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Post by Admin on Apr 24, 2021 3:05:13 GMT
Results DNA Preservation and Sequence Recovery. Of the 19 burials screened for DNA preservation, 4 provided sufficient sequence data for downstream analyses. These included burials 1, 2.1, 16A, and 18. Burial 1 represents the remains of a young to middle-aged female; burial 2.1 was a young adult male; burial 16A was a young adult female; and Burial 18 was a young to middle-aged female (16). Complete or nearly complete mitochondrial genomes were obtained from burials 1 (2,903 total mapped reads, 98.4% covered at 11.4-fold mean coverage) and 2.1 (1,199 total mapped reads, 99.3% covered at 6.9-fold mean coverage), and partial mitochondrial genome sequences could be recovered from burials 16A (128 total mapped reads, 29.3% covered at 0.8-fold mean coverage) and 18 (261 total mapped reads, 56.5% covered at 1.2-fold mean coverage) (Fig. S2). Sequence data have been deposited in the GenBank database.
Haplotype Assignments. For burials 1, 2.1, and 16A, we were able to identify the mtDNA haplotype to the highest resolution. Burial 1 and 16A could be unambiguously identified as belonging to haplogroup B4a1a1a3, a haplogroup present in 7 of the 20 individuals studied by Benton et al. (15). Burial 2.1 was identified as belonging to B4a1a1a, although with two unique mutations at positions 4,917 and 8,790. The B4a1a1a haplogroup was only found in three individuals by Benton et al. (15). Burial 18 could be identified to the level of B4a1a1, but single nucleotide polymorphisms (SNPs) required for more fine-scale identification were not covered. Burials 1 and 2.1 differ by seven mutations, and burials 1 and 16A differ by at least one mutation (Table S1 and Table S2). All burials showed specific SNPs identified by Benton et al. (15) as unique to Maori. Burials 1 and 16A display the 1185T mutation; burials 2.1 and 18 display 4769G. Although two conflicting reads with 4769A were identified in burial 2.1 (Table S1), this result is consistent with expected aDNA deamination damage.
Sequence Authenticity. Although strict precautions to avoid contamination of the laboratory experiments with present-day human DNA were taken, the teeth from which DNA was extracted were part of a museum collection for >50 y and may have been contaminated before entering our cleanroom facility. To estimate the level of contamination, we used five approaches.
First, throughout all experiments, the samples were handled alongside three no-template controls. None of these controls contained any reads mapping to the human mitochondrial genome, indicating no human contamination in our reagents.
Second, after identifying specific haplotypes, we evaluated the consistency of all haplotype-defining SNPs in the consensus sequences to determine whether more than one biological source could have contributed to the obtained consensus sequence (Table S1). None of the 68 haplotype-defining SNPs covered across all four analyzed burials was in unambiguous conflict with what was expected for the respective haplotype. However, we did identify two ambiguities. Position 263 in burial 2.1 was covered by two reads, one with the expected G, the other one with an A. The same combination could be observed for position 750 in burial 16A (Table S1). Both ambiguities are consistent with deamination damage.
Third, we evaluated the number of individual sequence reads that conflicted with the consensus sequences to identify potential contaminating molecules (Table S1). At 8 of the 68 informative sites (covered by a total of 438 reads), we found 15 reads that conflicted with the respective consensus sequence. All of these conflicting reads were either C to T or G to A mutations and are therefore consistent with deamination damage.
Fourth, we investigated the presence of increased C–T and G–A mutations at the 5′ and 3′ ends of all sequenced molecules. These mutations are characteristic for deamination-damaged ancient molecules and can be used to distinguish them from modern contamination. All four burials showed characteristic aDNA damage patterns at the sequence ends (Fig. S3). The observed C–T misincorporation frequency of ∼0.28–0.32 on the first base of the 5′ ends of all four samples is in good accordance with a rate of 0.1–0.3 (maximum of 0.4) “predicted” by Sawyer et al. (figure 4 in ref. 21) for samples between 500 and 2,000 y of age.
Fifth, we evaluated whether bait DNA could have been sequenced. We identified 19 positions at which the bait (haplotype T2b) differs from the identified sample haplotypes (Table S3). Of the 365 reads covering these informative positions, seven reads were consistent with the bait rather than the target. Two of those reads can be explained by DNA damage (burial 18 positions 1,888 and burial 2.1 position 14,905). However, position 4,917 in burial 2.1 is covered by five reads, all of which are consistent with T2b (G) rather than B4a1a1a (A). The mutation cannot be explained by deamination damage. Given the virtual absence of any other bait contamination, we are confident that this is a genuine mutation in burial 2.1.
Further measures of postmortem DNA degradation including the fragment length distribution and the base frequency at strand breaks were analyzed and were consistent with highly degraded DNA (Fig. S4 and Fig. S5).
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Post by Admin on Apr 24, 2021 6:56:19 GMT
Discussion A recent reevaluation of the dates for the colonization of East Polynesia suggests that, contrary to earlier studies positing a relatively long (2,000 y) chronology for the region, the settlement of most of East Polynesia occurred rapidly, in the period from A.D. ∼1190–1290 (22). The authors determined that the expansion event occurred from the Society Islands, which were only settled 70–265 y previously. This rapid and recent expansion event, they argue, explains the “remarkable uniformity of East Polynesian culture, human biology and language” (22). We report here complete ancient mitochondrial genomes from Polynesia, which likely represent the founding population of New Zealand and which date almost directly to this period of rapid expansion and settlement. Far from being uniform, we identified three distinct mtDNA haplotypes in the four burials from which we obtained sequence data. When combined with the increasing number of complete mitochondrial genomes from the Pacific and related populations (e.g., Madagascar), a more complex picture is emerging. Although all published mtDNA genomes sequenced to date from Maori belong to some branch on the B4a1a lineage, a recent analysis of ancient and modern mtDNA from the Gambier Islands in French Polynesia identified individuals with haplotype Q1, including one ancient sample dated to 1400–1450 cal A.D. (14). This haplotype has also been reported from modern Cook Island samples (6, 23, 24) and thus was likely to have existed in the source population for the East Polynesian expansion. It is possible that Q1 haplotypes were brought to New Zealand as well. Complete mtDNA analyses of these haplotypes in East Polynesia may indicate even more variation in the region. The four mitochondrial genomes presented here share two of the three unique “Maori” mutations identified by Benton et al. (15): 1185T in burials 1 and 16A and 4769G in burials 2.1 and 18. Although burial 1 has a haplotype already identified by Benton et al. (15), burials 2.1 and 16A have previously unidentified mutations and thus represent unique haplotypes, further increasing the known mtDNA variation within East Polynesia. Burials 1 and 2.1, for which complete mitochondrial genomes were sequenced, differ from the modern Polynesian mitochondrial genomes in GenBank by at least three positions (figure 2 in ref. 15). The Wairau Bar sequences are likely to represent a subset of the total mtDNA variation in the founding population of Aotearoa/New Zealand, which in itself is likely to be a subset of the variation present in the founding populations of East Polynesia. At least three of the four individuals sequenced from the Wairau Bar site were not recently maternally related. Burials 1 and 2.1 were recovered in the same burial group (Group 1) with similar grave goods, presumed to be of high status (25), yet these two individuals belonged to two different haplotypes (B4a1a1a3 and B4a1a1a) (Fig. 1). This finding indicates that the founding populations were unlikely to be from a single matrilocal source. Furthermore, all four individuals displayed SNPs that have so far been identified only in Maori. It is highly unlikely that such unique SNPs evolved and gained dominance in a population within <50 y. Thus, these SNPs must have been present on the canoes of the New Zealand founding populations. They therefore provide a link to the immediate origins of the first New Zealanders. With more sequence data from contemporaneous Polynesian voyagers, these mutations may allow us to retrace the last major human migration that ended on the shores of Aotearoa/New Zealand. Fig. 1. Map of the Pacific with statistical parsimony network of Pacific B4a1a haplotypes. Haplotypes are represented by ellipses. Two haplotypes are connected by a line if they are separated by one mutation; each additional mutation is indicated by a small black circle. The red line represents the separation of Polynesian motif on the right and other B4a1a haplotypes on the left. BOU, Bougainville; COK, Cook Islands; KAP, Kapingamarangi; MAD, Madagascar; MAR, Marshall Islands; PNG, Papua New Guinea; SAM, Samoa; TON, Tonga; TWN, Taiwan; TROB, Trobriand Islands; VAN, Vanuatu; WB, Wairau Bar. A particularly interesting SNP was identified in one of the Wairau Bar burials. Position 4917 in burial 2.1 was covered by five reads, all of which were consistent and indicate a G rather than the A typically found in the B4a1a1a haplotype. This mutation cannot be explained by deamination damage. While 4917G is a defining mutation for mitochondrial haplogroup T2b—the DNA used as bait in the hybridization enrichment of the Wairau Bar samples—given the virtual absence of any other bait contamination in any of the Wairau Bar samples, we assert that this is a genuine mutation in burial 2.1 (Table S3). This mutation is reported to be associated with insulin resistance (26). Type 2 diabetes (T2D) is a disease found at very high frequency in Maori and other Polynesian populations (27), and at least one other mtDNA mutation, which is a defining mutation for macrohaplogroup B (16189C) has also been associated with T2D in Asian populations (28). Interestingly, the recent analysis of mtDNA variation in modern Maori (15) did not report the 4917G variant, although their sample came from a single tribal group. It would therefore be particularly interesting to undertake further complete mtDNA genome sequencing of samples from Maori and other Polynesian populations to investigate the frequency of this mutation throughout Polynesia and to further assess its possible association with T2D and other metabolic disorders affecting Polynesians. In addition to having the mutations associated with insulin resistance, burial 2.1 showed skeletal evidence indicating that he also suffered from gout (16), another disease in the suite of metabolic disorders affecting modern Polynesians at remarkably high rates (29). These complete ancient mitochondrial genomes obtained from the first New Zealanders are exciting for a number of reasons. First, the preservation conditions for aDNA in the Pacific region are generally poor, so recovery of reliable aDNA sequences, particularly for human remains, is rare. Our results indicate that the average length of DNA fragments obtained from the Wairau Bar burials was <70 bp and therefore below a reasonable fragment length for PCR amplification and Sanger sequencing (30, 31). The application of next generation sequencing technology and hybridization capture as demonstrated here, however, may mean that Pacific samples previously analyzed using older protocols for which reliable results could not be obtained might yield results in the future. We were very pleased to find that, despite storage and handling conditions that were far from ideal with regard to aDNA preservation and contamination, reasonable-quality DNA could be recovered from 700-y-old samples stored and studied in a museum context. More importantly, the consistency of haplotype-determining SNPs across the respective mitochondrial genomes or genome fragments suggests that each individual sequence derived from a single biological source of Polynesian ancestry. At least three of the four burials differed from each other, suggesting that the sequence data are authentic and that contamination was minimal to nonexistent; thus, the pre-extraction decontamination treatments applied to the Wairau Bar samples and our specific laboratory protocols to avoid contamination were successful. This finding has implications for future aDNA studies of museum samples should those be requested by recognized descendant groups or by museums—for example, as part of repatriation projects. Most importantly, the degree of variation seen in this small, colonizing population from Wairau Bar was beyond what we might have expected based on previous analyses of variation within the HVR of the mtDNA in Maori (8). The settlement of the Pacific generally and East Polynesia specifically has been described as being the result of a series of successive bottleneck events. As a result, despite limited sampling in East Polynesia to support such a hypothesis, it has been suggested that little to no mtDNA variation would exist in the region—particularly in New Zealand, the last island group to be settled (9). Our results indicate that there was likely to be significant mtDNA variation within the founding population of Aotearoa/New Zealand, even if that variation may be within the B4a1a1a haplogroup. These first complete ancient mitochondrial genomes from Polynesia indicate that further complete mitochondrial genome sequencing from both modern and, where possible, ancient Polynesian populations will be valuable for testing current models of the settlement of Polynesia, which, we suggest, may require reassessment. We have now identified key mtDNA mutations in the founding populations that should allow us to locate the immediate origins of New Zealand Maori and better understand the history of disease susceptibility in Polynesian populations. These findings can perhaps even provide insight into the social and political structure of the founding communities of Aotearoa/New Zealand and of East Polynesia more generally.
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Post by Admin on Jul 2, 2022 1:06:20 GMT
Ms. Alyssa Taitano talks about her experience as a young scientist and CHamoru woman participating in the Micronesian ancient DNA project published July 1, 2022. Credit: Rosalind Hunter-Anderson, Ph.D., National Geographic Society grantee "It's an unexpected gift to be able to learn about cultural patterns from genetic data," said David Reich, a professor in the Department of Human Evolutionary Biology and a professor of genetics at Harvard Medical School. "Today, traditional communities in the Pacific have both patrilocal and matrilocal population structures and there was a debate about what the common practice was in the ancestral populations. These results suggest that in the earliest seafarers, matrilocality was the rule. The genetic analysis compared early seafarers from Guam, Vanuatu, and Tonga—living about 2500 to 3,000 years ago—revealing that their mitochondrial DNA sequences, which humans only inherit from their biological mother, differed almost completely while sharing much more of the rest of their DNA. The only way this can happen is if migrants who left their communities to marry into new ones were almost always males. "Females certainly moved to new islands, but when they did so they were part of joint movements of both females and males" explains Reich. "This pattern of leaving the community must have been nearly unique to males in order to explain why genetic differentiation is so much higher in mitochondrial DNA than in the rest of the genome." The new study from an interdisciplinary team of geneticists and archeologists quintuples the body of ancient DNA data from the vast Pacific region called Remote Oceania, the last habitable place on earth to be peopled. It also provides surprising insights into the extraordinarily complex peopling of one of Remote Oceania's major subregions. Humans arrived and spread through Australia, New Guinea, the Bismarck Archipelago, and the Solomon Islands beginning 50,000 years ago, but it wasn't until after 3,500 years ago that humans began living in Remote Oceania for the first time after developing the technology to cross open water in unique long-distance canoes. This expansion included the region called Micronesia: about two thousand small islands north of the Equator including Guam, the Marshall Islands, the Caroline Islands, Palau, and the Northern Mariana Islands. It's long been a mystery what the routes people took to arrive in the region. The revealing of five streams of migration into Micronesia helps bring clarity to this mystery and the origins of the people there today. "These migrations we document with ancient DNA are the key events shaping this region's unique history," said Liu, a post-doctoral fellow in Reich's lab and the study's lead author. "Some of the findings were very surprising." Of the five detected migrations, three were from East Asia, one from Polynesia, and a Papuan ancestry coming from the northern fringes of mainland New Guinea. The indigenous ancestry from New Guinea was a major surprise as a different stream of this migration—one from New Britain, an island chain to the east of New Guinea —was the source of the Papuan ancestry in the southwest Pacific and in Central Micronesia. The researchers also found that present-day Indigenous people of the Mariana Islands in Micronesia, including Guam and Saipan, derive nearly all their pre-European-contact ancestry from two of the East Asian-associated migrations the researchers detected. It makes them the "only people of the open Pacific who lack ancestry from the New Guinea region," Liu said. The researchers consulted with several Indigenous communities in Micronesia for the study. This is the fourth publication of original ancient DNA data from remote Pacific islands by Reich's group. "It's important that when we do ancient DNA work, we don't just write a paper about the population history of a region and then move on," Reich said. "Each paper raises as many new questions as it answers, and this requires long term commitment to follow up the initial findings. In the Pacific islands there are so many open questions, so many surprises still to be discovered." Explore further Ancient DNA sheds light on the peopling of the Mariana Islands More information: Yue-Chen Liu et al, Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers, Science (2022). DOI: 10.1126/science.abm6536. www.science.org/doi/10.1126/science.abm6536Journal information: Science
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Post by Admin on Jul 2, 2022 18:01:14 GMT
Modern humans arrived in Near Oceania at least 47,000 years before present (BP) and spread through Australia, New Guinea, the Bismarck Archipelago, and the Solomon Islands (1, 2). After 3500 to 3300 BP, humans expanded into previously unoccupied Remote Oceania (Fig. 1A). Fig. 1. Map and PCA. (A) Map showing five inferred streams of migration into Micronesia. (B) PCA results. Axes are computed with Dai, Nasioi, and Papuans; others are projected. In the southwest Pacific, the earliest archaeological sites are associated with artifacts of the Lapita complex, appearing in the Bismarck Archipelago as early as ~3350 BP and reaching the unoccupied islands of Remote Oceania by 3000 to 2850 BP (3, 4). Ancient DNA from 11 individuals from Vanuatu and Tonga 3000 to 2500 BP indicates that these pioneers were related distantly to Neolithic southeastern Chinese (5), more closely related to Neolithic and Iron Age people of Taiwan (6), and most closely related to the ancestors of present-day north-central Philippine groups such as Kankanaey Igorot (7–10). However, the primary ancestry of many southwest Pacific Islanders today is “Papuan” (our term to describe the primary ancestry of peoples of New Guinea, the Bismarck Archipelago, and the Solomon Islands), which genetic data has shown is due to a secondary expansion that began ~2500 BP (7–10). The first people to reach the Mariana Archipelago arrived around 3500 to 3200 BP (11–14). Their material culture (15) differed markedly from the Lapita assemblages in the southwest Pacific, with Marianas Redware ceramics being more similar to those found at sites in the Philippines and at the northern tip of Sulawesi (16). This study uses a revised chronology for the archaeology of the Mariana Islands that terms the earliest three periods of occupation from 3500 to 1600 BP “Unai” (table S1). The burials that we analyze date to 2800 to 2200 BP (Middle to Late Unai) and thus may not reflect the ancestry profile of Early Unai inhabitants. After 1100 BP, distinctive megaliths (latte) began to appear in the Mariana Islands, along with other material cultural changes marking the “Latte” period. The oldest evidence of human occupation in Palau in Western Micronesia dates to ~3000 BP (17). The oldest evidence in Central Micronesia is ~2000 BP; ceramics at these sites are similar to late Lapita pottery and shell artifacts and thus could reflect roots in earlier Lapita cultures in either northern New Guinea or in the southwest Pacific (18, 19). Linguistic relationships among Malayo-Polynesian (MP) languages that comprise all Austronesian languages outside of Taiwan provide an independent source of information about the cultural and geographic origins of Micronesian peoples (fig. S1). The CHamoru (20) language spoken by the indigenous people of the Mariana Islands is a first-order branch within MP; Palauan is another. All other Micronesian languages and languages of the southwest Pacific and Polynesia comprise a third major branch, Central-Eastern Malayo-Polynesian (CEMP) (21–23). Most Micronesian CEMP languages form a Nuclear Micronesian subgroup, which has been hypothesized to have developed somewhere between the Admiralty Islands and Vanuatu and to have spread near the end of the Lapita period ~2500 BP (24). By contrast, Yap’s language is believed to be an early offshoot of Proto-Oceanic derived directly from proto-languages that branched during the Lapita expansion, although Yapese was also subsequently affected by borrowings from other languages (25). The people of Kapingamarangi and Nukuoro atolls in the Caroline Islands speak Polynesian languages, suggesting replacement of the original languages by Polynesian immigration (26, 27). To test alternative models of population history, we generated genome-wide ancient DNA data for 164 individuals from five archaeological sites and coanalyzed them with published data from two ~2200 BP individuals from Guam (28). A total of 109 individuals (2800 to 300 BP) were from the Unai and Latte periods in Guam, 46 (600 to 200 BP) from the Latte period in Saipan, and 11 (500 to 300 BP) from Na Island and the nearby Nan Madol site in Pohnpei’s protected lagoon in Central Micronesia (20). We prepared samples in clean rooms, extracted DNA, built sequencing libraries, enriched for a common panel of ~1.2 million single-nucleotide polymorphisms (SNPs), and sequenced them (20). For individuals with evidence of high contamination, we restricted analysis to sequences with evidence of characteristic ancient DNA damage (20). The analyzed individuals had a median of 558,971 SNPs with data (table S2). We also genotyped 112 present-day Micronesians mainly from Guam, Palau, Chuuk, and Pohnpei (tables S3 and S4). We obtained 31 direct radiocarbon dates, 30 of which were on the same samples we analyzed for DNA (tables S5 and S6). We coanalyzed our newly produced data with published data from 95 prehistoric individuals and 1642 present-day individuals from globally diverse populations (table S7).
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Post by Admin on Jul 2, 2022 21:02:45 GMT
Overview of population structure We carried out principal components analysis (PCA) (Fig. 1B and figs. S2 and S3) by computing axes using shotgun data of present-day Dai (southern China), Nasioi (Solomon Islands), and New Guineans (from the Eastern Highlands and Middle Sepik areas) and then projecting other individuals. The first principal component (PC) corresponds to the proportion of East Asian–associated ancestry, henceforth “First Remote Oceanian (FRO)” (PC1; lower on left, higher on right); the second PC differentiates Papuan ancestry from the Solomon Islands to New Guinea (PC2; up to down). The Unai, Latte, and Lapita individuals cluster with present-day people from the Philippines (Kankanaey) and Taiwan (Ami and Atayal) on the right, corresponding to high East Asian–associated ancestry. Two clines are visible. The first (dashed blue) links groups with high proportions of FRO ancestry to New Britain, Vanuatu, and Polynesia; the second (dashed gray) links to groups from New Guinea, the Admiralty Islands, Palau, and a genetically homogeneous group of Central Micronesians (Chuuk, Pohnpei, and prehistoric Pohnpei). This suggests admixture in variable proportions between FRO and Papuan ancestry from at least two different sources—more related to New Britain in the first case and New Guinea in the second. f3-statistics reveal patterns qualitatively similar to those shown in the PCA (fig. S4 and table S8). We also computed the symmetry statistic f4(X, Kankanaey Igorot; New Guinea Highlanders, Dai) to test which individuals had significant Papuan admixture (using Kankanaey as a baseline with no evidence of Papuan ancestry) (table S9). Unai and Latte individuals had little or no Papuan ancestry; except for four Latte individuals, we observed non-significant Z-tests based on the normally distributed score being |Z| < 3 standard errors from zero. Lapita individuals from Vanuatu and Tonga had a small, but nonzero, proportion of Papuan ancestry (0.4 to 4.4% and 3.3 to 7.7%, respectively) (7–10). Papuan admixture was present in all prehistoric and present-day individuals from Pohnpei (~27%) and all present-day people from Chuuk (~27%) and Palau (~38%). In modern CHamoru, the inferred Papuan ancestry is consistent with zero, making CHamoru the only genetically analyzed indigenous Remote Oceanian group without evidence of such ancestry. Unsupervised clustering using ADMIXTURE recapitulates the patterns in the PCA and differentiates the FRO components of First Remote Oceanians (we show K = 9 clusters in Fig. 2; see also figs. S5 to S8). Two clusters correspond to East Asian–associated ancestry, with a light gray component maximized in Lapita individuals and a dark gray component maximized in Mariana individuals. Pohnpei and Chuuk in Central Micronesia primarily have a light gray Lapita-associated component. Modern CHamoru of Guam is the population with the highest proportion of dark gray, suggesting local continuity. Palau and Central Micronesia only have the green Papuan-associated component maximized in New Guinea, without the orange-blue-green mixture characteristic of New Britain, the southwest Pacific, and Polynesia, suggesting previously undocumented Papuan spreads into Micronesia. Fig. 2. Clustering analysis. Unsupervised ADMIXTURE (K = 9 clusters). New data are in boldface.
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