|
|
Post by Admin on Oct 9, 2017 18:57:27 GMT
 A female Neanderthal who lived in what is now Croatia 52,000 years ago is revealing that our "caveman" relatives may have passed on genes that play roles in cholesterol levels, eating disorders, arthritis and other diseases today, the researchers who sequenced her genome say. And some modern humans are carrying around more Neanderthal DNA than scientists had thought: The study found that the genomes of modern human populations that originated outside Africa hold between 1.8 and 2.6 percent Neanderthal DNA. That's much higher than previous estimates of 1.5 to 2.1 percent.  By extracting DNA from Neanderthal fossils, researchers sequenced the genomes of five Neanderthals. However, until now, just one of these yielded high-quality data — that of a woman found in Denisova Cave, in the Altai Mountains in Siberia. The fossil of the woman, who lived about 122,000 years ago, is known as the Altai Neanderthal. [Denisovan Gallery: Tracing the Genetics of Human Ancestors] Now, scientists have fully sequenced the genome of another female Neanderthal — this one from Vindija Cave, in Croatia — who lived about 52,000 years ago. Prior work suggested that Neanderthals lived in Vindija Cave until relatively late in their history. Scientists estimate that Neanderthals in Europe went extinct around 40,000 years ago. The new findings suggest that, compared with the Altai Neanderthal, the Vindija Neanderthal was more closely related to the Neanderthals who interbred with the ancestors of modern humans living outside Africa. This closer relation allowed the scientists to identify an additional 10 to 20 percent more Neanderthal DNA in modern humans.  The newly identified Neanderthal gene variants found in modern humans play roles in blood levels of vitamin D and "bad" LDL cholesterol, as well as in eating disorders, body fat levels, rheumatoid arthritis, schizophrenia and responses to antipsychotic drugs, the study found. Abstract To date the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50 thousand years ago from Vindija Cave, Croatia to ~30-fold genomic coverage. She carried 1.6 differences per ten thousand base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10-20% more Neandertal DNA to be identified in present-day humans, including variants involved in LDL cholesterol levels, schizophrenia and other diseases. Science 05 Oct 2017: eaao1887 |
|
|
|
Post by Admin on Oct 18, 2017 18:54:47 GMT
 DNA from our shorter, stockier cousins may be influencing skin tone, ease of tanning, hair color and sleeping patterns of those of present-day Europeans, according to a study from the Max Planck Institute for Evolutionary Anthropology published Thursday in the American Journal of Human Genetics. Scientists estimate that more than a few Homo sapiens ran into Neanderthals tens of thousands of years ago in Eurasia. They liked each other well enough to mate, and now Neanderthal DNA is thought to make up between 1 and 3 percent of the genetic code of most people who aren't indigenous Africans.  African people have very little Neanderthal DNA because their ancestors didn't make the trip through Eurasia, scientists think. Computational biologist Michael Dannemann, the lead author on the latest paper looking at the Neanderthal DNA that persists in modern humans, says that he wondered, well, does it do anything?  He and his colleagues looked for associations between Neanderthal DNA and human appearance and behavioral traits. The researchers analyzed information from over 100,000 people in the UK Biobank, a database that contains genetic information and people's answers to an extensive questionnaire, including questions about physical appearance and behavior. Dannemann and co-author, Janet Kelso, also at the Max Planck Institute for Evolutionary Anthropology, found genetic material from Neanderthals associated with traits like skin tone, hair color and sleeping patterns. |
|
|
|
Post by Admin on Nov 4, 2017 19:14:23 GMT
 Human papillomavirus (HPV) comes in hundreds of different strains, and infects almost everyone at some point in their lifetimes. For most people, the infection passes by without symptoms, due to the evolutionary mechanisms Homo sapiens have developed to combat the virus. But a particular variety called HPV16 can cause cervical and other cancers. A new study contends that the strain actually hopped to modern humans during sex with Neanderthals and Denisovans, our ancient cousins. The massive genetic-sequencing project indicates that the microbiology of the virus could tell us a bit about humanity’s family tree, the authors write in the latest issue of Molecular Biology and Evolution.  “Our results suggest that ancestral HPV16 already infected the ancestor of H. sapiens and H. neanderthalensis half a million years ago, and that two main HPV16 lineages codiverged with either human lineage,” they write. “When a population of modern humans migrated out of Africa some 60 to 120 thousand years ago… and interbred with Neanderthal/Denisovan populations in Europe and in Asia, a transfer of sexually transmitted pathogens occurred, in parallel with the genomic introgression.” The theory was based on 118 full sequences of HPV16 and five main lineage subtypes of it. They reconstructed the evolution of the virus over thousands of generations using computer algorithms, to understand how it changed over time.  One of the best pieces of evidence of the transmission of the cancer-causing HPV from ancient hominids to modern humans is the near-absence of the HPV16A strain in sub-Saharan Africa. Since the Neanderthals and Denisovans apparently spread the germ back to humans after they left Africa, the non-presence of the strain where modern humans began their rise fits the theory, said the scientists, from the Catalan Institute of Oncology and the French National Center for Scientific Research. Interbreeding between modern humans and Neanderthals was first identified in 2010, with the first sequencing of an entire Neanderthal genome from a bone. Since then, the evidence pointing toward an extended period of sex between the two species has emerged. Our extinct cousins currently make up as much of five percent of our genetic makeup – and have been blamed for a litany of modern problems, from depression to allergies. |
|
|
|
Post by Admin on Nov 5, 2017 19:31:48 GMT
 Interbreeding with Neandertals restored some genetic heirlooms that modern humans left behind in the ancient exodus from Africa, new research suggests. Those heirlooms are versions of genes, or alleles, that were present in humans’ and Neandertals’ shared ancestors. Neandertals carried many of those old alleles, passing them along generation after generation, while developing their own versions of other genes. A small number of humans left Africa around 100,000 years ago and settled in Asia and Europe. These migrants “lost” the ancestral alleles. But when the migrants or their descendants interbred with Neandertals, Eurasians reinherited the ancestral heirlooms along with Neandertal DNA, John “Tony” Capra reported October 20 at the annual meeting of the American Society of Human Genetics. Present-day Europeans have more than 47,000 of these reintroduced ancestral alleles, and East Asians — who have more Neandertal ancestry than Europeans (SN Online: 2/12/15) — carry more than 56,000, said Capra, an evolutionary geneticist at Vanderbilt University in Nashville.  Capra and others have evidence that Neandertal versions of genes make humans more prone to some diseases (SN: 3/5/16, p. 18). Of the thousands of ancestral variants reintroduced into modern humans, only 41 have been linked in genetic studies to diseases, such as skin conditions and neurological and psychiatric disorders, he said. The researchers can’t tell for sure whether the effect is from the ancestral variant or neighboring Neandertal DNA. Capra and Vanderbilt colleague Corinne Simonti’s analyses indicate that the Neandertal DNA is more likely to blame. Many of the ancestral alleles are still present in modern-day Africans, Capra said, “so they’re unlikely to be very, very bad.” |
|
|
|
Post by Admin on Nov 7, 2017 18:55:22 GMT
PgmNr 225: Neanderthal introgression reintroduced thousands of ancestral alleles lost in the out of Africa bottleneck. Authors: J. Capra; C. Simonti Affiliation: Vanderbilt University, Nashville, TN.  Anatomically modern humans (AMHs) interbred with Neanderthals approximately 50,000 years ago, and as a result, ~1–3% of the genomes of modern Eurasians are derived from of DNA introgressed from Neanderthals. Recent studies have focused on identifying and testing the effects of Neanderthal-derived alleles in AMHs, and these introgressed haplotypes have been shown to influence diverse phenotypes in AMHs including risk for many immune, skin, and neuropsychiatric diseases. However, recent analysis of an introgressed Neanderthal haplotype at the OAS locus revealed that the variant responsible for changes in gene expression is a reintroduced ancestral human allele, rather than a Neanderthal-derived allele.  Motivated by this observation of the reintroduction of a functional ancestral allele that was lost in Eurasian populations in the out of Africa bottleneck, we performed a genome-wide search for other lost alleles on introgressed Neanderthal haplotypes in 1000 Genomes Phase 3 European (EUR), East Asian (EAS), and South Asian (SAS) individuals. In each super-population, we identified between ~47,000 and ~57,000 ancestral introgressed alleles. Consistent with the greater levels of Neanderthal DNA in Asian populations, these groups had more reintroduced ancestral alleles. Additionally, we found that nearly 66% of the reintroduced ancestral variants identified in EUR individuals are polymorphic in at least one non-admixed African sub-population (Yoruba, Esan, or Mende). These variants represent an extreme scenario where the ancestral allele was completely lost either before or during the out of Africa transition, and reintroduced by Neanderthal introgression.  Many introgressed haplotypes carry more lost ancestral alleles than Neanderthal-derived alleles. Thus, we hypothesized that these alleles might influence phenotypes in modern Eurasian populations. To explore the potential function of these reintroduced ancestral alleles, we performed a phenome-wide association analysis on the introgressed alleles over more than 20,000 European-ancestry individuals with electronic health record data in Vanderbilt’s BioVU databank. We identified and replicated several novel associations with clinical phenotypes that are likely driven by these reintroduced alleles. |
|
