Eikonal Blog

2010.05.07

Human species interbreeding (Neanderthals, Denisovans and Sapiensis’, Oh My!)

2014

  • “Neanderthals Lived in Small, Isolated Populations, Gene Analysis Shows” by Dan Vergano (National Geographic; 2014.04.22) – http://news.nationalgeographic.com/news/2014/04/140421-neanderthal-dna-genes-human-ancestry-science/
      wilma-neanderthal-01_78945_600x450

    • Modern humanity’s ancient cousins, the Neanderthals, lived in small groups that were isolated from one another, suggests an investigation into their DNA. The analysis also finds that Neanderthals lacked some human genes that are linked to our behavior.
    • Compared to Neanderthals, humanity appears to have evolved more when it comes to genes related to behavior, … in particular that genes linked to hyperactivity and aggressive behavior in modern humans appear to be absent in Neanderthals. Also missing is DNA associated with syndromes such as autism.
    • The Neanderthal genes suggest that sometime after one million to 500,000 years ago, Neanderthal numbers decreased and the population stayed small, … A small population size would have been bad news for Neanderthals, … because it would have meant that “natural selection had less power to weed out bad mutations.”
    • Pääbo and colleagues looked at the genes of two ancient Neanderthals, one from Spain and one from Croatia. They compared the DNA of those individuals to that of a third Neanderthal who had lived in Siberia and whose DNA had been analyzed in an earlier study, and to the DNA of several modern humans. … “We find that [Neanderthals] had even less [genetic] variation than present-day humans,” … Genetic diversity among Neanderthals was about one-fourth as much as is seen among modern Africans, … and one-third that of modern Europeans or Asians.
    • The comparison also showed that modern people possess genes linked to heart health and metabolism that were absent in our ancient cousins. We also have genes for skin and hair color they lacked. “These mutations may contribute to differences in pigmentation among present-day humans,”
    • The Pääbo team also compared the Neanderthal and modern human DNA to that of a Denisovan, another early human cousin species that lived in Siberia as recently as 40,000 years ago and is known only from genetic maps and a few scraps of bones. The main genetic difference found in that comparison relates to the curvature of the lower back, according to the study. Essentially, Neanderthals looked a bit less sway-backed than do modern humans, Denisovans, and our other early ancestors.
    • … The PNAS study found, for instance, genetic differences between Neanderthals and modern humans in genes linked to aggression. But the authors caution that “if [the genes] affected activity or aggression levels, it is unclear whether they increased or decreased such traits.” They cannot say, for now, which species would have been the more aggressive one.
    • And there’s also the question of how often any genes present were actually used, called gene activity. In a recent study published in the journal Science, Israeli researchers teamed up with Pääbo’s group to look at gene activity in Neanderthals who lived 50,000 or more years ago. That study showed how differences in the expression of genes shared by modern people and our ancient cousins led to Neanderthals possessing bigger hands, shorter arms, and a more burly build.
  • “What made humans better than Neanderthals? Not mutation, say scientist” by Ruth Schuster (Haaretz; 2014.04.22) – http://www.haaretz.com/life/science-medicine/.premium-1.586682
    • Our genomes are 99% identical. It’s a question of how evolution turned our genes on and off, notably genes relating to brain.
    • With a nod to statistical probabilities, the human genome has been sequenced, and so have genomes of Neanderthals and Denisovans, with a high degree of accuracy. We can compare these genomes to see what genes we have in common, which turns out to be some 99%. We can see where mutations occurred that distinguish us from our sister species.
      It bears mention in this context that the human genome and the chimpanzee genome, which was sequenced in 2005, differ by only 4%; the last common ancestor to chimp and Wimp lived five to seven million years ago. Humans split with Neanderthals and Denisovans between 550,000 to 765,000 years ago.
    • [Researches have] reconstructed the epigenome (a “picture” of which genes were on and off) of the Neanderthal and the Denisovan for the first time. Then they compared these dead species’ epigenomes with that of modern humans. The scientists identified genes that existed in all three, but whose activity in humans was different. They found major differences in the patterns of gene expression governing the development of the brain and skull, as well as in the immune and cardiovascular systems. They didn’t find much change regarding the genes that govern the digestive system,
    • How did they do it, you wonder. Comparing genes, fine – but their regulation? How can they tell if a gene in a 50,000-year old body … had been on or off?
      … the solution lay in the fact that the Neanderthal and Denosivan DNA had been partly decomposed, … DNA consists of extremely long chains of nucleic acids. There are four types of nucleic acids, usually referred to simply as T, G, A and C. … as DNA decomposes, the acid known as C gets turned into either T if the gene is “on,” or U if the gene is “off.” … U stands for uracil and it has no business being in DNA. If it’s there, therefore, it replaced a C nucleic acid molecule in a dead body. The scientists re-replace all the U molecules with C’s (on the computer, not in the corpse) and calculate the ratios of C’s and T’s; thereby they can tell if an ancient gene had been on or off.
    • Their conclusion: our genes were much the same, but they were used in different ways.
    • … genes whose activity is unique to modern humans but not with the proto-humans include ones associated with Alzheimer’s disease, autism and schizophrenia, which are fairly common disorders today.

2013

  • “Oldest DNA obtained from human ancestor” b Richard Gray (The Telegraph; 2013.12.05) – http://www.telegraph.co.uk/earth/environment/archaeology/10495222/Oldest-DNA-obtained-from-human-ancestor.html
    • The oldest genetic sequence ever recovered from a human ancestor has been extracted from a 400,000 year old thigh bone
  • “Baffling 400,000-Year-Old Clue to Human Origins” – http://www.nytimes.com/2013/12/05/science/at-400000-years-oldest-human-dna-yet-found-raises-new-mysteries.html?_r=0
    • The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.
    • Based on the anatomy of the fossils, Dr. Arsuaga has argued that they belonged to ancestors of Neanderthals, which lived in western Asia and Europe from about 200,000 to 30,000 years ago.
  • “Ancient human relative’s DNA puzzles scientists” – http://www.cbc.ca/news/technology/ancient-human-relative-s-dna-puzzles-scientists-1.2452118
    • Genetic fingerprint of 400,000 year-old bone in Spain surprisingly different from Neanderthals’
  • “‘Pit of Bones’ Yields Oldest Known Human DNA” by Gillian Mohney (ABC News; 2013.12.04) – http://abcnews.go.com/Health/pit-bones-yields-oldest-human-dna/story?id=21093890
  • “Hominin DNA baffles experts” by Ewen Callaway (Nature; 2013.12.04) – http://www.nature.com/news/hominin-dna-baffles-experts-1.14294
  • “A mitochondrial genome sequence of a hominin from Sima de los Huesos” by Matthias Meyer, Qiaomei Fu1, Ayinuer Aximu-Petri, Isabelle Glocke1, Birgit Nickel1, Juan-Luis Arsuaga3, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonelland Svante Pääbo (Nature; 2013.12.04; doi:10.1038/nature12788) – http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12788.html
    • Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals4 dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
    • “Figure 1: Location of the Middle Pleistocene site of Sima de los Huesos (yellow) as well as Late Pleistocene sites that have yielded Neanderthal DNA (red) and Denisovan DNA (blue).” – http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature12788_F1.html
    • “Figure 4: Bayesian phylogenetic tree of hominin mitochondrial relationships based on the Sima de los Huesos mtDNA sequence determined using the inclusive filtering criteria.” – http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature12788_F4.html
    • “Extended Data Figure 6: Complete view of the mid-point rooted phylogenetic tree constructed with a Bayesian approach under a GTR + I + Γ model of sequence evolution using the Sima de los Huesos consensus sequence generated with inclusive filters as well as 54 present-day humans, 9 ancient humans, 7 Neanderthals, 2 Denosivans, 22 bonobos and 24 chimpanzees.” – http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature12788_SF6.html
  • “Neanderthals were pioneers of domestic bliss” by Richard Gray (The Telegraph; 2013.12.03) – http://www.telegraph.co.uk/earth/environment/archaeology/10492170/Neanderthals-were-pioneers-of-domestic-bliss.html
    • House proud Neanderthals lived in well organised homes rather than chaotic caves, new finds suggest
  • “Mystery humans spiced up ancients’ rampant sex lives” by Ewen Callaway (Nature; 2013.11.19) – http://www.nature.com/news/mystery-humans-spiced-up-ancients-rampant-sex-lives-1.14196
    • Genome analysis suggests interbreeding between modern humans, Neanderthals, Denisovans and a mysterious archaic population.
    • All humans whose ancestry originates outside of Africa owe about 2% of their genome to Neanderthals; and certain populations living in Oceania, such as Papua New Guineans and Australian Aboriginals, got about 4% of their DNA from interbreeding between their ancestors and Denisovans, who are named after the cave in Siberia’s Altai Mountains where they were discovered. The cave contains remains deposited there between 30,000 and 50,000 years ago.
    • David Reich, an evolutionary geneticist …, have now produced much more complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes. The high-quality Denisovan genome data and new Neanderthal genome both come from bones recovered from Denisova Cave.
    • The new Denisovan genome indicates that this enigmatic population got around: Reich said at the meeting that they interbred with Neanderthals and with the ancestors of human populations that now live in China and other parts of East Asia, in addition to Oceanic populations, as his team previously reported. Most surprisingly, Reich said, the new genomes indicate that Denisovans interbred with another extinct population of archaic humans that lived in Asia more than 30,000 years ago, which is neither human nor Neanderthal.
  • “Neanderthals, humans may have missed each other” by The Associated Press (CBC News; 2013.02.04) – http://www.cbc.ca/news/technology/neanderthals-humans-may-have-missed-each-other-1.1309554
    • New analysis suggests Neanderthals died out far earlier than thought
  • “Radiocarbon dating casts doubt on the late chronology of the Middle to Upper Palaeolithic transition in southern Iberia” by Rachel E. Wood, Cecilio Barroso-Ruíz, Miguel Caparrós, Jesús F. Jordá Pardo, Bertila Galván Santos, and Thomas F. G. Higham (PNAS; vol. 110 no. 8 > Rachel E. Wood, 2781–2786) – http://www.pnas.org/content/110/8/2781
    • It is commonly accepted that some of the latest dates for Neanderthal fossils and Mousterian industries are found south of the Ebro valley in Iberia at ca. 36 ka calBP (calibrated radiocarbon date ranges). In contrast, to the north of the valley the Mousterian disappears shortly before the Proto-Aurignacian appears at ca. 42 ka calBP. The latter is most likely produced by anatomically modern humans. However, two-thirds of dates from the south are radiocarbon dates, a technique that is particularly sensitive to carbon contaminants of a younger age that can be difficult to remove using routine pretreatment protocols. We have attempted to test the reliability of chronologies of 11 southern Iberian Middle and early Upper Paleolithic sites. Only two, Jarama VI and Zafarraya, were found to contain material that could be reliably dated. In both sites, Middle Paleolithic contexts were previously dated by radiocarbon to less than 42 ka calBP. Using ultrafiltration to purify faunal bone collagen before radiocarbon dating, we obtain ages at least 10 ka 14C years older, close to or beyond the limit of the radiocarbon method for the Mousterian at Jarama VI and Neanderthal fossils at Zafarraya. Unless rigorous pretreatment protocols have been used, radiocarbon dates should be assumed to be inaccurate until proven otherwise in this region. Evidence for the late survival of Neanderthals in southern Iberia is limited to one possible site, Cueva Antón, and alternative models of human occupation of the region should be considered.

2012

  • “Neanderthal genome may hold clues to human survival” by Susan Lunn (CBC News; 2012.12.29) – http://www.cbc.ca/news/technology/neanderthal-genome-may-hold-clues-to-human-survival-1.1148479
  • “New DNA analysis shows ancient humans interbred with Denisovans” by Katherine Harmon (Nature; 2012.08.31) – http://www.nature.com/news/new-dna-analysis-shows-ancient-humans-interbred-with-denisovans-1.11331
    • A new high-coverage DNA sequencing method reconstructs the full genome of Denisovans — relatives to both Neandertals and humans — from genetic fragments in a single finger bone.
  • “Genome of Denisovan cave girl sheds light on human ancestry” (CBC News; 2013.08.31) – http://www.cbc.ca/news/technology/genome-of-denisovan-cave-girl-sheds-light-on-human-ancestry-1.1288406
    • Researchers map genome of ancient people who shared genetic heritage with those of Southeast Asia, Oceania
  • “Neanderthals, humans didn’t make whoopee, study says” (CBC News; 2011.08.17) – http://www.cbc.ca/news/technology/neanderthals-humans-didn-t-make-whoopee-study-says-1.1256007
    • Interbreeding theory challenged despite evidence of shared DNA.
    • The researchers say the DNA crossover is actually a remnant from a common ancestor from half a million years ago, not a result of Homo sapiens and Neanderthals interbreeding. This common ancestor lived in parts of Africa and Europe, but divided into separate populations in Europe and Africa around 300,000 to 500,000 years ago, according to the latest study.
  • “The date of interbreeding between Neandertals and modern humans” by Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, David Reich (arXiv.org > q-bio > arXiv:1208.2238; 2012.08.10) – http://arxiv.org/abs/1208.2238
    • Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find 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 years ago. This supports the recent interbreeding hypothesis, and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

2011

  • “Hybrid humans: How our ancestors’ inter-species trysts affect us” (CBC News; 2011.10.24) – http://www.cbc.ca/news/technology/hybrid-humans-how-our-ancestors-inter-species-trysts-affect-us-1.1048087
  • “Ancient DNA reveals secrets of human history” by Ewen Callaway (Nature; 2012.08.09) – http://www.nature.com/news/2011/110809/full/476136a.html
    • Modern humans may have picked up key genes from extinct relatives.
  • “Mysterious ‘third species’ of caveman had sex with our Asian ancestors” by Simon Tomlinson (Mail online; 2011.10.02) – http://www.dailymail.co.uk/sciencetech/article-2056149/Mysterious-species-caveman-sex-Asian-ancestors.html

    • Denisovans spread DNA throughout Southeast Asia, study confirms
    • Experts examined genes from 1,500 modern humans from across the world
    • Southeast Asians had higher proportion of Denisovan-related gene variants
  • “Sex with Neanderthals boosted human immunity” (CBC News; 2011.08.26) – http://www.cbc.ca/news/technology/sex-with-neanderthals-boosted-human-immunity-1.996348
    • Neanderthals (…) died out 30,000 years ago. But many of their immune genes are common among humans outside Africa.
    • Hominins and hominids: Humans are part of a larger group of closely related human-like species, such as Neanderthals, called hominins. All hominins are themselves part of a larger group known as hominids that includes all the great apes such as chimpanzees and gorillas.
  • “Ancient DNA reveals secrets of human history” by Ewen Callaway (Nature; 2011.08.09; Nature 476, 136-137 (2011) | doi:10.1038/476136a ) – http://www.nature.com/news/2011/110809/full/476136a.html
    • Modern humans may have picked up key genes from extinct relatives.
  • “All Non-Africans Part Neanderthal, Genetics Confirm” by Jennifer Viegas (Discover News; 2011.07.18) – http://news.discovery.com/human/genetics-neanderthal-110718.html
  • “Europeans never had Neanderthal neighbours” by Ewen Callaway (Nature; 2011.05.09; doi:10.1038/news.2011.276) – http://www.nature.com/news/2011/110509/full/news.2011.276.html
    • Russian find suggests Neanderthals died out earlier than was thought.
  • “Extremely rare interbreeding events can explain Neanderthal DNA in modern humans” by Armando G. M. Neves and Maurizio Serva (arXiv.org > q-bio > arXiv:1103.4621; 2011.03.23) – http://arxiv.org/abs/1103.4621
      Abstract: Considering the recent experimental discovery of Green et al that present day non-Africans have 1 to 4% of their nuclear DNA of Neandertal origin, we propose here a model which is able to quantify the interbreeding events between the two subpopulations. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the Wright-Fisher drift process. By simulating the model we are able to apply it to the interbreeding of African and Neandertal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neandertal DNA in non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizable probability.

2010

2009

2008

  • “First complete Neanderthal genome sequenced” by Lucas Laursen (Nature; 2008.08.07; doi:10.1038/news.2008.1026 ) – http://www.nature.com/news/2008/080807/full/news.2008.1026.html
    • The first complete genome of a Neanderthal — specifically, the mitochondrial DNA found in a 38,000-year-old bone — has been sequenced.
    • Full nuclear sequence, offering clues about our relatives’ demise, expected within months.
  • “Neanderthals Wore Make-up and Liked to Chat” by Dan Jones (ABC News; 2008.03.27) – http://abcnews.go.com/Technology/story?id=4537206&page=1
    • Francesco d’Errico, an archaeologist from the University of Bordeaux, France, has found crafted lumps of pigment – essentially crayons – left behind by Neanderthals across Europe.

      He says that Neanderthals, who most likely had pale skin, used these dark pigments to mark their own as well as animal skins. And, since body art is a form of communication, this implies that the Neanderthals could speak, d’Errico says.

2007

2006

2000

A much older liason, but still in the family

Misc:


Here: Anthropology – https://eikonal.wordpress.com/2011/05/09/anthropology/

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1 Comment »

  1. […] “Mysterious New Human Coexisted with Neanderthals: Photos” by Jennifer Viegas (Discovery News; 2011.05.06) – http://news.discovery.com/archaeology/new-human-neanderthal-evolution-110505.html Here at this blog: Human species interbreeding – https://eikonal.wordpress.com/2010/05/07/human-species-interbreading/ […]

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    Pingback by Anthropology « Eikonal Blog — 2011.05.09 @ 10:44


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