Mal'ta Boy (ANE): Origins of Native Americans

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Mal'ta Boy (ANE): Origins of Native Americans Nov 13, 2016 20:54:36 GMT

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Y-DNA Haplogroup R1 (specially R1b) is the second most predominant Y haplotype found after Q. Western Eurasian genetic signatures in modern-day Amerindians such as R1b derive mostly from a mixed ancestry of the First Americans or Canadians, rather than post-Columbian admixture as it's commonly thought. Raghavan et al. (2014) found that 14 to 38% of Native American ancestry may originate through gene flow from an ancient European population (MA-1). MA-1 had haplogroup R* (Y-DNA) that diverged before the hg R1 and R2 split. MA-1 belongs to Y-DNA haplogroup R* and mtDNA haplogroup U. Haplogroup U is a typical haplogroup of European hunter-gatherers and Y-DNA haplogroup R* is the ancestral haplogroup for R1a and R1b and no East Asian haplogroup such as Q was present in the MA-1 genome. West Siberian populations such as Mansi and Khants have the high frequency of hg U4, which is a West Eurasian haplogroup inherited from ancient European hunting-gatherers. The presence of hg C, which is a typical Asian haplogroup, is a result of population admixture which goes back to 6,000–10,000 years ago. Ancient Siberians who lived around 24,000-10,000 years ago had no East Asian admixture. Raghavan et al. (2014) found that MA-1 is basal to modern-day western Eurasians and it's also related to modern-day Native Americans (14-38%). Native Americans carry a high frequency of R1 (R-M173), which may be partly derived from the Mal'ta boy (MA-1) in addition to post-Columbian admixture. Haplogroup R-M173 (R1) is common among some Native American tribes (38-79%) and R1 is also widespread among certain south-central Siberian groups.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1–3, there is no consensus with regard to which specific Old World populations they are closest to4–8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 13. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10–12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find 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. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought.

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 MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2,13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

In 2009 we visited Hermitage State Museum in St. Petersburg, Russia, and sampled skeletal remains of a juvenile individual (MA-1) from the Mal’ta Upper Palaeolithic site in south-central Siberia. Mal’ta, located along the Belaya River near Lake Baikal, was excavated between 1928 and 1958 (ref. 9) and yielded a plethora of archaeological finds including 30anthropomorphic Venus figurines, which are rare for Siberia but found at a number of Upper Palaeolithic sites across western Eurasia15–17 (Fig. 1a and Supplementary Information, section 1). Accelerator mass spectrometry (AMS) 14C dating of MA-1 produced an age of 20,240 ± 60 14C years before present or24,423–23,891calendar years before present (cal. bp) (Supplementary Information, section 2).

DNA from 0.15 g of bone from MA-1 was sequenced to an average depth of 13 (Supplementary Information, section 3). From one library (referred to as MA-1_1stextraction in Supplementary Information, section 3.1), approximately 17% of the total reads generated mapped uniquely to the human genome, in agreement with good DNA preservation (see Supplementary Information Table 2). Low contamination rates were inferred for both mitochondrial DNA (mtDNA) (1.1%) and the X chromosome (1.6 to 2%; MA-1 is male) (Supplementary Information, section 5). The overall error rate for the data set was estimated to be 0.27%, with the most dominant errors being transitions typical of ancient DNA damage deriving from post-mortem deamination of cytosine18 (Supplementary Information, section 6.1).

Phylogenetic analysis of the MA-1 mtDNA genome (76.6X) places it within mtDNA haplogroup U without affiliation to any known subclades, implying a lineage that is rare or extinct in sampled modern populations (Supplementary Information, section 7 and Supplementary Fig. 4a). Present-day distribution of haplogroup U encompasses a large area including North Africa, the Middle East, south and central Asia, western Siberia and Europe (Supplementary Fig. 4b), although it is rare or absent east of the Altai Mountains; that is, in populations living in the region surrounding Mal’ta. Haplogroup U has also been found at high frequency (>80%) in ancient hunter-gatherers from Upper Palaeolithic and Mesolithic Europe10–12. Our result therefore suggests a connection between pre-agricultural Europe and Upper Palaeolithic Siberia. The Y chromosome of MA-1 was sequenced to an average depth of 1.5X, with coverage across 5.8 million bases. Acknowledging the low depth of coverage, we determined the most likely phylogenetic affiliation of the MA-1 Y chromosome to a basal lineage of haplogroup R (Supplementary Information, section 8 and Supplementary Fig. 5a). The extant sub-lineages of haplogroup R show regional spread patterns within western Eurasia, south Asia and also extend to the Altai region in southern Siberia (Supplementary Fig. 5b). The sister lineage to these extant sub-lineages of haplogroup R, haplogroup Q, is the most common haplogroup in Native Americans5 and it was recently shown that, in Eurasia, haplogroup Q lineages closest to Native Americans are found in southern Altai7.

We reconstructed admixture graphs using TreeMix21 to relate the population history of MA-1 to 11 modern genomes from worldwide populations22, 4 new genomes from Eurasia (Mari, Avar, Indian and Tajik ancestry) and the Denisova genome22 (Supplementary Information, section 11). The maximum-likelihood population tree inferred without admixture events places MA-1 on a branch that is basal to western Eurasians (Supplementary Fig. 12). However, a significant residual was observed between the empirical covariance for MA-1 and Karitiana, a Native American population, and the covariance predicted by the tree model (Supplementary Fig. 12). Consequently, gene flow between these lineages was inferred in all graphs incorporating two or more migration events (Fig. 2 and Supplementary Fig. 13). Bootstrap support for the migration edge from MA-1 to Karitiana, rather than from Karitiana to MA-1, was 99% in this analysis.

We investigated further the population history of MA-1 by conducting sequence read-based D-statistic tests23 on proposed tree-like histories comprising MA-1 and combinations of 11 modern genomes (Supplementary Information, section 13). In agreement with the TreeMix results, these tests reject the tree ((X, Han), MA-1) where X represents Avar, French, Indian, Mari, Sardinian and Tajik, consistent with the MA-1 lineage sharing more recent ancestry with the western Eurasian branch after the split of Europeans and east Asians (Supplementary Table 13). This result also holds true when the Han Chinese is replaced with Dai, another east Asian population (Supplementary Table 13). Notably, we can also reject the tree ((Han, Karitiana), MA-1) (Z 5 10.8), suggesting gene flow between MA-1 and ancestral Native Americans, in accordance with the admixture graphs (Supplementary Table 13). This result is consistent with allele frequency-based D-statistic tests20 on SNP arrays for 48 Native American populations of entirely First American ancestry19, indicating that all tested populations are equally related to MA-1 and that the admixture event occurred before the population diversification of the First American gene pool (Fig. 3a, Supplementary Information, section 14.4 and Supplementary Fig. 24).

The genetic affinity between Native Americans and MA-1 could be explained by gene flow after the split between east Asians and Native Americans, either from the MA-1 lineage into Native American ancestors or from Native American ancestors to the ancestors of MA-1. However, MA-1, at approximately 24,000 cal. bp, pre-dates time estimates of the Native American–east Asian population divergence event24,25. This presents little time for the formation of a diverged Native American gene pool that could have contributed ancestry to MA-1, suggesting gene flow from the MA-1 lineage into Native American ancestors. Such gene flow should also be detectable using modern-day western Eurasian populations in place of MA-1. Consistent with this, D-statistic tests estimated from outgroup-ascertained SNP data20 reveal significant evidence (Z == 3) for Middle Eastern, European, central Asian and south Asian populations being closer to Karitiana than to Han Chinese20 (Fig. 3b and Supplementary Information, section 14.5).

Similar signals were also observed when we replaced modern-day Han Chinese with data from chromosome 21 from a 40,000-yearold east Asian individual (Tianyuan Cave, China), which has been found to be ancestral to modern-day Asians and Native Americans26 (Supplementary Information, section 14.5). Thus, if the gene flow direction was from Native Americans into western Eurasians it would have had to spread subsequently to European, Middle Eastern, south Asian and central Asian populations, including MA-1 before 24,000 years ago. Moreover, as Native Americans are closer to Han Chinese than to Papuans (Fig. 3c), Native American-related gene flow into the ancestors of MA-1is expected to result in MA-1 also being closer to Han Chinese than to Papuans. However, our results suggest that this is not the case (D (Papuan, Han; Sardinian, MA-1) = 20.002 ± 0.005 (Z = 20.36)), which is compatible with all or almost all of the gene flow being into Native Americans (Supplementary Information, section 14.6). Similar results are obtained when MA-1 is replaced with most modern-day western Eurasian populations, except populations with recent admixture from east Asia (Russian, Adygei and Burusho) and Africa (Middle Eastern populations) (Fig. 3c). The most parsimonious explanation for these results is that Native Americans have mixed origins, resulting from admixture between peoples related to modern-day east Asians and western Eurasians. Admixture graphs fitted with MixMapper27 model Karitiana as having 14–38% western Eurasian ancestry and 62–86% east Asian ancestry, but we caution that these estimates assume unadmixed ancestral populations (Supplementary Information, section 12).

Importantly, in addition to the low contamination rates and rare or extinct uniparental lineages, we exclude modern DNA contamination as being the source of the observed population affinities of MA-1 for three reasons. First, we corrected the sequence read-based D-statistics tests for differing amounts of contamination, using a European individual as the contamination source (Supplementary Information, section 13.5). We find similar outcomes for corrected and uncorrected tests (Supplementary Fig. 20), even when contamination levels larger than that estimated for MA-1 are considered, confirming that our results are not affected by contamination from a European source. Second, restricting the PCA to sequences with evidence of post-mortem degradation gives results that are comparable with those using the complete data set (Supplementary Information, section 15). Finally, the genome sequence of the researcher (Indian ancestry) who carried out DNA extraction and library preparation of MA-1 enables us to exclude the researcher as a source of contamination (Supplementary Information, sections 11 and 13). In addition, we exclude post-Columbian European admixture (after 1492 ad) as an explanation for the genetic affinity between MA-1 and Native Americans for three reasons. First, for SNP array-based analyses, we take recent European admixture into account by using a data set masked for inferred admixed genomic regions19. Second, allele frequency-based D-statistic tests20 show that all 48 tested modern-day populations with First American ancestry19 are equally related to MA-1 within the resolution of our data (Supplementary Information, section 14.4), which would not be expected if the signal was driven by recent European admixture. Third, MA-1 is closer to Native Americans than any of the 15 tested European populations (Supplementary Information, section 14.8).

Human dispersals in northeast Asia immediately before and after the LGM are most likely to have led to the settlement of Beringia, and ultimately the Americas28. As MA-1 pre-dates the LGM, we investigated whether the genetic composition of southern Siberia changed during the LGM by generating a low-coverage data set (~0.1X) of a post-LGM individual from Afontova Gora-2 (AG-2) (ref. 14), located on the western bank of the Enisei River in south-central Siberia (Fig. 1a). We obtained a direct AMS 14C date of 13,810 ± 35 14C years before present or 17,075–16,750 cal. bp for AG-2 (Supplementary Information, section 2). Despite substantial present-day DNA contamination in this sample (Supplementary Information, section 5), we find that AG-2 shows close similarity to the genetic profile of MA-1 on a PCA (Supplementary Information, section 15 and Supplementary Fig. 29) and is significantly closer to Karitiana than to Han (D (Yoruba, AG-2; Han, Karitiana) = 0.078 ± 0.004, Z = 19.9) (Supplementary Information, section 15). We observe consistent results when restricting analyses to sequences with evidence of post-mortem degradation (Supplementary Information, section 15 and Supplementary Fig. 29), implying that southern Siberia may have experienced genetic continuity through the environmentally harsh LGM.

Our study has four important implications. First, we find evidence that contemporary Native Americans and western Eurasians share ancestry through gene flow from a Siberian Upper Palaeolithic population into First Americans. Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations29. Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans13 derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis30. Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.

Nature. 2014 Jan 2; 505(7481): 87–91.

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Mal'ta Boy (ANE): Origins of Native Americans Dec 14, 2016 20:30:13 GMT

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Post by Admin on Dec 14, 2016 20:30:13 GMT

Y-DNA haplogroup R1 (M173) is found predominantly in North American groups like the Ojibwe (50-79%), Seminole (50%), Sioux (50%), Cherokee (47%), Dogrib (40%) and Tohono O'odham (Papago) (38%). R1 (M173) was not introduced by European settlers as it has been previously believed, because R1b and R1a, which most Europeans belong to, are descendant lineages of haplogroup R1 (M173), which is much older than R1b and R1a. R1 most likely entered the Americas through prehistoric Amerindian migrations from Asia through Beringia. The First Americans received ancient gene flow from the MA-1 lineage into Native American ancestors (Raghavan et al. 2014). Haplogroup R is the Y-DNA haplogroup of MA-1, which is basal to modern-day western Eurasians and near the root of most Native American lineages. The Mal'ta boy (MA-1) lived in south-central Siberia around 24,000 years ago and 14 to 38% of Native American ancestry originated through gene flow from this ancient population.

Figure SI 5a An unrooted Neighbor Joining tree of 24 Y chromosomes from the
publicly available Complete Genomics dataset1 and MA-1. The tree is based on
22492 Y chromosome SNPs and constructed with MEGA using default parameters.
MA-1 is ancestral to haplogroup R, based on 5 sites that are in ancestral state
compared to all other individuals belonging to this haplogroup. The phylogenetic
analysis of sites underlying the tree resulted in a pruned dataset of 4301 informative
positions. The derived (d) or ancestral (a) states of called (non-N) sites in the MA-1 Y
chromosome are noted on the edges of the tree. The overall number of informative
sites at those edges is shown in parentheses. For example, “(232) MA-1: 109a, 1d,
122N ” on the hg Q edge means that out of the 232 positions in derived state at this
edge, 109 were ancestral, one derived and 122 N in MA-1.

SI 8. Y chromosome haplogroup of MA-1

Due to low depth-of-coverage of the MA-1 individual (1.5X on 5.8 million bases),
genotyping at each site on the Y chromosome was performed by selecting the allele
with the highest frequency of bases with a base quality of 13 or higher. Additionally,
a multi-fasta file was generated from the variable positions on the Y chromosomes
available from 24 Complete Genomics public genomes1. SNPs were filtered for
quality (using VQHIGH as the threshold, as defined by Complete Genomics), with
tri-allelic positions excluded and only those Y chromosome regions determined as
being phylogenetically informative being used2. This yielded a final dataset of 22492
positions. MA-1 Y chromosome data was then included, and MEGA phylogenetic
software3 was used to construct a Neighbor Joining (NJ) tree with default parameters
(Figure SI 5a). MA-1 is placed as a basal lineage to hg R2,4. Phylogenetically
informative positions and their state in MA-1 were then determined to confirm the
placement of MA-1 on the tree. In the course of this analysis, the original dataset was
severely pruned. Non-informative positions, including those with more than four Ns
in the public dataset, were excluded (633 positions). Moreover, the following
positions were also excluded which were 1) in reference state in all individuals
including MA-1 (7172 positions); 2) N in MA-1 and either N or reference state
among the rest of the individuals (9682 positions); 3) ‘N-ref’ – those with only N or
reference state among all individuals (586 positions) and ‘N-alt’ - positions with
alternative alleles, but difficult to classify (11 positions); 4) reference specific (79
positions); and, 5) recurrent (28 positions). This resulted in 4301 positions being
retained that were classified according to their hg affiliations. Among those
phylogenetically informative positions, 1889 non-N positions were retrieved from
MA-1. When counting from the split of hg DE on the unrooted phylogenetic tree,
MA-1 is determined to be carrying the derived allele in 183 sites and the ancestral
allele in 1706 sites. The position of MA-1 on the phylogenetic tree is established by
the state of the 313 basal mutations separating hgs DE and R, where MA-1 has 143
informative positions. Of these, 138 are in the derived and 5 in the ancestral state,
placing MA-1 as a lineage basal to hg R. With only a few exceptions characterized
below, all other informative positions in MA-1 are in the ancestral state, further
supporting the phylogenetic positioning of MA-1 on the tree.

Among the derived markers in the final dataset only a few (11) mutations were
detected that are likely to be false positives based on the phylogenetic analysis, where
it is assumed that recurrent mutation is less likely than a sequencing error. One
position among the 35 private to MA-1 is characteristic of a distant hg – namely
C3c14. Based on current data, 10 additional phylogenetically non-concordant
positions in MA-1 were found – 1 position for hgs E, G, Q, R1b, R1 each, 2 defining
positions for hg I and 3 private mutations for R1b individuals (shown in red on Figure
SI 5a). Additionally, among the mutations originally excluded (the reference-private
mutations), two positions were found where MA-1 is in derived state.

Figure SI 4 mtDNA haplogroup placement of MA-1.
(a)Placement of the ancient mtDNA lineages of MA-1 and Dolni Vestonice 14 (DV14)1
, for comparison, on a phylogenetic tree depicting the main extant branches of hg
U. The haplogroup nomenclature usage is in accordance with the mtDNA tree Build
15 (Sept 30, 2012)2. The age estimates (kiloyears, +/- SD) shown on the branches of
different sub-hgs of hg U are from Behar et al.3. The regional frequency data of hg U
sub-hgs is pooled into four frequency classes (shown in the legend) and comprises
data from previous studies and unpublished data from Estonian Biocentre (indicated
with asterisks): Northern Africa4-7; Caucasus and Middle East7-16,* ; West Europe6,9,17-28;
Scandinavia9,19,24,29-36,*; East Europe and Baltic9,24,37-42,*; Central and South
Europe9,16,22,43-59,*; West Siberia60-62,*; Central and South Siberia63-65,
*; Central Asia14,66-68,*; South Asia14,15,69; East Asia63,67-77

SI 7. mtDNA haplogroup of MA-1

Sequence reads from MA-1 were mapped to the revised Cambridge Reference
Sequence (rCRS, NC_012920.1) and, filtered for PCR duplicates and paralogs
requiring a minimum mapping quality of 25 (SI 4.1). A file of variants, filtered for a
minimum depth of 10, was generated. Indels were excluded from the analysis. MA-1
carries all the three SNPs characterizing hg U (A11467G, A12308G and G12372A).
For comparison, we included in the analysis the individual Dolni Vestonice 14 (DV14;
GenBank accession number KC521458), which has been shown to be basal to the
extant hg U51. Both the MA-1 and DV-14 sequences were analyzed for the presence
of diagnostic mutations of the major sub-hgs of extant hg U lineages, using
information from mtDNA tree Build 15 (Sept 30, 2012)2. A phylogenetic tree wasbuilt,
with the age estimates (kiloyears, +/- SD) of different sub-hgs of hg U3,including
all major extant branches of mtDNA hg U lineages from its root and also he two ancient
hg U lineages (Figure SI 4a).

The mtDNA sequences of MA-1 and DV-14 share only the three basal mutations inside hg U
with each other, and do not belong to any known modern branch of hg U.
To show the present spread of hg U and its different sub-hgs (Figure SI 4b), the
average frequencies, divided into four frequency classes, were calculated in regional
groups, using a dataset consisting of ca. 30,000 partial mtDNA genomes4-78. Today,
hg U is a pan western Eurasian haplogroup, with distribution across Europe, the
Middle East, South and Central Asia, western Siberia and North Africa (Figure SI
4b). The overall frequency of hg U is low or absent in extant central and south
Siberian populations, i.e. the region close to where MA-1 originated, as well as in
East Asia (Figure SI 4b).

Archaeologists need a new theory for the colonization of the Americas. Plant and animal DNA buried under two Canadian lakes squashes the idea that the first Americans travelled through an ice-free corridor that extended from Alaska to Montana.

The analysis, published online in Nature on 10 August and led by palaeogeneticist Eske Willerslev of the University of Copenhagen, suggests that the passageway became habitable 12,600 years ago1. That’s nearly 1,000 years after the formation of the Clovis culture — once thought to be the first Americans — and even longer after other, pre-Clovis cultures settled the continents.

Some 14,000 years ago, as North America was emerging from the last Ice Age, twin glaciers that blanketed central Canada receded, creating the ice-free corridor before the appearance of Clovis people across what is now the central United States. “That coincidence seemed too powerful to ignore,” says archaeologist and co-author David Meltzer of Southern Methodist University in Dallas, Texas. “People who have been cooling their heels in Alaska for thousands of years see this new land open up and they come blasting down this corridor into the new world.”

The ice-free-corridor theory began to crack in the 1990s, when researchers made a case that humans lived at Monte Verde in Chile more than 14,000 years ago. The discovery of other possible pre-Clovis sites in North America further shook the theory that Clovis people were the first Americans. But the idea that their ancestors at least trekked through the corridor persisted, says Meltzer, even though there was little consensus on when the passage opened or when it became habitable. “It’s 1,500 kilometres. You can’t pack a lunch and do it in a day.”

To build a picture of the habitat as it crept out of the Ice Age, Willerslev’s team analysed DNA in cores taken from beneath two lakes in what was the last stretch of the corridor to melt. The first plant life — thin grasses and sedges — dates back just 12,600 years. The region later became lusher, with sagebrush, buttercups and even roses, followed by willow and poplar trees. This habitat attracted bison first, and later mammoths, elk, voles and the occasional bald eagle. Around 11,500 years ago, the corridor began to resemble the pine and spruce boreal forests of today’s landscape.

The region’s bounty must eventually have tempted hunter-gatherers. But the dates rule out its use as a corridor by Clovis people and earlier Americans to colonize the Americas, says Willerslev. Instead, both probably skirted the Pacific coast, perhaps by boat.

Last Edit: Jun 1, 2018 20:40:39 GMT by Admin

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Mal'ta Boy (ANE): Origins of Native Americans Jan 19, 2017 20:25:28 GMT

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Post by Admin on Jan 19, 2017 20:25:28 GMT

Beringia, a vast region stretching from the Lena River in Siberia to the Mackenzie River in the Yukon Territory [1, 2], is thought to have played a pivotal role in the initial dispersal of human populations from Asia to North America. The exact timing of the initial dispersal remains uncertain, however. Recent genetic and palaeogenetic analyses [3–10], as well as dental morphological evidence [11], confirm that human populations migrating into North America originated in Siberia. They also suggest that dispersing groups reached Beringia during the LGM (dated to ca. 18,000–24,000 cal BP) where they were genetically isolated for up to 8,000 years before moving south of the ice-sheets into North America [3–11]. Unfortunately, archaeological support for the standstill hypothesis is scarce [12]. Recent archaeological discoveries prove that humans were able to adapt to high-latitude, Arctic environments by at least 45,000 cal BP [13]. The Yana River sites, in Siberia, demonstrate that modern human populations had reached Western Beringia by 32,000 cal BP [14, 15], i.e., well before the LGM. Human activity is not recorded again in Western Beringia until the post-LGM period, however, with occupations of two open-air sites, Berelekh and Ushki, dated to ca. 14–13,000 cal BP [16–18]. In Eastern Beringia, the oldest currently accepted human occupations occur in the Tanana valley (interior Alaska) at Swan Point, Broken Mammoth and Mead [19–21], and at the Little John site, located 2 km east of the international border in the Yukon Territory [22]; these sites are no older than ca. 14,000 cal BP, however [19–22]. The only potential candidate for an earlier, LGM occupation of Beringia is the controversial Bluefish Caves site.

Excavated from 1977 to 1987 under the direction of Jacques Cinq-Mars (Archaeological Survey of Canada), the Bluefish Caves site (northern Yukon Territory, 67°09’N 140°45’W) occupies a unique place in Eastern Beringian prehistory. The site is comprised of three small karstic cavities, not exceeding 30 m3 in volume, located in the Keele range about 54 kilometres southwest of Old Crow village. The caves are situated at the base of a limestone ridge about 250 meters above the right bank of the Bluefish River [23–27]. All three cavities contain a loess layer (Unit B) up to one meter thick, deposited on bedrock (Unit A) and overlain by a humus layer mixed with cryoclastic debris (Unit C) and finally, a modern humus layer (Unit D) [25, 27]. The loess deposit (Unit B) can be differentiated into three sub-layers based on granulometric and sedimentological examinations and was excavated in 5 cm spits [23]. Small artefact series were excavated from the loess in Cave I (MgVo-1) and Cave II (MgVo-2) and rich faunal assemblages were recovered from all three caves [23–27]. The lithic assemblages (which number about one hundred specimens) include microblades, microblade cores, burins and burin spalls as well as small flakes and other lithic debris [23–26]. Most of the artefacts were recovered from the loess of Cave II at a depth comprised between about 30 to 155 cm. The deepest diagnostic pieces–a microblade core (B3.3.17), a burin (B3.6.1) and a core tablet (B4.16.4) found inside Cave II, as well as a microblade (E3.3.2) found near the cave entrance–derive from the basal loess at a depth of about 110 to 154 cm below datum, according to the CMH archives [28]. While the artefacts cannot be dated with precision [24, 25, 29], they are typologically similar to the Dyuktai culture which appears in Eastern Siberia about 16–15,000 cal BP, or possibly earlier, ca. 22–20,000 cal BP [30]. There are no reported hearth features [24]. Palaeoenvironmental evidence, including evidence of herbaceous tundra vegetation [31, 32] and vertebrate fauna typical of Pleistocene deposits found elsewhere in Eastern Beringia [27, 33, 34], is consistent with previously obtained radiocarbon dates which suggest that the loess layer was deposited between 10,000 and 25,000 14C BP (radiocarbon years Before Present), i.e., between 11,000 and 30,000 cal BP [23–27, 35] (Table 1).

Table 1. Previous radiocarbon dates obtained on bone from Bluefish Caves I (MgVo-1) and II (MgVo-2).

A total of 36,000 mammal bones from Caves I and II were analysed for this research. As previously reported [23–27], the faunal spectrum of the Bluefish Caves is diversified and includes several carnivore taxa. Our taphonomic analysis indicates that wolves, lions and, to a lesser degree, foxes were the main agents of bone accumulation and modification, but that humans also contributed to the bone accumulations in both caves, partially confirming earlier taphonomic studies [26, 39]. The caves were probably used as den sites for Ursids in winter and Canids in spring and summer. The archaeozoological evidence, together with the small size of the lithic assemblages, suggests that human occupation of Caves I and II was probably sporadic and brief.

The effects of weathering and cryoturbation were observed in both caves but didn’t alter the bone surfaces significantly [39]. In Cave II, however, the extent of root etching on the bone surfaces was very high and will have affected the preservation of cut marks: root etching was recorded on 70% of the bone material in this cavity and affected more than half of the surface in 27% of cases. The bone assemblage of Cave I was less affected by this biological agent with only 4% of the bones affected. On the other hand, 57% of the bones in Cave I and only 18% in Cave II were abraded. Rodent gnawing was minimally present, while carnivore tooth marks were observed on 38 to 56% of the bone material of Cave I and 14 to 32% of the material of Cave II. Thus, carnivore gnawing, root etching and abrasion were mainly responsible for the bone alterations in Cave I and II (see also S1 Graph). In both cavities, however, human modifications were also identified.

Fig 1. Cut marks on a horse mandible from Cave II.

The specimen (# J7.8.17) is dated to 19,650 ± 130 14C BP (OxA-33778). The bone surface is a bit weathered and altered by root etching but the cut marks are well preserved; they are located on the medial side, under the third and second molars, and are associated with the removal of the tongue using a stone tool [48].

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Mal'ta Boy (ANE): Origins of Native Americans Jan 20, 2017 20:24:16 GMT

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Post by Admin on Jan 20, 2017 20:24:16 GMT

Six of the cut-marked bones were selected for AMS dating (Fig 3). The results range from 10,490 ± 55 14C BP to 19,650 ± 130 14C BP, i.e., between 12,000 and 24,000 cal BP, and are consistent with previously reported dates for Bluefish Caves (Table 1) [23–27, 35]. An old date that was obtained by the RadioIsotope Direct Detection Laboratory on a cut-marked horse metatarsal from Cave I (17,440 ± 220 14C BP; RIDDL-278) is now strengthened by two new dates performed on the same specimen (Figure D in S1 Fig): 17,660 ± 100 14C BP (OxA-33774) and 17,610 ± 100 14C BP (OxA-33775).

Fig 3. New radiocarbon determinations obtained on bone from Bluefish Caves I and II.

The oldest date we obtained (19,650 ± 130 14C BP, OxA-33778) came from the cut-marked horse mandible (J7.8.17) from Cave II (Fig 1) and is consistent with the stratigraphic position of the bone, which is reported to have been found in the basal loess, at a depth of 142 cm below datum [28]. Unfortunately, the exact depth at which the other bone specimens we dated in this study were found could not be established from the archival records at our disposal, but the vast majority of the faunal material derives from the bone beds contained in the lower loess layers in both caves [28].

It is highly unlikely that the cut marks observed on the Bluefish Caves faunal material were generated by nonhuman agents or natural processes. In Cave II, the horse mandible (J7.8.17) (Fig 1) and a caribou pelvis (I5.6.5) (Fig 2) date the human presence to the LGM, ca. 24–22,000 cal BP (Fig 3). The traces identified on these bones are clearly not the result of climato-edaphic factors or carnivore activity. The presence of multiple, straight and parallel marks with internal microstriations observed on both specimens eliminates carnivores as potential agents. The relatively high breadth ratio (12 and 18 μm, respectively), as well as the depth (91 and 95 μm, respectively) and opening angle (144 and 139 μm, respectively) that we measured are in the range of marks produced by stone tools reported by experimental and archaeological studies [58]; the breadth ratio also differs from marks produced by carnivore teeth [52]. Sedimentary abrasion or trampling are also eliminated since the caribou coxal bone shows no other signs of abrasion and the long, parallel striae on the horse mandible are simply too regular. Furthermore, the anatomical location and orientation of the marks are consistent with filleting marks in the case of the caribou bone, while the presence of multiple cut marks on the medial side of the horse mandible indicates the removal of the tongue [48]. Previous cementochronological analysis of one of the teeth from this mandible indicated that the animal was killed in spring/summer [35], thus suggesting a human presence in Cave II during the warm season.

In Cave I, three other bone specimens are dated to the end of the Pleistocene, ca. 22–15,000 cal BP. A horse humerus (J7.1.1), a horse metatarsal (K8.1.13) and a caribou metacarpal (K8.1.27) bear straight, V-shaped cut marks on the shaft (no more than two on each bone) that cannot result from natural processes; again, morphometrical analyses show consistency with marks produced by stone tools [52, 58] and the relatively deep and narrow incisions can hardly result from trampling [44]. Instead, the marks observed on the humerus and metacarpal indicate filleting activity (Figures C and H in S1 Fig) while the cut-marked metatarsal may reflect stripping of tendons [48] (Figure D in S1 Fig).

Finally, the youngest date (ca. 12,000 cal BP) was obtained on a bone fragment (K6.1.20) from Cave I, bearing eight clear, curved and parallel striae obliquely oriented on the bone shaft and illustrating filleting activity. The specimen couldn’t be taxonomically identified but might be a wapiti bone judging by the thickness and curvature of the shaft fragment (Figure F in S1 Fig). Cut marks were also observed on a wapiti premaxilla (undated) recovered from the same cavity and reflecting skinning activity (Figure A in S1 Fig).

Last Edit: Apr 12, 2018 20:33:08 GMT by Admin

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Mal'ta Boy (ANE): Origins of Native Americans Jan 21, 2017 20:26:06 GMT

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Post by Admin on Jan 21, 2017 20:26:06 GMT

Discussion

The small percentage of cut-marked bones at Bluefish Caves I and II is not surprising. Our taphonomic analysis suggests that natural processes, particularly root etching and scavenging activities, may have destroyed some of the evidence of human activity. In other Beringian archaeological sites dated to the Late Pleistocene/Early Holocene, taphonomic studies show that cut marks are scarce (less than 1%) [73] or even absent in bone assemblages highly affected by natural processes [74, 75]. Furthermore, the Bluefish Caves, like other Beringian cave sites [73, 74, 76], were probably only used occasionally as short-term hunting sites. Thus, they differ from the open-air sites of the Tanana valley in interior Alaska and the Little John site in the Yukon Territory, where hearth features, large lithic collections, bone tools and animal butchery have been identified, reflecting different cultural activities and a relatively longer-term, seasonal occupation [19–22].

In conclusion, while the Yana River sites indicate a human presence in Western Beringia ca. 32,000 cal BP [14, 15], the Bluefish Caves site proves that people were in Eastern Beringia during the LGM, by at least 24,000 cal BP, thus providing long-awaited archaeological support for the “Beringian standstill hypothesis”. According to this hypothesis, a human population genetically isolated existed in Beringia from about 15,000 to 23,000 cal BP [9], or possibly earlier [3–5, 10], before dispersing into North and eventually South America after the LGM [3–12,77–79].

Central Beringia may have sustained human populations during the LGM since it offered relatively humid, warmer conditions and the presence of woody shrubs and occasional trees that could be used for fuel [12, 33, 37]. However, this putative core region was submerged at the end of the Pleistocene by rising sea levels making data collection difficult. Bluefish Caves, situated in Eastern Beringia, may have been located at the easternmost extent of the standstill population’s geographical range. The seasonal movements of human hunters from a core range, hypothetically located in Central Beringia, into adjoining, more steppic regions such as Eastern Beringia would explain the sporadic nature of the occupations at Bluefish Caves [12].

The scarcity of archaeological evidence for LGM occupations in both Western and Eastern Beringia suggests that the standstill population was very small. This is consistent with the genetic data, which suggest that the effective female population was only about 1000–2000 individuals [5, 6, 10] and that the standstill population didn’t exceed a few tens of thousands of people in Beringia [10]. The size of the standstill population is thought to have increased after the LGM, leading to renewed dispersals into the Americas [4–6, 10]. Our results indicate that human hunters continued to use Bluefish Caves as the climate improved. While some prey species became extinct by ca. 14,000 cal BP (e.g. horse) [80], human hunters could continue to rely on different species such as caribou, bison and wapiti.

By around 15–14,000 cal BP an ice-free corridor formed between the Laurentide and Cordilleran ice sheets potentially allowing humans to disperse from Beringia to continental North America; arguably, this corridor wouldn’t have been biologically viable for human migration before ca. 13–12,500 cal BP, however [77–79]. It is now more widely recognized that the first inhabitants of Beringia probably dispersed along a Pacific coastal route, possibly as early as ca. 16,000 cal BP, and settled south of the ice sheets before the ice-free corridor became a viable route [3–12,77–79].

Our results, therefore, confirm that Bluefish Caves is the oldest known archaeological site in North America and furthermore, lend support to the standstill hypothesis. More research effort is required in Beringia clearly, to substantiate the existence of a standstill population and fully understand the prehistory of the first people of the Americas.

Bourgeon L, Burke A, Higham T (2017) Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada. PLoS ONE 12(1): e0169486. doi:10.1371/journal.pone.0169486

Last Edit: Apr 12, 2018 20:33:38 GMT by Admin