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cjkekgg22h · Posted: Fri 6:02, 11 Oct 2013 Post subject:

+ The Denisova Cave is in a remote region of southern Siberia's Altai Mountains north of the border between China and Kazakhstan.The cave contains cultural material, which infers episodic hominid occupation from ca 125Ka ago or "possibly earlier. The distal, manua phalanx of the fifth digit of a human, a lithic assemblage, numerous bone implements and personal ornaments were retrieved from level 11.2. The stone tool industry is difficult to classify, because it contains Levallois, Mousterian and Upper Palaeolithic components. It could be a transitional industry or some of the artifacts have been displaced by post depositional disturbance. [There is a wedge of disturbed sediment by the Denisova finger in level 11.2 and the cave has a natural "chimney" opening; A Gibbons,2011]. The chronology for level 11.2 is conjectural. A realistic approximation might be ca 40050BCE +/-8.0Ka,cal 2011. The mtDNA diversity of Neanderthals is low, when compared to Homo sapiens and Denisovans. Comparisons suggest that across the geographic range Neanderthals had a population history that was distinct from Denisovans [J Krause, 2010].
A DNA sample was extracted from the Denisova cave finger bone. Analyses indicated that the mtDNA fragments belonged to a one individual, who appears to have predated the Neanderthals. There were no indications that the sample had been subjected to significant contamination [ibid].
The nuclear genome of the Denisovan finger bone sample was sequenced to ascertain its relationship to extant humans and Neanderthals.The draft genome sequence can identify features, that are ancestral in the Denisovan genome and that are derived in Homo sapiens. On average the Denisovan nuclear genome shares more in common with the recent ancestor of Neanderthals than with modern humans.Research revealed, that the archaic component of the European gene pool is not as closely related to Denisovans as it is to Neanderthal.The Denisovan genome was compared to 938 present day people from 53 populations. Papuan and Bougainville islanders were distinct from almost all samples outside of Africa [no Australian specimens were incorporated into the study].Comparisons with five extant humans revealed, that Denisovans and Melanesians shared some alleles, which Neanderthals did not have in common with Melanesians. The Denisovan nuclear genome varies from its mtDNA phylogeny [D Reich,2010].
Two teeth were recovered from the south gallery of the Denisova cave level 11.1. The young adult tooth is a second or third molar. The crown is trapezoidal and tapers strongly distally, with bulging, lingual and buccal walls, which gives the tooth an inflated appearance. The short roots are robust and strongly flaring. If the very large tooth is a third molar, it compares to Australopithecines. If it is the second molar,it is within the Homo erectus range. The other very large molar has many unusual cusps. Genetic analyses revealed that both teeth are Denisovan and were distinct from modern humans and Neanderthals [D Reich,2010].
Preliminary evaluations of a toe bone from Denisova cave infers that it belonged to a Neanderthal. It has similarities to a Neanderthal toe bone from Iraq. The presence of the bones, which have been designated as Homo floresiensis in Indonesia and the Denisovans, Homo sapiens and Neanderthals in the Siberian cave [ during different eras?] indicates that at least four hominid lineages inhabited Eurasia coevally.The diverse variants of the HLA gene system provides significantly more detail about population histories than Y chromosome and mtDNA studies. HLA-B*73 is rare in Africa and constitutes up to 5.0% of all the genes known variants among western Asians. It has been identified as a Denisovan gene sequence. Comparisons of the HLA genes of archaic humans and modern Homo sapiens suggest that it evolved from fraternization between Denisovans and [link widoczny dla zalogowanych] Homo sapiens. However other HLA types, which emerged from ancient interbreeding ,occur in much higher frequencies. Certain archaic traits have become a dominant form. HLA-A*11 is virtually absent in Africa and represents up to 64% of variants in East [link widoczny dla zalogowanych] Asia and Oceania, with the highest frequency in Papua New Guinea. It is deemed to have been advantageous to modern people and therefore it attained a significant presence [L Abi Rached, 2011].
D Reich [2011] analysed the genome wide data of 243 individuals from 33 populations in Oceania, Australia, South and SE Asia [one Australian group is from the Northern Territories and the other location has not been identified]. The SNP array for the samples was merged with chimpanzees,Denisovans and Neanderthals. Mainland East Asians, western Negritos [Jehai and Onge] and western Indonesian specimens do not have a significant Denisovan genetic component. SE Asian and western Indonesia were populated by an influx of Neolithic newcomers, who may not have harboured appreciable number of Denisovan genes. However Australians, New Guineans, Fijians, Nusa Tenggaras islanders [east Indonesia], Philippine Mamanwa [Negrito] and Philippine Manobo specimens yielded strong evidence of a Denisovan genetic contribution [D Reich,2011].
New Guineans and Australians have a similar Denisovan component [ca3.0+/-0.8%], which infers a common ancestry, that may trace to before their entry into Sahul. An admixture graph model suggests additional gene flow into Australians/New Guineans, after their ancestors and the Philippine Mamanwa forebearers split from people, who did not have Denisovan genes. The model infers that these people were closer to Andamanese and Malaysian Negritos than to East Asians. Neanderthal admixture averaged 1.3% [ibid].
Genome wide SNP genotype data is available for [link widoczny dla zalogowanych] a relatively wide cross section of the world's population. Analysis of the genetic variation of extant humans using genotype data [link widoczny dla zalogowanych] from a diverse selection of modern human people identified an archaic admixture signal among coeval East Asians. Although Papuans had the highest Denisovan allele frequency, the south China, Yizu,appear to have a similar Denisovan component to Melanesians from Bougainville. Research indicated, that generally a signal of archaic ancestry may only [link widoczny dla zalogowanych] be discernible between two populations, with a similar magnitude of genetic drift. This study shows that complex signals of archaic ancestry emerge in the analysis of human genetic variations. Moreover ascertainment bias and genetic drift can result in artificial variations between populations with similar admixture histories [P Skoglund, 2011].
When more genetic variants are shared among some Eurasians, than with contemporary sub-Sahara Africans, a degree of archaic admixture might be implied. Archaic introgression probably does not impact on all loci equally. Post breeding, recombination and genetic drift will leave a patchwork of loci, which carry an introgression signal. [link widoczny dla zalogowanych] The innate immune gene, OAS1, which has an important antiviral function and an archaic introgression signature, is possibly a suitable candidate for studies of local adaption and differentiation among populations. A 7kb region encompassing the OAS1 gene was [link widoczny dla zalogowanych] re-sequenced in 88 individuals from the San, Baika Pygmy, Mandenka Senegal, French Basque, Han Chinese and Paua New Guinea populations [F Mendez, 2012].
This research discovered an ancient, previously unknown genetic variation. The unique diversity patterns of the 5' region of this gene include higher levels of nuclear diversity in Papuans on either side of the rooted network and a divergent Melanesian haplotype, that shares SNPs with the Denisovan OAS1 sequence. Extensive re-sequencing on a ca 18kb region, that commences ca 9.1kb upstream of OAS1 and that encompasses the entire Melanesian gene panel, [link widoczny dla zalogowanych] revealed more than a 12kb section with SNPs common to Melanesians and Denisovans. Computationally phased [link widoczny dla zalogowanych] sequences were used to generate a median-joining network of haplotypes. A long branch separated a fraction of Papuan haplotypes from a cluster with all remaining haplotypes. The authors refer to this basal Papuan branch as the "deep lineage" [ibid].
There is a 90kb block where "deep lineage" and Denisovan SNPs are in accord. They both evolved from the ancestral sequence of all humans by the inclusion of three mutations in the core sequence [R104G, P129R and E183D], with only the "deep lineage" having a two-base-pair at position 11841650. There is a possibility that "deep lineage" was introduced to the ancestor s of the Melanesians by an archaic source, that probably resided in Asia [Denisovans or a common ancestor?]. The 5' region OAS1 gene has five SNPs with the ancestral allele, that have only been observed in Papuans . In addition there are seven SNPs, that are exclusive to Papuans and that have occurred more than once. Sequence analysis of 72 worldwide group samples revealed that the divergent Papuan haplotype was largely confined to Melanesia, eastern Indonesia,with a small presence in Australia, two samples in Pakistan and one specimen in Sri Lanka [F Mendez,2012].
L Abi-Rachel et al [2011] conducted research to ascertain,whether the highly polymorphic HLA class 1 genes [HLA-A,-B and -c] of the major histocompatibility complex could be used to detect possible admixture between archaic and modern humans.HLA-B*73:01 is a highly divergent HLA-B allele.HLA-B*73:01 combines ancient sequence divergence with modern sequence homogeneity properties,which is compatible with extant humans having acquired HLA-B*73:01 through introgression.It is concentrated in the present populations of western Asia and is absent or rare in other territories [ibid].
There is linkage disequilibrium between HAL-B*73:01 and HAL-C*15:05,which is an allele with a wider distribution in west/SE Asia than HAL-B*73:01.These distributions could be compatible with admixture between archaic and modern humans.About 98% of people harbouring HAL-B*73:01 also have HAL-C*15:05.The former has not been recorded among the sub-Sahara Khoisan-speakers and Pygmy populations,which may imply that HLA-B*73:01 was not present in Africa, when early Homo sapiens migrated to Asia.They might have acquired HLA-B*73:01 by admixture in western Asia ibid].
The archaic HLA class 1 for Denisova was characterized. All four combinations of the Denisovan HLA-A and HLA-C occur in Asia and Oceania.They are rare in Europe and to date have not been observed in sub-Sahara Africa.Both alternate pairs are common among Melanesians and attain a frequency of about 20% in Papua New Guinea.It appears that Denisovan admixture made an appreciable contribution to the HAL components of Asians and Amerindians[ibid].
The Denisovan HAL-A*11 allele is common in many Asian regions.It reaches frequencies of 50-60% in China and Papua New Guinea.Denisovan alleles HLA-C*15 and HLA-C*12:02 have also been recorded among extant Asians,with an appreciable component in Papua New Guinea.Their Asian dispersal extends further west than HLA-A*11,with a low presence in Africa and a much higher haplotype diversity in Asia than in Africa [ibid].
HAL-C*15:05 and HAL-C*12:02 are the two modern HLA-C alleles in the strongest linkage disequilibrium with the HAL-B*73:01 allele. The latter might have been introduced to modern humans via ancient admixture with archaic individuals,but to date HAL-B*73:01 has not been identified in Denisovan [ibid]. This might indicate the presence of another unidentified, archaic population in eastern Eurasian [conjectural].
I Alves et al [2012] contend that over estimates of divergence time and population admixture size bear an almost linear relationship to the admixture rate.A divergence time of 1600 generations can be recovered with a reasonable degree of accuracy,when no admixture is involved. However it is over estimated by about 350 generations,when the admixture rate is approximately 5%.Admixture has the potential to erroneously increase the divergence time estimates [ibid].
Most methods to detect recent episodes of selection in humans assume that adaptions are primarily driven by classical positive selection.However the [link widoczny dla zalogowanych] human genome does not exhibit many sites that are fixed between human populations.Moreover fixed variations tend to be between human populations from different continents.This [link widoczny dla zalogowanych] implies that strong adaptive events are rare [link widoczny dla zalogowanych] in response to local adaption.Regions with high levels of variation between continents are not associated with high levels of linkage equilibrium.This infers that allele frequency shifts have an ancient origin and are not the result of adaptive events.Diversity reduction may be related to background selection,which eliminates strongly deleterious mutations in the functional regions.There is mounting evidence that background selection "might" explain many aspects of human genetic diversity,in association with other selective processes [ibid].More complex software will be required to incorporate the above recommendationsinto future studies.

M Meyer et al [August,30 2012] published an article,which has altered perceptions of Denisovan genetics.The sample from Denisovan girl's finger bone yielded a high 70% DNA preservation. Meyer developed a procedure to commence the sequencing process with single strands DNA,rather than the standard double strand application.By binding special molecules to the ends of a single strand,the ancient DNA retained its position,while enzymes were copied from its sequence.The DNA sequence from the sample was augmented by 6 to 22 fold.Consequently 99.9% of the mappable nucleotide positions in the genome were recovered at least once and 92% of the sites were retrieved at less twenty times.Equal portions of her parents DNA were determined.This rivals the recovery rate for an extant person and exceeds that for Neanderthals [M Meyer,2012].
A high coverage [30x] genome sequence of [link widoczny dla zalogowanych] the Denisovan girl was reconstructed.The reference base was comprised of the deep genome sequences of eleven,diverse,post-San individuals.The authors estimated that the Denisovan ancestry in Papuans was about 3% [no estimate was provided for Australians-3%??].Western Eurasians had a 1.0+/-0.3% archaic DNA content,which was assigned to Neanderthal admixture.Eastern Eurasians had an additional 0.7+/-0.2% archaic content,which had a closer affinity to Neanderthals than to Denisovans [ibid].Since Neanderthals largely inhabited western Eurasia,there may have been a third [unidentified] archaic population, who lived in eastern Eurasia,with a closer genetic resemblance to Neanderthals than to Denisovans [speculation].The Han and Dai in mainland China might only have a trace of Denisovan ancestry [M Meyer,2012].
The relatively high quality Denisovan DNA facilitated endeavours to differentiate between the materal and paternal chromosomes.The girl's parents were genetically very similar,but they were not closely related.Autosomes are often inherited equally from both parents and X chromosomes are inherited twice as often from the mother.The Denisovan ancestry contribution tothe Papuans was largely in the [link widoczny dla zalogowanych] autosomes [3.0+/-0.8%] and not in the X chromosome [0.0+/-0.9%].Denisovan-Papuan admixture may have had a sexual bias between Denisovan males and Papuan females and/or the unions were not genetically compatible,with natural selection discriminating against some of the X cromosomes [ibid]. Whether either of the above premises are appicable is a moot point.
Investigations revealed that Denisovans had 23 pairs of chromosomes,which is similar to modern humans.Denisovans are more closely related to each other than to Homo sapiens. Denisovans have a closer genetic affinity to Neanderthals than to Homo Sapiens. Denisovans have fewer differences from chimpanzees than present day people.The girl's lineage had less time to acquire mutations and her bone collagen provided an estimate of 82-74Ka ago for the time of her death [this chronology is tenuous]. The divergence of Yoruba [Africa] from Neanderthals and Denisovans has been calculated to be ca440-170Ka.Using a much lower mutation rate an estimate of ca700-440Ka was obtained.Both calculations fall within the plausible range of divergence for ancestral Neanderthal and Denisovan populations from Homo sapiens.The critical component in divergence estimates is the poorly defined mutation rate [M Meyer,2012].
Denisovans have a low diversity,when compared to the eleven extant humans in the reference data base.Natural selection was also deemed to be less effective among Denisovans.Both of these factors are compatible with a small Denisovan population size or with a series of bottle necks.Denisovan population numbers are postulated to have declined significantly as Homo sapiens expanded.
The authors have identified 100,000 locations on the genome of present day Homo sapiens that vary from Denisovans.However only 260 are in locations that provide information about proteins.The majority of the changes are in the genes that involve development of the nervous system,the eyes and the skin. The authors have proposed that the Denisovan girl "might" have had dark brown hair, brown eyes,dark skin and no freckles [ibid].
The allele B*73:01,which is structurally divergent from other alleles of HLA-B,has a relatively high frequency among the Lebanese people.In contrast to most other populations allele B*73:01 associates with both C*15:05:01 and C*12:02:02 in the Lebanese,which suggests that this allele could have evolved in western Asia and spread to other territories from this region. The allele has been identified in the Denisovan DNA.Admixture between the Denisovans and Homo sapiens may [?] have occurred in western Asia [M Vina,2012].
Research into archaic admixture with [link widoczny dla zalogowanych] Homo sapiens is in the embryonic stage and there will probably be numerous revisions to the above.

Archaic and Homo sapiens Admixture Island SE AsiaArticle Summary: The recovery of well preserved DNA from a Denisovan girl's finger in an Altai Mountain cave has provided genetic data,which suggests that there may have been admixture between Denisovans and some Island SE Asians/Australians.
Article Source: uPublish.info
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