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Research news (2014-2015) relevant to early humans in Franco-Iberia
Part 1: genomic evidence
Caves and Castles, 2015
Roy Larick, Lecturer
Archaeological Tours study tour
Research news relevant to early humans in Franco-Iberia
Part 1 addresses the genomic basis for understanding Pleistocene Eurasians
We are at the peak of modeling ancient gene flow based on modern and 'fossil' DNA. Addressed is the genetic makeup of prehistoric modern humans Neandertalsand Denisovans.
Presentation generally follows publication order.
Bare-bones summaries of current research papers. Basic data, graphics and links only. News items to be fleshed out on tour.
Includes links to the original abstracts--the online papers usually lie behind a paywall.
Siberia: sequenced genomes from two woolly mammoths (Mammuthus primigenius)
‘Signatures of Demographic and Genetic Declines in the Woolly Mammoth’
Palkopoulou et al. Current Biology, May 18, 2015
The Wrangel mammoth shows a 20% reduction in heterozygosityas well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity.
The Wrangel Island population (last surviving woolly mammoths) was subject to reduced genetic diversity shortly before it became extinct.
our finding of an overall reduced genomesurviving mammoths constitutes the first direct observation of genetic stochasticityits extinction. Given that small population sizes in wild animals often lead to reduced individual fitness [33], it seems plausible that the low genetic variation detected in this study may have had a negative impact on the fitness of the and thus may have contributed to its subsequent extinction. The results presented here also highlight the value of sequencing ancient genomes from specimens that predate population declines to establish baseline levels of genomebiology, this approach can be used to directly quantify the amount of diversity lost in threatened species.
Parallel demographic trajectories reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation.
a number of Hs genomic regions may have been affected by positive selection for Hngenes in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development
Nucleotide substitutions inferred to have occurred on the evolutionary lineages leading to the Neandertals, the human, and the chimpanzee genomes.
(A) The three bones from Vindija from which Neandertal DNA was sequenced. (B) Map showing the four archaeological sites from which bones were used and their approximate dates
Neandertalsof presentEurope and western Asia before disappearing 30,000 years ago. We present a draft sequence of the than 4 billion nucleotides from three individuals. Comparisons of the genome to the genomes of five presenthumans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertalspresentpresentsuggesting that gene flow from into the ancestors of nonbefore the divergence of Eurasian groups from each other.
gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Distributions of divergence from the human genome reference sequence among segments of 100 kb for three Neandertalsand five present-day humans.
This individual is from a group that shares a common origin with Neanderthals.
The ‘Denisovans’ may have been widespread in Asia during the Late Pleistocene epoch
Denisovans were notinvolved in the gene flow from Neanderthals into Eurasians; however, they contributed 4–6% of its genetic material to the genomes of present-day Melanesians
Using DNA extracted from a finger bone found in we have sequenced the genome of an archaic hominin to about 1.9coverage.that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4genetic material to the genomes of presentthis hominin population ‘suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that evolutionary history distinct from Neanderthals and modern humans.
Denisova, Altai
A tooth found in Denisova Cave carries a mtDNA genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans
(B) Admixture graph of population history fitted to ancient genomes showing more hunter-gatherer admixture in Neolithic Scandinavian farmers than in central European farmers
The MAwhich is at high frequency among Upper Mesolithic European hunterchromosome of MAEurasians and near the root of most Native American lineagesis basal to modernclosely related to modernclose affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more norththought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MAexplain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east another southapproximately 17,000 years autosomalregion was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modernAmericans derive not only from postas commonly thought, but also from a mixed ancestry of the
(A) locations of ancient human remains included in the population model.
The MA-1 mitochondrial genome (haplogroup U) is basal to modern-day western Eurasians and near the root of most Native American lineages. Autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago. 14 to 38% of Native American ancestry may originate through gene flow from this ancient population.
An almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos
Closely related to the lineage leading to mitochondrial genomes of Denisovans.
Excavations of a complex of caves in the Sierra de unearthed hominin fossils that range in age from the early Pleistocene to the Holocenelos world’s largest assemblage of Middle Pleistocene hominin at least 28 300,000 years share a number of morphological features with fossils classified heidelbergensisNeanderthaldetermine an almost complete mitochondrial genome sequence of a hominin from that it is closely related to the lineage leading to mitochondrial genomes of Denisovansgroup to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
Sites yielding Neanderthal DNA (red) Denisovan DNA (blue)
Bayesian phylogenetic tree of hominin mitochondrial relationships based on the Sima de los Huesos mtDNA sequence determined using the inclusive filtering criteria.
Complete view of the mid-point rooted phylogenetic tree constructed with a Bayesian approach using the Sima de los Huesos consensus sequence generated with 54 present-day humans, 9 ancient humans, 7 Neanderthals, 2 Denosivans, 22 bonobos and 24 chimpanzees.
modern humans do not greatly differ genetically from our cousins
We’re a whole lot more Neo-African than we are Neanderthal or Denisovan
human phylogeny is more properly defined as a graph than a tree.
We present a highsequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of halfmating 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 presentseveral gene flow events occurred among Neanderthals, modern humans, possibly including gene flow into archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the highgenome 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
Three Neantertal sample sites
mating among close relatives was common among her recent ancestors.
several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group.
interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene
The complete genome sequence of a Neanderthal from the Altai Mountains
Genomic studies have shown that Neanderthals interbred with modern humans, and that nonAfricans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred However, Neanderthal distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal the genomes of 1,004 presentthat harbor a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to nonenvironments. We identify multiple Neanderthalderived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of
Eurasian Hs has paler skins partly due to Hn BNC2, providing efficiency in generating vitamin D from sunlight
several genes make Hs susceptible to type 2 diabetes, lupus and Crohn's disease
http://www.newscientist.com/article/mg22129542.600-neanderthalhuman-sex-bred-light-skins-and-infertility.html#.VRHKmvnF84Jaspects of human health, including psoriasis and
Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sanchez et al. Nature 14 August 2014
Haplotype network based on the number of pairwisedifferences between the 40 most common haplotypes
Haplotype network based on the number of pairwisedifferences between 43 unique haplotypes defined from the 20 most differentiated SNPs between Tibetans and the 14 populations (1000 Genomes Project
Genealogical structure in a model with gene flow from Denisovans to Tibet.
Tibetan gene conferring high altitude oxygen processingis of Denisovan origin.
Genome sequence of a 45,000-year-old modern human from western Siberia
Q. Fu, et al.Nature 19 October 2014
Ust’-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000 years ago to populate the rest of the world, but later went extinct.
about 2% of his genome comes from Neanderthals. This is roughly the same level that lurks in the genomes of all of today’s non-Africans, owing to ancient trysts between their ancestors and Neanderthals. The Ust’-Ishim man probably got his Neanderthal DNA from these same matings, which, past studies suggest, happened after the common ancestor of Europeans and Asians left Africa and encountered Neanderthals in the Middle East, between 50,000 and 60,000 years ago.
Companion piece:Selection and Reduced Population Size Cannot Explain Higher Amounts of East Asian than in European Human PopulationsBernardAJHG
It has been hypothesized that the greater proportion of Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious NeandertalUsing simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertaldata.
Ancient DNA Holds Clues to Gene Activity in Extinct Humans
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
David Gokhman, et al.Science 17 April 2014
Methylation is a DNA chemical modification during the lifetime of the individual.
Using the two high-quality genomes that exist for Neandertals and Denisovans, methylationcan be mapped in relation to that for modern humans.
Methylation maps may reveal the genomic base for skeletal differences between Neandertals and modern humans.
Many more ancient methylomes must be mapped to determine which methylome is representative of these species, and more work needs to be done to show that methylation really does underlie these skeletal differences.
Characteristics of DMRs. (A) Distribution of methylation in housekeeping promoters in various human tissues (blue) and in the Neandertal and the Denisovan (red). The distribution of methylation in the Neandertal and the Denisovan falls within the variability across human tissues. (B) The numbers of present-day human–, Neandertal-, and Denisovan-specific DMRs. (C) Intergenic DMRs colocalize with enhancer and insulator marks. Overlap of intergenic DMRs with insulator mark (CTCF) and with five different enhancer marks (histonemodifications H3K4me1 and H3K27ac, histone variant H2A.Z, binding by p300, and DNase I sensitivity). DMRs are divided according to the number of enhancer marks they overlap.
Massive migration from the steppe was a source for Indo-European languages in Europe
Wolfgang Haak, et al.Nature 02 March 2015
Western and Eastern Europe came into contact 4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced 75% of their ancestry to the documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least 3,000 years ago, and is ubiquitous in presentresults provide support for a steppe origin of at least some of the IndoEurope
Massive migration from the steppe was a source for Indo-European languages in Europe
Evan GallowayNature 17 February 2015
Two fresh studies — one of ancient human DNA, the other a newly constructed genealogical ‘tree’ of languages — point to the steppes of Ukraine and Russia as the origin of this major language family, rekindling a long-standing debate.
Deletions: chunks of DNA in ancestral lineages later erased through evolutionary processes. Today, specific deletions are ‘present’ in some human genomes and missing from others
several genes make Hs susceptible to type 2 diabetes, lupus and Crohn's disease
all common (>5% allele frequency) deletion variation
deletion variants were
deletions are shared with archaic hominin
specific positive selection. genomic structural variants that are shared between
Compare Hs DNA with Hn and Denisovans. genetic deletions associated with various aspects of human health, including psoriasis and Crohn's disease, likely originated in a common ancestor of the three species.
The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction
Pat Shipman, UCSD (2015)
Modern humans domesticated dogs soon after Neanderthals began to disappear (33 ka)
This alliance between two predator species, gave moderns success in hunting large Ice Age mammals--a distinct and ultimately decisive advantage for human invaders at a time when climate change made both humans and Neanderthals vulnerable.
Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs
Robert Wayne, Beth Shapiro, et al.Nature, 2013
Dogs split from European wolves 30-18 ka Modern humans hunted grassland steppe
hoping to widen scope with more DNA from fossils outside of Europe, while also looking at the genes of living dogs that might hold important clues.
Some wolves began to scavenge left carcasses. As they migrated along with people, some were isolated from others.
Ice-age Europeans roamed in small bands of fewer than 30, on brink of extinction
Francesca JennerHorizon 26 March 2015
Ancient h-g genomes indicate a high level of inbreeding in comparison to modern populations. Present study has more and more ancient genomes sampled from diverse locations to add confidence to the original conjecture
Why the homogeneity? Probably on the huge broad northern expanse of hominin habitationcharacterized by extinction and resettlement from survivor lineages was very common. There is circumstantial evidence from wolves that the same happened to them. Why? This might simply be a amongPleistocene.
Europeans emerged in their current form in the past ~5,000 years or so. The northheterozygositymay then be a function not of serial founder effects from the expansion of the Pleistocene higher fraction of hunterancestry in Northern Europeans, who exhibited decrease genetic diversity due to the bottlenecks.
H-g genomes sequenced from Hungary and Swis, 14 000 to 7 500 ka are close to specimens from Denmark or Sweden from the same period.Suggest that post LGM genetic diversity was very limited, major demographic bottleneck triggered by LGM human isolation and extinction.http://horizon-magazine.eu/article/ice-age-europeans-roamed-small-bands-fewer-30-brink-extinction_en.html
Major transitions in human evolution revisited: A tribute to ancient DNA
Ermini, Der Sarkissian, Willerslev & Orlando Journal of Human Evolution 26 March 2015
aDNA: traits in Hn evolution:Hn/Hs split, 550-765 kaHn ranged from Iberia to the AltaiHn dist sparsely in small groupspatrilocal and/or interfamilial breedingHn/Hd split, 381-473 ka
Why the homogeneity? Probably on the huge broad northern expanse of hominin habitationcharacterized by extinction and resettlement from survivor lineages was very common. There is circumstantial evidence from wolves that the same happened to them. Why? This might simply be a amongPleistocene.
Melanesian genomes Denisovan ancestry = ~4-6%
Neanderthal ancestry = ~2%
aDNA supports Hs multiple dispersal theory for E AsiaAustralian ancestors into E Asia about 62-75 ka, admixing with Denisovans and arriving in Australia ~50 kyr ago. mainland Asian ancestors followed independently 25-38 ka.
archaic introgression into Cameroon pygmies, Khoisan-Hadza and Tanzania Sandawe: ancestors admixed with one or more archaic human populations