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Post by Admin on Apr 4, 2022 22:03:00 GMT
Fig. 2. Schematic phylochronology of Y-chromosome haplogroup I2a1b-M423. For detailed branching at the tips, see SI Appendix, Fig. S15. The software qpAdm (38) summarizes f4-statistics (which are similar to D-statistics) in order to estimate the direction and magnitude of gene flow, or admixture, from one population to another. We modeled admixture fractions with qpAdm using the three major components demonstrated by ADMIXTURE; Steppe, “Anatolian Neolithic Farmer” (ANF), and “Western Hunter-Gatherer” (WHG) (SI Appendix, Fig. S6 and Dataset S1F). The LoN comprised ∼55% of their ancestry from the Steppe, 33% from ANF, and 12% from WHG, broadly similar to published BA samples from across Britain (13). The populations that contributed to the LoN population were likely admixtures of those three components. To identify more proximal sources for the LoN, we modeled various potential Early Neolithic versus Late Neolithic/EBA source populations (Table 2). The Orcadian BA samples could be plausibly modeled as ∼4 to 7% local Neolithic and ∼93 to 96% Scottish BBC populations, but also as 1 to 5% local Neolithic and ∼95 to 99% French BBC populations or ∼1% local Neolithic and ∼99% Danish BA populations. Despite the uncertainty indicated by the SEs, these results clearly imply very high levels of replacement of the Neolithic people by people related to continental BBC immigrants by the EBA, with only ∼5% assimilation at most of the local autosomal gene pool. However, by the time the descendants of the BBC immigrants reached Orkney, they appear to have lost their Beaker cultural affiliation, as reflected in the dearth of Beaker-associated material culture in Orkney (6).
Table 2. Putative BA and Neolithic ancestry of LoN MBA and Lop Ness EBA (13) samples modeled with qpAdm
Target Neolithic population Neolithic proportion Late Neolithic/BA population BA proportion SE P value LoN British Neolithic 0.039 Scotland BBC 0.961 0.032 0.079759 LoN Orkney Neolithic 0.038 Scotland BBC 0.962 0.031 0.080413 Lop Ness Orkney Neolithic 0.075 Scotland BBC 0.925 0.045 0.151044 LoN British Neolithic 0.005 France BBC 0.995 0.031 0.124343 LoN Orkney Neolithic 0.006 France BBC 0.994 0.031 0.124541 Lop Ness Orkney Neolithic 0.052 France BBC 0.948 0.046 0.066244 Lop Ness Orkney Neolithic 0.013 Denmark BA 0.987 0.032 0.284911
Only feasible and significant results are displayed. The strong apparent similarity between the Orkney MBA LoN samples and the southern France BBC samples is likely not due to common ancestry but possibly due to the higher levels of Neolithic assimilation in the latter (SI Appendix, Fig. S2B); the reason for the similarity with the Danish BA is unclear. Thus, the picture from the genome-wide analyses suggests a substantial replacement of the Orcadian population between the Late Neolithic and the BA, similar to that seen in mainland Britain (13). However, there are striking and unexpected differences between the patterns displayed by the uniparental marker systems, which can illuminate in more detail how this process took place.
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Post by Admin on Apr 5, 2022 17:22:06 GMT
Mitochondrial DNA Variation. Early Neolithic Orkney (n = 21) includes mitochondrial DNAs (mtDNAs) characteristic of the European Neolithic, suggesting predominantly settlement from the western Neolithic but with a minor contribution from the Danubian Neolithic (SI Appendix, Section S5). By contrast, the BA LoN suite of lineages (n = 20) is very different (Datasets S1G and S2). There are a number of minor H lineages, including H39 (four individuals), H58a, H+195, and two individuals with H1n1. There are also two with J1c2a, three with T2a1b1a—matching the EBA individual from Lop Ness (the only previously published BA Orkney sample) (13), two with T2b21, two with U5b2a3, one with K1a3a, one with K1a29a, and one with K1c2. Eight of these individuals (three of the H39 individuals, all three T2a1b individuals, one of the two U5b2a3 individuals, and the K1a3a individual) were part of a multiple burial, of which two were related (see below). The males from the multiple burial also all carried Y-chromosome haplogroup I2a1b-M423/I2a1b1-S185.
The age and geographic distribution of the clusters to which most of the BA LoN lineages belonged suggest that most of them were not inherited from the local Neolithic but arrived later. Many are associated in ancient DNA studies with continental Corded Ware Culture, BBC, or BA populations (SI Appendix, Section S5). For example, T2a1b1 is seen in the German Corded Ware, whereas T2b21 matches German and Czech BBC lineages. While H39 and K1c2 lineages have not been seen in published ancient DNA data, the modern lineages are restricted to northern Europe and date to ∼3000 BC and 2600 BC, respectively, again suggesting a source in the Corded Ware expansion across northern Europe at 2500 to 3000 BC. Several lineages, such as J1c2*, K1a3a, H1n1, H58a, and H+195, are harder to resolve, but their distribution is in each case consistent with a BBC arrival, although we cannot currently conclusively rule out a local Neolithic source. The IA KoS remains (n = 3) include two identical H1b lineages and one U5a1b1a, both of which can be attributed to either the BBC or the Corded Ware on the Continent.
The lineage most likely to date to before the Beaker Age in Orkney, seen in two LoN individuals, is U5b2a3 + 16319, which we name here U5b2a3b (Dataset S3). U5b2a3 dates to ∼8500 BC and is seen in Early Neolithic individuals from both Scotland (13) and Wales (39), and so the Orkney individuals represent potential continuity from the British Neolithic into the BA. Intriguingly, U5b2a3b is also seen in one modern individual from the British Isles (40), as well as an individual from Virginia, United States (founded as a British colony), indicating potential continuity through to the present day. Indeed, with U5b2a* found in Neolithic Orkney (32) and Scotland (13) and, notably, Mesolithic Ireland (41) and U5b2a3 itself also seen in Neolithic Ireland (41), along with the presence of U5b2 lineages in modern Orkney and Shetland (Dataset S2), it is possible that some U5b2 lineages, including U5b2a3b, may signal some of the most ancient lineages surviving in present-day Britain and Ireland, potentially even from the local Mesolithic.
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Post by Admin on Apr 5, 2022 19:23:21 GMT
Y-Chromosome Variation. There are 16 known Y-chromosome (Y-DNA) haplotypes from Neolithic Orkney, of which 14 appear to be well resolved (13, 32). All 14 belong to haplogroup I2a, of which seven are I2a1b-M423, four are I2a1b1-S185, one is I2a2-S33, one is I2a2a1b-CTS10057, and one is I2a2a1a2-Y3679 (the remaining two are poorly resolved I and I2). In BA LoN, even though the majority of genome-wide and female lineages most likely arrived in Britain and Orkney with the BBC or BA, all but one of the nine Y-DNA lineages belong to haplogroup I2a1b-M423, with just one belonging to R1b-M269 (SI Appendix, Section S6 and Dataset S1H). We found four distinct haplotypes within I2a1b: I2a1b-M423, I2a1b1-S185, and the more derived I2a1b1a1b-A1150 and I2a1b1a1b1-A8742. This predominance of I2a1b-M423 is surprising because it is completely absent elsewhere in CA/BA Europe, where the Y-DNA landscape is heavily dominated by R1b-M269 (Figs. 2–4 and SI Appendix, Figs. S13–S15). For example, in a dataset of 21 BBC males from Britain, 20 carry the R1b-M269 lineage and only one I2a, which is on the distinct I2a2a-M223 lineage. If we include CA and EBA Britain and Ireland, 41 out of 43 males carried R1b-M269, two I2a2a-M223, and none I2a1b-M423. Fig. 3. Distribution of Mesolithic and Neolithic Y-chromosome lineages, and their Bronze Age descendants. (A) Britain and Ireland with (B) zoom in on Orkney. Colors represent different Y-chromosome lineages, and distinct outlines represent the time period of the sample. Each circle represents one individual, except for Trumpington Meadows, Cambridgeshire (66), where two brothers are represented by a single circle. Maps prepared with GADM tools (https://gadm.org/data.html) (67) using data from SRTM (68).
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Post by Admin on Apr 5, 2022 21:57:39 GMT
Fig. 4. Distribution of prehistoric I2a1b-M423 Y-chromosome lineages in Europe. Each circle represents one individual carrying I2a1b. Map modified from Mapswire.com (https://mapswire.com/), which is licensed under CC BY 4.0. Thus, except for the single R1b-M269 lineage, all sampled LoN BA males carried a subset of the Neolithic Y-DNA pool. These are very unlikely to have been brought to Orkney by BBC or BA migrants from further south in Britain. Not only has I2a1b-M423 not been seen in the European BBC or BA, but it was a minority lineage even during the European Neolithic. Among 389 published male genomes from the European Neolithic, only 12% (47 of them) carry I2a1b-M423, of which 40% (19/47) are from Britain or Ireland (42), and most of those in Britain are from Orkney (Figs. 3 and 4). Even in Britain and Ireland, outside of Orkney most Neolithic Y-DNA lineages belong to haplogroup I2a2-S33 or I2a2a-M223 (Fig. 3), although, curiously, our Neolithic individual from Skye belongs to the very rare I2a2b-S154, seen elsewhere only in Middle Neolithic France (43). I2a1b-M423 seems to be largely restricted to western Neolithic Britain and Ireland, where it occurs rarely alongside I2a2a-M223, as well as I2a1a-CTS595 (41), which has not yet been found in Neolithic Britain. This perhaps suggests a relict distribution, shared by Orkney, Ireland, and western and northern Britain. A consequence is that not only was the assimilation of Neolithic male lineages very rare during the BBC spread in Britain, but assimilation of I2a1b-M423, which formed a small minority of Neolithic British mainland lineages, must have been even rarer, if it ever happened at all. We conclude that the I2a1b-M423 lineages at BA LoN had most likely persisted from the local Orcadian Neolithic and were not contributed to this population by mainland British Neolithic groups. By contrast, the two sampled males at the IA KoS site, also on Westray, belonged to the R1b-M269 lineage. I2a1b-M423 likely arrived in Orkney with the first farmers. In the Neolithic, I2a1b-M423 was largely distributed in an arc around the Atlantic façade of Europe, from the western Mediterranean to the Baltic. Outside Britain, most I2a1b-M423 lineages are from Middle/Late Neolithic Spain and France, with one from Germany and a small number from Sweden, where, at a megalithic site on Gotland, all four genotyped males belonged to I2a1b-M423 (Fig. 4) (32). It is also present in several hunter-gatherers in northern and central Europe, including Mesolithic Ireland. This distribution, the molecular-clock age of the two major subclades (I2a1b1-S185 and I2a1b2-S392 both date to ∼7 ka) (YFull YTree version 8.06.01, 27 June 2020; www.yfull.com/tree/), and evidence that the ancestral lineage survives today only in Iberia (YFull tree) suggest assimilation from hunter-gatherers during the spread of the Neolithic into southwest Europe, followed by Neolithic dispersal into northwest and northern Europe, although some further assimilation in northern Europe is also possible.
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Post by Admin on Apr 6, 2022 18:23:07 GMT
Runs of Homozygosity and Kinship. We assessed runs of homozygosity (ROH) using the program hapROH (44). ROH profiles of BA LoN samples indicate a small effective population size but give no evidence for recent consanguinity, up to third cousin unions (SI Appendix, Fig. S7). HapROH estimated the effective population size to be ∼400. This is a large decrease from Neolithic Orkney and also much lower than elsewhere in Neolithic, BBC, or BA Britain and northwest Europe (SI Appendix, Table S2). These results suggest a small, endogamous population.
We estimated kinship using Relationship Estimation from Ancient DNA (READ) software (45), coupled with uniparental markers and the age-at-death osteoarchaeological profile. The READ analysis identified almost no evidence for close kinship. Even among the seven individuals in the multiple inhumation who passed the criteria for DNA analysis (out of 11), the only first- or second-degree relationship involved two full siblings: a brother and sister, where the former died in adolescence and the latter soon after birth. The siblings shared an identical, rare mtDNA haplotype (within H39), and the male carried the most common Y-DNA haplotype at the cemetery (I2a1b1-S185). An infant from outside of the multiple burial carried a slightly distinct lineage of mtDNA H39, but we could find no evidence of close kinship using READ (SI Appendix, Fig. S8A).
The low Y-DNA diversity and multiple sharing of rare mtDNA haplotypes both suggest a small, close-knit community, notwithstanding the relatively recent arrival (within the previous millennium) of most of the mtDNAs from overseas. However, the most significant signal remains the contrast between the autochthonous male lineages versus higher-diversity nonlocal female lineages, pointing to ongoing patrilocal marriage patterns, not only in the BA but, by inference from the persistence of I2a1b-M423, at the end of the Neolithic too. We note that although the contrast between the largely indigenous Y-DNA and the largely continental mtDNA and autosomal fraction is very striking, a level of ∼95% continental genome-wide ancestry could be achieved by the marrying out of indigenous men with immigrant women in only five generations, or 100 to 150 y, which the results suggest were followed by isolation and endogamy (SI Appendix, Section S3.10).
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