in humans are also more often expressed in the ventricular zone of the developing neocortex, compared to fixed synonymous changes.
“It has been claimed20 that genes with fixed non-synonymous changes in humans are also more often expressed in the ventricular zone of the developing neocortex, compared to fixed synonymous changes.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
Protein-coding changes in cell cycle-related genes are highly relevant candidates for human-specific traits, with the brain being specifically sensitive to such changes.
“It has been proposed previously that protein-coding changes in cell cycle-related genes are highly relevant candidates for human-specific traits1,20, with the brain being specifically sensitive to such changes61.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
Based on observed general concordance between selection time estimates and aDNA evidence, the authors developed an overall chronicle of human genome adaptation based on positive selection signals, three AMH aDNA genomes, and the Neanderthal genome consensus.
“Based on the observed general concordance between the selection time estimates and aDNA evidences, we developed an overall chronicle of human genome adaptation that is based on PS signals, the three AMH aDNA genomes and the Neanderthal genome consensus 40 (Fig. 4).”
From A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years (2015) · cites this paper as [40]
The approach of defining putatively introgressed alleles as those that differ between Altai Neandertal and all Yoruba individuals and overlap with the Neandertal introgression map enriches for alleles of Neandertal origin.
“Although it is possible that a subset of sites are mis-labeled due to error, incomplete lineage sorting, and the divergence between introgressing and sequenced Neandertal genomes [14], this approach enriches for alleles of Neandertal origin.”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [14]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
Self-citationInference of human population history from individual whole-genome sequences
Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590 · see citing works
Self-citationRate of de novo mutations and the importance of father’s age to disease risk
Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S. A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., et al. (2012) · Nature · doi:10.1038/nature11396 · Cited by 2,134 · see citing works
Genetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991 · see citing works
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Self-citationAnalysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., et al. (2010) · Science · doi:10.1126/science.1186802 · Cited by 1,084 · see citing works
Self-citationPatterns of damage in genomic DNA sequences from a neandertal
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981 · see citing works
Self-citationGreat ape genetic diversity and population history
Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdós, B., Veeramah, K. R., Woerner, A. E., O’Connor, T. D., Santpere, G., et al. (2013) · Nature · doi:10.1038/nature12228 · Cited by 873 · see citing works
Self-citationThe complete mitochondrial DNA genome of an unknown hominin from southern Siberia
Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010) · Nature · doi:10.1038/nature08976 · Cited by 792 · see citing works
Self-citationRecurrent 16p11.2 microdeletions in autism
Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A., Gilliam, T. C., Nowak, N. J., Cook, E. H., Dobyns, W. B., et al. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm376 · Cited by 731 · see citing works
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684 · see citing works
Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.005 · Cited by 656 · see citing works
Self-citationLangergraber, K. E., Prüfer, K., Rowney, C., Boesch, C., Crockford, C., Fawcett, K. A., Inoue, E., Inoue-Muruyama, M., Mitani, J. C., Muller, M. N., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211740109 · Cited by 638 · see citing works
Self-citationRevising the human mutation rate: implications for understanding human evolution
Scally, A., & Durbin, R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3295 · Cited by 610 · see citing works
DNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608 · see citing works
Self-citationA Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 601 · see citing works
Self-citationRevisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?
Leffler, E. M., Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., & Przeworski, M. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001388 · Cited by 577 · see citing works
Genomic Runs of Homozygosity Record Population History and Consanguinity
Kirin, M., McQuillan, R., Franklin, C. S., Campbell, H. J., McKeigue, P., & Wilson, J. F. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013996 · Cited by 553 · see citing works
Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA
Gansauge, M.-T., & Meyer, M. (2013) · Nature Protocols · doi:10.1038/nprot.2013.038 · Cited by 541 · see citing works
Self-citationThe shaping of modern human immune systems by multiregional admixture with archaic humans
Abi-Rached, L., Jobin, M. J., Kulkarni, S., McWhinnie, A., Dalva, K., Gragert, L., Babrzadeh, F., Gharizadeh, B., Luo, M., Plummer, F. A., et al. (2011) · Science · doi:10.1126/science.1209202 · Cited by 537 · see citing works
Self-citationTargeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maričić, T., Stenzel, U., Lalueza‐Fox, C., Rudan, P., Brajković, D., Kućan, Ž., et al. (2009) · Science · doi:10.1126/science.1174462 · Cited by 501 · see citing works
Self-citationRemoval of deaminated cytosines and detection of in vivo methylation in ancient DNA
Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1163 · Cited by 491 · see citing works
Self-citationThe Date of Interbreeding between Neandertals and Modern Humans
Sankararaman, S., Patterson, N., Li, H., Pääbo, S., & Reich, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002947 · Cited by 460 · see citing works
Self-citationHublin, J. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904119106 · Cited by 448 · see citing works
ABCtoolbox: a versatile toolkit for approximate Bayesian computations
Wegmann, D., Leuenberger, C., Neuenschwander, S., & Excoffier, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-116 · Cited by 407 · see citing works
Remains of Homo erectus from Bouri, Middle Awash, Ethiopia
Asfaw, B., Gilbert, W. H., Beyene, Y., Hart, W. K., Renne, P. R., WoldeGabriel, G., Vrba, E. S., & White, T. D. (2002) · Nature · doi:10.1038/416317a · Cited by 287 · see citing works
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Kircher, M., Stenzel, U., & Kelso, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r83 · Cited by 271 · see citing works
Self-citationCortical progenitor expansion, self-renewal and neurogenesis—a polarized perspective
Fietz, S. A., & Huttner, W. Β. (2010) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2010.10.002 · Cited by 270 · see citing works
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249 · see citing works
Self-citationHaplotype-resolved genome sequencing of a Gujarati Indian individual
Kitzman, J. O., MacKenzie, A. P., Adey, A., Hiatt, J. B., Patwardhan, R. P., Sudmant, P. H., Ng, S. B. H., Alkan, C., Qiu, R., Eichler, E. E., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1740 · Cited by 244 · see citing works
Self-citationAnalysis of High-Throughput Ancient DNA Sequencing Data
Kircher, M. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-516-9_23 · Cited by 236 · see citing works
Self-citationDirect Measure of the De Novo Mutation Rate in Autism and Schizophrenia Cohorts
Awadalla, P., Gauthier, J., Myers, R. A., Casals, F., Hamdan, F. F., Griffing, A. R., Côté, M., Henrion, É., Spiegelman, D., Tarabeux, J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.07.019 · Cited by 235 · see citing works
Eriksson, A., & Manica, A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200567109 · Cited by 221 · see citing works
Estimating the human mutation rate using autozygosity in a founder population.
Campbell, C. D., Chong, J. X., Malig, M., Ko, A., Dumont, B. L., Han, L., Vives, L., O'Roak, B. J., Sudmant, P. H., Shendure, J., et al. (2012) · Nature Genetics · doi:10.1038/ng.2418 · Cited by 215 · see citing works
Self-citationKokovay, E., Wang, Y., Kusek, G., Wurster, R., Lederman, P. L., Lowry, N. A., Shen, Q., & Temple, S. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.06.016 · Cited by 199 · see citing works
FIP200 is required for maintenance and differentiation of postnatal neural stem cells
Wang, C., Liang, C.-C., Bian, Z. C., Zhu, Y., & Guan, J.-L. (2013) · Nature Neuroscience · doi:10.1038/nn.3365 · Cited by 169 · cited 1× · see citing works
“They include, for example, the gene RB1CC1 (also called FIP200 ) which encodes a transcription factor which, like VCAM1 , is essential for maintenance of neuronal stem cells in the adult subventricular zone 35 .”
Archaic human ancestry in East Asia
Skoglund, P., & Jakobsson, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108181108 · Cited by 168 · see citing works
Gabunia, L., Antón, S. C., Lordkipanidze, D., Vekua, A., Justus, A., & Swisher, C. C. (2001) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.1030 · Cited by 155 · see citing works
Mezmaiskaya Cave: A Neanderthal Occupation in the Northern Caucasus
Golovanova, L. V., Hoffecker, J. F., Kharitonov, V. M., & Romanova, G. P. (1999) · Current Anthropology · doi:10.1086/515805 · Cited by 138 · see citing works
Self-citationAncient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity
Yang, M. A., Malaspinas, A.-S., Durand, E. Y., & Slatkin, M. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss117 · Cited by 101 · see citing works
Self-citationESR dating at Mezmaiskaya Cave, Russia
Skinner, A. R., Blackwell, B. A. B., Martin, S., et al. (2004) · Applied Radiation and Isotopes · doi:10.1016/j.apradiso.2004.08.008 · Cited by 75 · see citing works
A database and API for variation, dense genotyping and resequencing data
Ríos, D., McLaren, W. M., Chen, Y., Birney, E., Stabenau, A., Flicek, P., & Cunningham, F. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-238 · Cited by 37 · see citing works
A proximal pedal phalanx of a Paleolithic hominin from denisova cave, Altai
Mednikova, M. B. (2011) · Archaeology Ethnology and Anthropology of Eurasia · doi:10.1016/j.aeae.2011.06.017 · Cited by 34 · see citing works
Waddell, P. J., & Tan, X. L. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1212.6820 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
Haber, M., Mezzavilla, M., Xue, Y., & Tyler-Smith, C. (2016) · Genome Biology · doi:10.1186/s13059-015-0866-z · Cited by 1,924 · see citing works
Massive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940 · see citing works
Self-citationThe Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works
Self-citationAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
Self-citationAltitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., et al. (2014) · Nature · doi:10.1038/nature13408 · Cited by 1,208 · see citing works
Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
Camp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Bräuninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1520760112 · Cited by 1,130 · see citing works
Self-citationRuns of homozygosity: windows into population history and trait architecture
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.109 · Cited by 1,006 · see citing works
Genome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023 · see citing works
Self-citationThe genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107 · see citing works
Self-citationInsights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020 · see citing works
Self-citationThe genetic history of Ice Age Europe
Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., et al. (2016) · Nature · doi:10.1038/nature17993 · Cited by 959 · see citing works
Self-citationGenomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955 · see citing works
Self-citationAn early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802 · see citing works
Self-citationA high-coverage Neandertal genome from Vindija Cave in Croatia
Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719 · see citing works
Self-citationTracing the peopling of the world through genomics
Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works
A genomic history of Aboriginal Australia
Malaspinas, A.-S., Westaway, M. C., Muller, C., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., et al. (2016) · Nature · doi:10.1038/nature18299 · Cited by 650 · see citing works
Self-citationThe major genetic risk factor for severe COVID-19 is inherited from Neanderthals
Zeberg, H., & Pääbo, S. (2020) · Nature · doi:10.1038/s41586-020-2818-3 · Cited by 636 · see citing works
Self-citationThe Evolution of Animal Domestication
Larson, G., & Fuller, D. Q. (2014) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-110512-135813 · Cited by 640 · see citing works
Human-specific gene <i>ARHGAP11B</i> promotes basal progenitor amplification and neocortex expansion
Florio, M., Albert, M., Taverna, E., Namba, T., Brandl, H., Lewitus, E., Haffner, C., Sykes, A., Wong, F. K., Peters, J., et al. (2015) · Science · doi:10.1126/science.aaa1975 · Cited by 632 · see citing works
Ancient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577 · see citing works
Self-citationNuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2016) · Nature · doi:10.1038/nature17405 · Cited by 584 · see citing works
Self-citationHuman-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., Novak, A. M., van den Bout, A., Bishara, A., Rosenkrantz, J. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.051 · Cited by 595 · see citing works
Self-citationGenomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, M. C., Malaspinas, A.-S., et al. (2015) · Science · doi:10.1126/science.aab3884 · Cited by 540 · see citing works
Evolution of the Human Nervous System Function, Structure, and Development
Sousa, A. M. M., Meyer, K. A., Santpere, G., Gulden, F. O., & Sestan, N. (2017) · Cell · doi:10.1016/j.cell.2017.06.036 · Cited by 517 · see citing works
The prehistoric peopling of Southeast Asia
McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al. (2018) · Science · doi:10.1126/science.aat3628 · Cited by 517 · see citing works
Self-citationThe Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
Sankararaman, S., Mallick, S., Patterson, N., & Reich, D. (2016) · Current Biology · doi:10.1016/j.cub.2016.03.037 · Cited by 465 · see citing works
Self-citationEvidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521 · see citing works
Self-citationSouthern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Vicente, M., Steyn, M., Soodyall, H., et al. (2017) · Science · doi:10.1126/science.aao6266 · Cited by 519 · see citing works
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., et al. (2016) · Science · doi:10.1126/science.aad9416 · Cited by 459 · see citing works
Self-citationSchmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015) · Genome Biology · doi:10.1186/s13059-015-0776-0 · Cited by 509 · see citing works
Self-citationNatural selection interacts with recombination to shape the evolution of hybrid genomes
Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G., et al. (2018) · Science · doi:10.1126/science.aar3684 · Cited by 412 · see citing works
Self-citationGenetic adaptation and Neandertal admixture shaped the immune system of human populations
Quach, H., Rotival, M., Pothlichet, J., Loh, Y.-H. E., Dannemann, M., Zidane, N., Laval, G., Patin, E., Harmant, C., Lopez, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.024 · Cited by 475 · see citing works
Self-citationThe Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · see citing works
On the origin of modern humans: Asian perspectives
Bae, C. J., Douka, K., & Petraglia, M. D. (2017) · Science · doi:10.1126/science.aai9067 · Cited by 471 · see citing works
Genomic insights into the peopling of the Southwest Pacific
Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., Clark, G. R., Reepmeyer, C., Petchey, F., Fernandes, D., et al. (2016) · Nature · doi:10.1038/nature19844 · Cited by 414 · see citing works
Self-citationOrlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411 · see citing works
Self-citationUpper Palaeolithic genomes reveal deep roots of modern Eurasians
Jones, E. R., Gonzalez-Fortes, G., Connell, S., Siska, V., Eriksson, A., Martiniano, R., McLaughlin, R. L., Gallego Llorente, M., Cassidy, L. M., Gamba, C., et al. (2015) · Nature Communications · doi:10.1038/ncomms9912 · Cited by 417 · see citing works
The evolution of modern human brain shape
Neubauer, S., Hublin, J.-J., & Gunz, P. (2018) · Science Advances · doi:10.1126/sciadv.aao5961 · Cited by 389 · see citing works
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture
Browning, S. R., Browning, B. L., Zhou, Y., Tucci, S., & Akey, J. M. (2018) · Cell · doi:10.1016/j.cell.2018.02.031 · Cited by 381 · see citing works
The phenotypic legacy of admixture between modern humans and Neandertals
Simonti, C. N., Vernot, B., Bastarache, L., Bottinger, E., Carrell, D. S., Chisholm, R. L., Crosslin, D. R., Hebbring, S. J., Jarvik, G. P., Kullo, I. J., et al. (2016) · Science · doi:10.1126/science.aad2149 · Cited by 330 · see citing works
Multiple Deeply Divergent Denisovan Ancestries in Papuans
Jacobs, G. S., Hudjashov, G., Saag, L., Kusuma, P., Darusallam, C. C., Lawson, D. J., Mondal, M., Pagani, L., Ricaut, F.-X., Stoneking, M., et al. (2019) · Cell · doi:10.1016/j.cell.2019.02.035 · Cited by 346 · see citing works
Global diversity, population stratification, and selection of human copy-number variation
Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., et al. (2015) · Science · doi:10.1126/science.aab3761 · Cited by 345 · see citing works
Self-citationA high-coverage Neandertal genome from Chagyrskaya Cave
Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309 · see citing works
Self-citationPrehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324 · see citing works
Genomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works
The outer subventricular zone and primate-specific cortical complexification
Dehay, C., Kennedy, H., & Kosik, K. S. (2015) · Neuron · doi:10.1016/j.neuron.2014.12.060 · Cited by 314 · see citing works
The Strength of Selection against Neanderthal Introgression
Juric, I., Aeschbacher, S., & Coop, G. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006340 · Cited by 309 · see citing works
Zhirnov, V., Zadegan, R. M., Sandhu, G. S., Church, G. M., & Hughes, W. L. (2016) · Nature Materials · doi:10.1038/nmat4594 · Cited by 307 · see citing works
The influence of evolutionary history on human health and disease
Benton, M. L., Abraham, A., LaBella, A. L., Abbot, P., Rokas, A., & Capra, J. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00305-9 · Cited by 291 · see citing works
Early Neolithic genomes from the eastern Fertile Crescent
Broushaki, F., Thomas, M. G., Link, V., López, S., van Dorp, L., Kirsanow, K., Hofmanová, Z., Diekmann, Y., Cassidy, L. M., Díez-del-Molino, D., et al. (2016) · Science · doi:10.1126/science.aaf7943 · Cited by 288 · see citing works
Dannemann, M., Andrés, A. M., & Kelso, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.015 · Cited by 249 · see citing works
Self-citationPatterns of coding variation in the complete exomes of three Neandertals
Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405138111 · Cited by 247 · see citing works
Self-citationGünther, T., & Nettelblad, C. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008302 · Cited by 228 · see citing works
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Chen, L., Wolf, A. B., Fu, W., Li, L., & Akey, J. M. (2020) · Cell · doi:10.1016/j.cell.2020.01.012 · Cited by 254 · see citing works
Ancient Genomics of Modern Humans: The First Decade
Skoglund, P., & Mathieson, I. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021749 · Cited by 246 · see citing works
Ancient biomolecules: Their origins, fossilization, and role in revealing the history of life
Briggs, D. E. G., & Summons, R. E. (2014) · BioEssays · doi:10.1002/bies.201400010 · Cited by 223 · see citing works
Neanderthal language revisited: not only us
Dediu, D., & Levinson, S. C. (2018) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2018.01.001 · Cited by 218 · see citing works
Limits of long-term selection against Neandertal introgression
Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814338116 · Cited by 211 · see citing works
Self-citationAdhikari, K., Fuentes-Guajardo, M., Quinto-Sánchez, M., Mendoza-Revilla, J., Camilo Chacón-Duque, J., Acuña-Alonzo, V., Jaramillo, C., Arias, W., Lozano, R. B., Pérez, G. M., et al. (2016) · Nature Communications · doi:10.1038/ncomms11616 · Cited by 200 · see citing works
Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Gittelman, R. M., Schraiber, J. G., Vernot, B., Mikacenic, C., Wurfel, M. M., & Akey, J. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.10.041 · Cited by 181 · see citing works
Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans
Enard, D., & Petrov, D. A. (2018) · Cell · doi:10.1016/j.cell.2018.08.034 · Cited by 208 · see citing works
Genomic insights into population history and biological adaptation in Oceania
Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A. M.-S., Harmant, C., Laurent, R., Verdu, P., et al. (2021) · Nature · doi:10.1038/s41586-021-03236-5 · Cited by 208 · see citing works
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
McCoy, R. C., Wakefield, J., & Akey, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.01.038 · Cited by 200 · see citing works
The Contribution of Neanderthals to Phenotypic Variation in Modern Humans
Dannemann, M., & Kelso, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.09.010 · Cited by 193 · see citing works
Self-citationThe Human Condition—A Molecular Approach
Pääbo, S. (2014) · Cell · doi:10.1016/j.cell.2013.12.036 · Cited by 197 · see citing works
Self-citationHominin taxic diversity: Fact or fantasy?
Wood, B., & K. Boyle, E. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22902 · Cited by 196 · see citing works
Multiple episodes of interbreeding between Neanderthal and modern humans
Villanea, F. A., & Schraiber, J. G. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0735-8 · Cited by 192 · see citing works
The evolution and population diversity of human-specific segmental duplications
Dennis, M. Y., Harshman, L., Nelson, B. J., Penn, O., Cantsilieris, S., Huddleston, J., Antonacci, F., Penewit, K., Denman, L., Raja, A., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0069 · Cited by 159 · see citing works
Self-citationRiesenberg, S., & Maricic, T. (2018) · Nature Communications · doi:10.1038/s41467-018-04609-7 · Cited by 174 · see citing works
Pendleton, A. L., Shen, F., Taravella, A. M., Emery, S., Veeramah, K. R., Boyko, A. R., & Kidd, J. M. (2018) · BMC Biology · doi:10.1186/s12915-018-0535-2 · Cited by 156 · see citing works
Brain Plasticity and Human Evolution
Sherwood, C. C., & Gómez-Robles, A. (2017) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-102215-100009 · Cited by 170 · see citing works
Genome Sequences Reveal Cryptic Speciation in the Human Pathogen <i>Histoplasma capsulatum</i>
Sepúlveda, V. E., Márquez, R., Turissini, D. A., Goldman, W. E., & Matute, D. R. (2017) · mBio · doi:10.1128/mbio.01339-17 · Cited by 175 · see citing works
Self-domestication in Homo sapiens: Insights from comparative genomics
Theofanopoulou, C., Gastaldon, S., O’Rourke, T., Samuels, B. D., Messner, A., Martins, P. T., Delogu, F., Alamri, S., & Boeckx, C. (2017) · PLOS ONE · doi:10.1371/journal.pone.0185306 · Cited by 174 · see citing works
Evidence for recent, population-specific evolution of the human mutation rate
Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165 · see citing works
Brain ontogeny and life history in Pleistocene hominins
Hublin, J.-J., Neubauer, S., & Gunz, P. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0062 · Cited by 173 · see citing works
Mondal, M., Casals, F., Xu, T., Dall'Olio, G. M., Pybus, M., Netea, M. G., Comas, D., Laayouni, H., Li, Q., Majumder, P. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3621 · Cited by 149 · see citing works
Complex History of Admixture between Modern Humans and Neandertals
Vernot, B., & Akey, J. M. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.01.006 · Cited by 149 · see citing works
Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., et al. (2017) · doi:10.1101/106955 · Cited by 144 · see citing works
Self-citationThe nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 145 · see citing works
Genetic Changes Shaping the Human Brain
Bae, B.-I., Jayaraman, D., & Walsh, C. A. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.01.035 · Cited by 135 · see citing works
Sams, A. J., Dumaine, A., Nédélec, Y., Yotova, V., Alfieri, C., Tanner, J. E., Messer, P. W., & Barreiro, L. B. (2016) · Genome Biology · doi:10.1186/s13059-016-1098-6 · Cited by 140 · see citing works
Using hominin introgression to trace modern human dispersals
Teixeira, J. C., & Cooper, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1904824116 · Cited by 136 · see citing works
An evolutionary anthropological perspective on modern human origins.
Marean, C. W. (2015) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-102313-025954 · Cited by 135 · see citing works
Genetic Markers of Human Evolution Are Enriched in Schizophrenia
Srinivasan, S., Bettella, F., Mattingsdal, M., Wang, Y., Witoelar, A., Schork, A. J., Thompson, W. K., Zuber, V., Winsvold, B. S., Zwart, J.-A., et al. (2016) · Biological Psychiatry · doi:10.1016/j.biopsych.2015.10.009 · Cited by 129 · see citing works
Hubisz, M. J., Williams, A. L., & Siepel, A. (2020) · PLOS Genetics · doi:10.1371/journal.pgen.1008895 · Cited by 130 · see citing works
Detecting archaic introgression using an unadmixed outgroup
Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M. H., & Durbin, R. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007641 · Cited by 125 · see citing works
Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity
Gunz, P., Tilot, A. K., Wittfeld, K., Teumer, A., Shapland, C. Y., van Erp, T. G. M., Dannemann, M., Vernot, B., Neubauer, S., Guadalupe, T., et al. (2019) · Current Biology · doi:10.1016/j.cub.2018.10.065 · Cited by 117 · see citing works
“Neandertals and modern humans show that they encountered each other outside Africa and interbred [6, 15, 16].”
Self-citationMondal, M., Bertranpetit, J., & Lao, O. (2019) · Nature Communications · doi:10.1038/s41467-018-08089-7 · Cited by 124 · see citing works
Ancient Biomolecules and Evolutionary Inference
Cappellini, E., Prohaska, A., Racimo, F., Welker, F., Pedersen, M. W., Allentoft, M. E., de Barros Damgaard, P., Gutenbrunner, P., Dunne, J., Hammann, S., et al. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012002 · Cited by 118 · see citing works
Self-citationHsieh, P., Woerner, A. E., Wall, J. D., Lachance, J., Tishkoff, S. A., Gutenkunst, R. N., & Hammer, M. F. (2016) · Genome Research · doi:10.1101/gr.196634.115 · Cited by 105 · see citing works
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
Schaefer, N. K., Shapiro, B., & Green, R. E. (2021) · Science Advances · doi:10.1126/sciadv.abc0776 · Cited by 106 · see citing works
Self-citationDetecting adaptive introgression in human evolution using convolutional neural networks
Gower, G., Picazo, P. I., Fumagalli, M., & Racimo, F. (2021) · eLife · doi:10.7554/elife.64669 · Cited by 95 · see citing works
Self-citationDental evolutionary rates and its implications for the Neanderthal–modern human divergence
Gómez-Robles, A. (2019) · Science Advances · doi:10.1126/sciadv.aaw1268 · Cited by 104 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Self-citationFunctional implications of Neandertal introgression in modern humans
Dannemann, M., Prüfer, K., & Kelso, J. (2017) · Genome biology · doi:10.1186/s13059-017-1181-7 · Cited by 92 · see citing works
Self-citationJoint estimates of heterozygosity and runs of homozygosity for modern and ancient samples
Renaud, G., Hanghøj, K., Korneliussen, T. S., Willerslev, E., & Orlando, L. (2019) · Genetics · doi:10.1534/genetics.119.302057 · Cited by 101 · see citing works
Self-citationJinam, T. A., Phipps, M. E., Aghakhanian, F., Majumder, P. P., Datar, F., Stoneking, M., Sawai, H., Nishida, N., Tokunaga, K., Kawamura, S., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx118 · Cited by 103 · see citing works
Human evolution: a tale from ancient genomes
Llamas, B., Willerslev, E., & Orlando, L. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0484 · Cited by 100 · see citing works
Zanella, M., Vitriolo, A., Andirko, A., Martins, P. T., Sturm, S., O’Rourke, T., Laugsch, M., Malerba, N., Skaros, A., Trattaro, S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw7908 · Cited by 101 · see citing works
Testing for ancient selection using cross-population allele frequency differentiation
Racimo, F. (2016) · Genetics · doi:10.1534/genetics.115.178095 · Cited by 96 · see citing works
Self-citation
- Authors
- Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- University of California, Berkeley (US)
- Broad Institute (US)
- University of Washington (US)
- Chinese Academy of Sciences (CN)
- Harvard University (US)
- National Institutes of Health (US)
- University of California, Santa Cruz (US)
- Max Perutz Labs (AT)
- Emory University (US)
- Fondation Jean Dausset-CEPH (FR)
- Howard Hughes Medical Institute (US)
- Allen Institute for Brain Science (US)
- Russian Academy of Sciences (RU)
- Corresponding author
- Slatkin, Montgomery
- Reich, David
- Pääbo, Svante
- ORCID
- Prüfer, Kay
- Racimo, Fernando
- Patterson, Nick
- Jay, Flora
- Sankararaman, Sriram
- Sawyer, Susanna
- Renaud, Gabriel
- Sudmant, Peter H.
- Li, Heng
- Mallick, Swapan
- Dannemann, Michael
- Fu, Qiaomei
- Kircher, Martin
- Kuhlwilm, Martin
- Lachmann, Michael
- Meyer, Matthias
- Moorjani, Priya
- Mullikin, James C.
- Vohr, Samuel H.
- Green, Richard E.
- Hellmann, Ines
- Kitzman, Jacob O.
- Shendure, Jay
- Eichler, Evan E.
- Lein, Ed S.
- Bakken, Trygve E.
- Golovanova, Liubov V.
- Doronichev, Vladimir B.
- Shunkov, Michael V.
- Viola, Bence
- Slatkin, Montgomery
- Reich, David
- Kelso, Janet
- Pääbo, Svante
- Venue
- Nature
- Published
- 2013-12-18
- Volume
- 505
- Issue
- 7481
- Pages
- 43-49
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4031459
- OpenAlex
- W2047998066
- Cited by
- 2,254
- References
- 46
- Citations by year
- 2026: 127 · 2025: 157 · 2024: 193 · 2023: 180 · 2022: 138 · 2021: 221 · 2020: 159 · 2019: 170 · 2018: 195 · 2017: 202 · 2016: 199 · 2015: 159 · 2014: 144 · 2013: 7 · 2012: 1
- FWCI
- 792.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Human Genome Research Institute (HG006283, HG002385, R01HG006283, R01HG002385)
- National Institute of General Medical Sciences (R01GM040282, GM100233, R01GM100233, R01‑GM40282)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Neanderthal genome, Denisovans, Denisova Cave, Altai Mountains, inbreeding, interbreeding, gene flow, modern human ancestry, toe bone
- MeSH terms
- Africa, Animals, Female, Fossils, Gene Frequency, Heterozygote, Humans, Inbreeding, Models, Genetic, Phylogeny, Population Density, Siberia, Genome, Toe Phalanges, Gene Flow, DNA Copy Number Variations, Neanderthals, Caves
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
