Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

  title={Resurrecting Surviving Neandertal Lineages from Modern Human Genomes},
  author={Benjamin Vernot and Joshua M. Akey},
  pages={1017 - 1021}
Neandertal Shadows in Us Non-African modern humans carry a remnant of Neandertal DNA from interbreeding events that have been postulated to have occurred as humans migrated out of Africa. While the total amount of Neandertal sequence is estimated to be less than 3% of the modern genome, the specific retained sequences vary among individuals. Analyzing the genomes of more than 600 Europeans and East Asians, Vernot and Akey (p. 1017, published online 29 January) identified Neandertal sequences… 

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

This work 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, and recovered Neandertal and Denisovan DNA.

A high-coverage Neandertal genome from Vindija Cave in Croatia

The genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, is sequenced to ~30-fold genomic coverage, allowing 10 to 20% more Ne andertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.

The Divergence of Neandertal and Modern Human Y Chromosomes

Limits of long-term selection against Neandertal introgression

It is shown that there has been no long-term genome-wide removal of Neandertal DNA, and that the previous result was due to incorrect assumptions about gene flow between African and non-African populations.

Humans and Neanderthals interbred following the emergence of humans in Eurasia 60,000-

This study presents a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and showed that they can be traced back to multiple introgression events, and is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.

Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans

An introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity, in agreement with earlier results that suggested that deletions evolve under more constraint than insertions.

Reconstructing the Genetic History of Late Neandertals

It is found that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 year ago.

Complex history of admixture between modern humans and Neandertals.

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes

It is concluded that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgressive patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes.

The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes

Analysis of Icelandic genomes reveals chromosome fragments of Neanderthal and Denisovan origin, the latter of which occurred through Denisovan gene flow either into ancestors of the Neanderthals or directly into humans.



A Draft Sequence of the Neandertal Genome

The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

The results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations.

The Date of Interbreeding between Neandertals and Modern Humans

The extent of linkage disequilibrium (LD) in the genomes of present-day Europeans is measured and it is found that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000-65,000 year ago.

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

A model of admixture during a spatial expansion is used to study the hybridization of Neanderthals with modern humans during their spread out of Africa and finds that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding.

Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations

An alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration is examined.

A Haplotype at STAT 2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

A DNA sequence analysis of the innate immune gene STAT2 is provided and it is shown that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2.

Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity.

Simulations show that the dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixtures with Neanderthals accounts for the greater similarity of Neanderthal to non- Africans than Africans.

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

Targeted sequencing improves Neandertal mitochondrial DNA retrieval and reveals low diversity among individuals, and together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Ne andertals was smaller than that of modern humans and extant great apes.