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Major trends and growth projections by region and countryKey winning strategies followed by the competitorsWho are the key competitors in this industry?What shall be the potential of this industry over the forecast tenure?What are the factors propelling the demand for theDigital Genome Market ?What are the opportunities that shall aid in significant proliferation of the market growth?What are the regional and country wise regulations that shall either hamper or boost the demand for Digital Genome Market?How has the covid-19 impacted the growth of the market?Has the supply chain disruption caused changes in the entire value chain?

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Global Digital Genome Market Set for Rapid Growth, to reach Value around $29.1 Billion by 2025 | Exclusive Report by Esticast Research The Grundy...

image:Figure 1: The three ancient populations that form the contemporary European gene pool, with the addition of Siberian (peculiar to the Estonian genomes analysed in this study) are represented here along with the inferred contribution (increase, decrease or nothing) they made to a number of body and health traits in present day individuals. For eye and hair colour, symbols point to the shade most likely contributed by a given ancestry. view more

Credit: Davide Marnetto

A study recently published in Current Biology described the impact of ancient migrations on some complex traits (physiology and appearance) of contemporary Europeans. The study was led by Dr. Davide Marnetto from the Institute of Genomics of the University of Tartu, Estonia and University of Turin, Italy and Prof. Luca Pagani from the University of Padova, Italy.

Background

Most of the contemporary European genetic makeup was shaped by movements that occurred in the last 10,000 years when local European Hunter-Gatherers mixed with incoming Anatolian Neolithic farmers and Pontic Steppe pastoralists. These populations were separated for thousands of years and evolved in different directions. Following this encounter, their DNA, or genome, came in contact and genetic variants characterising each of them intermixed.

What is novel

Previous studies, relying on the information contained in ancient genomes, described some biological traits of these source populations, elucidating the origins and the natural selection forces acting on traits like lactase persistence, height, and skin, eye or hair pigmentation. With our study, instead, we asked how the physiology and appearance of contemporary Europeans are influenced by these ancient footprints that are still embedded in their genomes, said Dr. Marnetto, first author of the study.

What has been done

As a case study, we used the Estonian population, which also displays some genetic components frequent in present-day Siberian populations, because of the rich data provided by the Estonian Biobank, where we could find the genome and trait characterization for more than 50,000 samples. We specifically measured whether having a certain feature, e.g. high cholesterol, is coupled with having inherited more variants from a specific ancestry, exactly in those DNA regions influencing cholesterol levels, continues Marnetto.

What the results say

Our results show that the ancient populations that formed contemporary Europeans were differentiated enough to contribute their own signature to the physiology and appearance of contemporary individuals, says Prof. Luca Pagani, senior author of the study. For example, Steppe ancestry seems to have contributed to a strong build, with tall stature and increased hip and waist circumferences, but also to higher blood cholesterol, which on the other hand tends to be lower in individuals carrying Hunter-Gatherer ancestry at specific genes. The latter seems also linked with higher body mass index (BMI), among others. The best connections made for the Anatolian ancestry are instead a reduced (BMI-corrected) waist-hip ratio and lower heart rate.We also find substantial differences in ancestry or evidence for recent natural selection in eye and hair pigmentation, body caffeine intake, age at menarche and sleep patterns.

What the results do not say

Importantly, we drew our conclusions relying on specific parts of the genome, while using the rest of the genome as control, to observe subtle effects by contrast. This means that it is misleading and naive at best to use any given trait to guess the dominant ancestry across ones genome, says Prof. Mait Metspalu, co-author of the study. He follows up by reminding that to give a biological outcome, it does not just matter how much of a certain ancestry one has in their genome, rather where and which genes this ancestry contributed, even for complex traits encoded by many genes. Metspalu also emphasises that for the same reason it is simplistic to interpret trait patterns across Europe only as the abundance of one ancestry or the other without considering environment and other evolutionary forces. Furthermore, it is important to remark that the link we made between a given trait and a given ancestry does not imply that such a trait was predominant in a particular ancient population or absent in all other groups.

The authors conclude by pointing out that their focus on the Estonian and ultimately European population is connected with the sheer amount of data available, in contrast with the dramatic underrepresentation of other ethnicities in genetic studies.There is absolutely no evidence indicating that Europe encompasses higher genetic diversity and more complex heritage than other continents: an increased coverage of samples from across the world is crucial to enhance our understanding on how past human history shaped the trait variability displayed by contemporary individuals said Marnetto.

Experimental study

Not applicable

Ancestral contributions to contemporary European complex traits

8-Feb-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Excerpt from:
Ancient mixing of ancestries shaped present-day European body and health traits - EurekAlert

This article was originally published here

PLoS One. 2022 Feb 7;17(2):e0263606. doi: 10.1371/journal.pone.0263606. eCollection 2022.

ABSTRACT

Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system with genetics and environmental determinants. Studies focused on the neurogenetics of MS showed that mitochondrial DNA (mtDNA) mutations that can ultimately lead to mitochondrial dysfunction, alter brain energy metabolism and cause neurodegeneration. We analyzed the whole mitochondrial genome using next-generation sequencing (NGS) from 47 Saudi individuals, 23 patients with relapsing-remitting MS and 24 healthy controls to identify mtDNA disease-related mutations/variants. A large number of variants were detected in the D-loop and coding genes of mtDNA. While distinct unique variants were only present in patients or only occur in controls, a number of common variants were shared among the two groups. The prevalence of some common variants differed significantly between patients and controls, thus could be implicated in susceptibility to MS. Of the unique variants only present in the patients, 34 were missense mutations, located in different mtDNA-encoded genes. Seven of these mutations were not previously reported in MS, and predicted to be deleterious with considerable impacts on the functions and structures of encoded-proteins and may play a role in the pathogenesis of MS. These include two heteroplasmic mutations namely 10237T>C in MT-ND3 gene and 15884G>C in MT-CYB gene; and three homoplasmic mutations namely 9288A>G in MT-CO3 gene, 14484T>C in MT-ND6 gene, 15431G>A in MT-CYB gene, 8490T>C in MT-ATP8 gene and 5437C>T in MT-ND2 gene. Notably some patients harboured multiple mutations while other patients carried the same mutations. This study is the first to sequence the entire mitochondrial genome in MS patients in an Arab population. Our results expanded the mutational spectrum of mtDNA variants in MS and highlighted the efficiency of NGS in population-specific mtDNA variant discovery. Further investigations in a larger cohort are warranted to confirm the role of mtDNA MS.

PMID:35130313 | DOI:10.1371/journal.pone.0263606

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Next-generation sequencing of the whole mitochondrial genome identifies functionally deleterious mutations in patients with multiple sclerosis -...

Significance

The Orcadian Neolithic has been intensively studied and celebrated as a major center of cultural innovation, whereas the Bronze Age is less well known and often regarded as a time of stagnation and insularity. Here, we analyze ancient genomes from the Orcadian Bronze Age in the context of the variation in Neolithic Orkney and Bronze Age Europe. We find clear evidence for Early Bronze Age immigration into Orkney, but with an extraordinary pattern: continuity from the Neolithic on the male line of descent but immigration from continental Europe on the female side, echoed in the genome-wide picture. This suggests that despite substantial immigration, indigenous male lineages persisted for at least a thousand years after the end of the Neolithic.

Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From 3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By 2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.

Benefiting from the tail end of the Holocene climatic optimum, the British Early Neolithic spread rapidly through Britain and Ireland from the south over 300 to 400 y from 4050 BC (13). The settlers brought with them domesticated wheat, barley, sheep, and cattle, as well as knowledge of carinated bowl ceramics and causewayed enclosures (15), pointing to a likely source in northern France or Belgium.

The Orkney Islands, lying to the north of the Scottish mainland, flourished during the Neolithic (3800 to 2500 BC), becoming a major cultural center (69). Underpinned by a successful farming economy and long-range contacts, the earliest permanent settlements were constructed in wood, followed by stone-built dwellings from 3300 cal. (calibrated) BC onward (9, 10). The use of stone appears to have been a conscious design choice (9, 11, 12) and has resulted in an extraordinary level of archaeological preservation.

While recent genome-wide studies (13) have demonstrated the extent and tempo of continental migration into Britain during the Beaker period, after 2500 BC, there has so far been little or no recognition of the archaeological implications of this for Orkney. The paucity of Beakers and associated material culture in the archaeological record has been taken as an indication that the cultural and population shifts occurring elsewhere in Britain at this time had little direct impact in Orkney (8, 1418) and indeed may have been locally resisted (6). As a result, Orkney has been seen to have developed along a largely insular trajectory during the second millennium BC.

Significant changes in funerary practice did begin to emerge at this time, and research has concentrated on funerary remains. Barrow cemeteries, some of the largest in northern Britain, appeared in Orkney around the end of the third millennium BC. These earthen mounds contained multiple burials, added sequentially and most frequently comprising cremated remains in pits or stone-lined cists (18). Flat cist cemeteries were also in use for both inhumation and cremation burials, and often graves contained the remains of several individuals, but grave goods were infrequent.

Until recently, the low visibility of settlement sites had led to the idea that this was a period of environmental and cultural recession (19). The balance has begun to be redressed through focused environmental analyses (20) and reports on settlements such as at Crossiecrown (9) and Tofts Ness (21). Opportunities to correlate settlement and funerary remains are very rare, and few sites extend across the Neolithic and Bronze Age (BA) periods, making it difficult to draw a coherent picture of change over time. In this respect, the ongoing investigations at the Links of Noltland (LoN) are providing valuable new insights.

The LoN is located on Westray, the northwesterly most island of the Orkney archipelago. The exceptional conditions have preserved extensive settlement and cemetery remains dating from at least 3300 cal. BC up to about 500 BC (2225). While no direct overlap has yet been detected between Neolithic and BA phases of settlement, there is no evidence for a major hiatus in occupation. The BA settlement, distinguished on architectural grounds and dating from 2500 to 1200 cal. BC, includes three separate conglomerations of domestic and ancillary buildings, which, like their Neolithic counterparts, were spread across a contemporary farmed landscape. Built from a mix of stone and earthen banks, often arranged in pairs, they were in use until at least 1200 cal. BC. A cemetery located among these settlements, used between at least 2150 BC and 850 BC, comprised >50 burials, including >100 individuals. Both cremation and inhumation were practiced, at times contemporaneously, and multiple burials within a single grave were common. Material evidence of the Beaker complex, seen across mainland Britain, is scant in Orkney; a few sherds from two Beaker vessels were recovered from the wider area (19), dated to 2265 to1975 cal. BC, but no further pottery or recognizable artifacts have been found in association with the cemetery or settlement.

The study of ancient genomes has shown that across much of Europe, including mainland Britain, the arrival of Metal Age culture was accompanied by the introduction of new ancestry from the Pontic-Caspian Steppe and a predominance of Y-chromosomal haplogroup R1b-M269 (13, 2631). We investigated genomic variation in the Orkney archipelago within the context of this framework. Genome-wide SNP (singlenucleotide polymorphism) capture and shotgun data were available from 21 Early Neolithic Orcadians (13, 32), but only one from the BA (13). To investigate BA Orkney, we generated whole-genome shotgun sequence data from 22 samples from the LoN cemetery and analyzed them alongside these published data. We also included new data from three Iron Age (IA) samples from the multiperiod ritual complex and cemetery site of Knowe of Skea (KoS), on the west coast of Westray, and 12 further prehistoric samples from Scotland and northern England.

We present shotgun genome data from 29 samples from prehistoric Scotland and eight from northern England: 22 from the BA LoN in Westray, Orkney, dating to 1400 to 1700 BC (LoN); three from the IA KoS in Westray, Orkney, dating to the first two centuries AD; one from IA Milla Skerra (MS), Unst, Shetland; one from IA High Pasture Cave (HPC), Isle of Skye in the Hebrides (33); one from Neolithic Strath Glebe (SG), also Skye; a Pictish sample from Rosemarkie Cave (RC), Black Isle in northern Scotland, dating to 430 to 630 AD; a Beaker burial sample from Low Hauxley (LH), Northumberland; three BA samples from West Heslerton (WH), North Yorkshire; two IA samples from Knapton Wold (KW), North Yorkshire; and two IA samples from Carsington Pasture Cave (CPC), Derbyshire. Whole-genome coverage varied greatly from 0.0007 to 0.8207. We undertook genome-wide analysis on samples above 0.009, with samples averaging 0.194. All samples passed contamination tests (Table 1, SI Appendix, Table S1, Dataset S1 A and B, and SI Appendix, Fig. S1). We analyzed these in the context of genome data from Early Neolithic Orkney (n = 21) (13, 32) and Neolithic, Chalcolithic (CA), and BA Europe and 1,856 new mitogenomes from modern Orkney (n = 1,356) and Shetland (n = 500) (Datasets S1C and S2).

Summary of ancient samples reported in this study

ADMIXTURE analysis (Fig. 1A) showed that the samples from BA Orkney closely resembled other northern European BA people in their overall genome-wide profiles and were highly distinct from Neolithic Orkney samples, which resembled more our Neolithic sample from Skye and other British and Irish Neolithic samples. Neolithic samples all lacked the CHG (Caucasus hunter-gatherer) component (in blue) that most clearly signals admixture from Pontic-Caspian Steppe pastoralists (34). The CHG fraction in Orkney (both BA and IA) is somewhat higher (40%) than in other Scottish CA and EBA (Early Bronze Age) samples but within the wide range of values for England (Fig. 1A and SI Appendix, Fig. S2A). Modern Orcadians have an even higher fraction of the CHG component, reflecting medieval Norse settlement, estimated from modern genome-wide surveys at 20 to 25% (35) and 25 to 30% of modern Y chromosomes (36, 37). Geographical and chronological trends are portrayed more clearly in the PCA (principal component analysis) (Fig. 1B and SI Appendix, Fig. S3). LoN BA samples broadly clustered with northern and central European Bell Beaker, CA, and BA samples, and KoS IA samples fell within the same broad cluster.

Visualization of Orkney genome-wide data in context. (A) Unsupervised ADMIXTURE plot (K = 7) of European Mesolithic, Neolithic, BA, and IA samples. The red component maximizes in the WHG, green in the ANF, and blue in the CHG; profiles to the right of each label are from the same population. (B) PCA showing first two principal components of European Mesolithic, Neolithic, and BA samples, projected on present-day European variation. The figure shows a zoom-in of the full plot (SI Appendix, Fig. S3), excluding outlier Yamnaya and Mesolithic samples. LBK, Linearbandkeramik.

(C) Map displaying outgroup-f3 statistics for the LoN samples, showing the close relationship with Bell Beaker and BA samples from the British and Irish mainland and northwestern continental Europe.

D-statistics quantify shared genetic drift among genomes and can thus also be used to estimate the degree of similarity among individuals. We calculated symmetry D-statistics by comparing potential outlier samples (as noted in the ADMIXTURE analysis) to the rest of the LoN using the form D(Mbuti, Test; Potential Outlier, LoN). The LoN samples consistently formed a clade, indicating that they were statistically indistinguishable from each other (SI Appendix, Fig. S4A and Dataset S1D). With D-statistics of the form D(Mbuti, LoN; European BA, European BA), after closest matches to the slightly older published Lop Ness BA sample from Sanday, Orkney, the most common significant similarities were with British Bell Beaker complex (BBC) samples, the Scottish BA, and Orkney KoS IA, as well as to a few continental individuals such as French BBC and the Dutch BA (SI Appendix, Fig. S4B and Dataset S1E). Outgroup-f3 statistics showed a similar pattern, with LoN closest to eastern British, Welsh, Irish, and northwest European BBC and BA samples, albeit with overlapping errors across European BBC and BA samples (Fig. 1C and SI Appendix, Fig. S5A). This indicates that the Orkney BA was most likely settled via the British mainland (possibly the eastern side) by people who arrived in Britain during the Beaker period.

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).

Putative BA and Neolithic ancestry of LoN MBA and Lop Ness EBA (13) samples modeled with qpAdm

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.

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 T2a1b1amatching 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.

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. 24 and SI Appendix, Figs. S13S15). 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.

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).

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 faade 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; https://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.

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).

We have investigated genomic variation in BA and IA Orkney and compared it with the available evidence for the preceding Orcadian Neolithic, in the context of Mesolithic, Neolithic, BA, and IA variation from across Europe. Both the mtDNA and Y-DNA variation of Neolithic Orkney point to settlement primarily from the Mediterranean/Rhne/Atlantic dispersal route, via the British mainland, in line with genome-wide analyses for Neolithic Britain as a whole (13, 39). Although this process was largely one of colonization, we find some evidence for potential assimilation and survival of indigenous Mesolithic maternal lineages. The presence of an apparently ancient local branch of mtDNA haplogroup U5b complements genome-wide observations of hunter-gatherer assimilation in western Scotland (39) and Ireland (41).

This study confirms that the drastic shift in the British population in the BA, evident in both the genome-wide (13) and mtDNA patterns, also occurred in Orkney. Orkney was largely resettled from the British mainland by people of substantially recent continental ancestry. Although this demographic shift may have taken place over centuries, it was likely sustained relatively unchanged into the IA; although we have analyzed only three IA samples, they all show a similar pattern.

Unexpectedly, despite this wave of immigration, local Neolithic male lineages persisted well into the BA, at least in Westray. While we do see evidence for male newcomers, in the presence of a single R1b-M269 Y-DNA lineage (in an infant burial), the other males all carry the indigenous I2a1b-M423 lineage. This lineage survived in a single fifth or sixth century Pictish sample from Birsay, northwest Mainland (46), but is only seen in a single family (among 407 males tested) in Orkney today.

The I2a1b-M423 lineage almost vanished elsewhere in western Europe after the end of the Neolithic. None are seen in post-Neolithic European archaeological remains. It is seen at only 1% in modern Britain and is almost absent in most of modern western Europe, although one recent subclade of I2a1b2-S392 has undergone dramatic expansion with Slavic populations in the Balkans (Figs. 24 and SI Appendix, Fig. S13) (47).

A possible explanation can be found in the continuity, stability, and self-sufficiency of farming settlements, such as LoN. These successful household groups, while undoubtedly participating in an Orkney-wide Neolithic society, also developed strong local identities, manifested in locally variant art styles, material culture, architecture, and ritual activity. They may, for example, have pursued their own long-range contacts, as suggested, for example, by the importation of aurochs and local tomb art, distinctive within Orkney and most directly comparable with that found at Br na Binne in Ireland, where patrilineal descent has recently also been inferred from genetic data (41). From a position of strength during the Neolithic, such settlements may have been better placed to mediate inward migration and to make specific choices with regards to the management of lineage.

We propose that we may be seeing the surviving remnants of well-established Neolithic household groups in BA Orkney: a number of distinct male lineages that have persisted when almost the whole of the rest of the population (and genome) has been replaced. While the archaeological signs of these groups may not have been especially ostentatious, the persistence of their lineages for at least a thousand years beyond the point when the vast majority of male lineages elsewhere in Britain were replaced by newcomers might imply a more protracted and perhaps more negotiated process of assimilation than elsewhere, as well as pointing to much less insularity than has often been assumed for the Orcadian BA (25).

There are several caveats to this suggestion. Firstly, we are describing the situation in one of the most remote parts of the Orkney archipelago and at a particular moment in time. It is a snapshot and may not be representative of Orkney as a whole. While the single Lop Ness sample (from another island in the archipelago) confirms the overall pattern of continental immigration, the individual is female and therefore provides no information on the male lineage. Further investigations can help to fill out the picture.

Secondly, there are numerous cremation burials at the site for which DNA analysis cannot be carried out. Is it possible that newcomer R1b-M269 males were mostly cremated? This seems unlikely; substantial numbers of BBC and EBA inhumation burials have been analyzed from England and Scotland, and the males carried almost exclusively R1b-M269 Y-DNA lineages. However, even if this were the case, the persistence in inhumations of the I2a1b-M423 lineage, in the face of an almost 95% replacement at the genome-wide (and probably also the mtDNA) level, remains extraordinary.

Within the European context, the Orkney BA stands in stark contrast as a location, at the northwestern extreme of the continent, where the majority of the genome was overwritten between the Late Neolithic and the end of the EBA but the male lineages somehow persisted. Even so, we can understand this phenomenon in terms of the same patrilocal marriage practices that we see throughout west Eurasia. The ancestral distribution in Orkney demonstrates deliberate marriage patterns involving local men and incoming women. This process of preferential assimilation seems likely to have continued for many generations, given the extent of replacement of the remainder of the Orcadian Neolithic genome.

The existence of a powerful and likely strongly hierarchical strand in Neolithic society has been proposed on the basis of the discovery of an incestuous first-degree union at Newgrange in Ireland (41) and was prefigured by earlier analyses of Ireland and other megalithic cultures in both northwest and central Europe (32, 48). Cassidy et al. (41) argue that it encompassed the whole of Ireland, adding that it may have incorporated the similar megalithic communities of Wales and Orkney, most likely originating in Brittany (1, 49). I2a1b-M423 is seen in both Mesolithic and Neolithic Ireland, and the main cluster seen in Late Neolithic Ireland, I2a2a1a1-M284found in the putative elite lineage at Newgrangematches an Orcadian Neolithic lineage from the Isbister Chambered Cairn (Tomb of the Eagles) on South Ronaldsay (Fig. 3 and SI Appendix, Fig. S13) (13). Both our data from BA Orkney and the Neolithic circumcoastal distribution of the Y-chromosome I2a1b-M423 haplogroup lend further support to this suggestion. European Neolithic society, at one extreme (but hardly peripheral) edge of its distribution, may have been patrilineal, patrilocal, and hierarchical long before the arrival of the Beaker complex and (most likely) Indo-European speech (27, 28, 31, 50).

Our data suggest that Neolithic lineages persisted within particular farming households, which, although not obviously elite, appear to have retained control of specific landholdings over many generations. This linkage of lineage with specific place is strongly suggestive of preferential inheritance along the male line. The continuity which this engendered is likely to have contributed significantly to the longevity of settlements between the third and first millennia BC. The indigenous male lineages remained in place while their people, their culture, their language, and even their genomes were transformed to resemble more and more those of the European mainland from which the newcomers had come.

Our findings both demonstrate EBA migration into Orkney and amplify the recognition that the expansion of the Beaker complex cannot be described by a simple one-to-one mapping of an archaeologically defined material culture to a genetically homogenous population (51). They also highlight that population influx may have occurred even where few archaeological traces have been identified. This prompts a critical reassessment of the origins of Orcadian BA practices, which have hitherto been viewed either as insular development, imitative of distant elites, or the result of gradual filtering-in of influences. The circumstances surrounding the emergence of novel monument types such as barrows and burnt mounds, for example, will need to be reconsidered.

If more widely borne out, these findings suggest that BA Orkney is likely to have seen regular and sustained migration, engaged in long-distance exchange networks, and adopted novel practices. The perseverance of Neolithic lineagesand, potentially, identitiesinto this period adds a further layer of cultural complexity, the implications of which remain to be fully explored.

We describe the archaeological samples and materials and methods fully in SI Appendix. Briefly, we extracted DNA from 37 samples using existing protocols (33, 52, 53). We constructed and UDG (uracilDNA glycosylase) treated next-generation sequencing libraries (42, 54, 55), pooled equimolarly, and sequenced all libraries on an Illumina HiSeq4000 (100-bp, paired-end sequencing; Macrogen). We trimmed sequence reads of adapter sequences and merged them using AdapterRemoval (version 2.1.7) (56). We mapped reads to the human reference genome (UCSC [University of California Santa Cruz] hg19) and the human mitochondrial reference genome (the revised Cambridge reference sequence or rCRS, NC_012920.1) (57) using BWA aln (BurrowsWheeler alignment tool) (version 0.7.12-r1039) (58) and filtered for mapping quality (56, 59). We examined molecular damage patterns to establish data authenticity and levels of mtDNA and whole-genome contamination. As expected from UDG-treated samples, observed damage patterns were minor (SI Appendix, Fig. S9). We carried out uniparental marker analysis and molecular sex determination (60) following established methods. We used GATK (version 3.8) to call pseudohaploid genotypes at known SNP positions, which were then merged with the Human Origins dataset (61), the 1000 Genomes Project data, and realigned published ancient samples (SI Appendix). We investigated population relationships between newly reported samples and other ancient and modern individuals using smartPCA and ADMIXTURE (version 1.3) (62), with D and f statistics calculated using ADMIXTOOLS (63) to formally confirm relationships, and quantified admixture using qpAdm (34). A list of published samples we used in analyses is in Dataset S1I. We inferred kinship relationships using READ (45) and assessed ROH and effective population size with hapROH (44). We describe construction of Y-chromosome phylochronology for I2a and R1b-M269 in SI Appendix, Section S6 and Figs. S10S16. We extracted the modern mitogenomes from the whole-genome Orkney Complex Disease Study (ORCADES) for Orkney (64) and the VIKING study for Shetland (65).

Raw sequencing reads of ancient samples produced for this study have been deposited in the European Nucleotide Archive under accession no. PRJEB46830. Modern mitochondrial genomes generated as part of this study have been deposited in GenBank, accession nos. MZ846240 to MZ848095.

We thank Steve Birch, Jenny Murray, and Sue Black for help with samples; Harald Ringbauer for advice on hapROH; and Joyce Richards for comments on an early draft. Excavations at LoN and KoS are directed by H.M. and G.W., EASE (Environment and Archaeology Services), grant funded by Historic Environment Scotland. M. Ni Challanain, M. McCormick, and D. Gooney undertook osteological identifications and sample selection. K.D., M.G.B.F, P.J., M.S., G.O.-G, A.F., and S.R. were supported by a Leverhulme Trust Doctoral Scholarship program awarded to M.B.R. and M.P. DNA sequencing was also supported by the UK Natural Environment Research Council Biomolecular Analysis Facility (NBAF) at the University of Liverpool, under NBAF Pilot Scheme NBAF685, awarded to C.J.E. whilst at the University of Oxford. P.S., M.P., and M.B.R. acknowledge FCT (Fundao para a Cincia e a Tecnologia) support through project PTDC/EPH-ARQ/4164/2014, partially funded by FEDER (Fundo Europeu de Desenvolvimento Regional) funds (COMPETE 2020 project 016899). PS was supported by FCT, European Social Fund, Programa Operacional Potencial Humano, and the FCT Investigator Programme and acknowledges FCT/MEC (Ministrio da Educao e Cincia) for support to CBMA through Portuguese funds (PIDDAC: Programa de Investimentos e Despesas de Desenvolvimento da Administrao Central)PEst-OE/BIA/UI4050/2014. V.M. and D.G.B. acknowledge the Science Foundation Ireland/Health Research Board/Wellcome Trust Biomedical Research Partnership Investigator Award No. 205072 to D.G.B., Ancient Genomics and the Atlantic Burden. The ORCADES was supported by the Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710), a Royal Society University Research Fellowship to J.F.W., the MRC (Medical Research Council) Human Genetics Unit quinquennial programme QTL in Health and Disease, Arthritis Research UK, and the EU FP6 EUROSPAN project (contract no. LSHG-CT-2006-018947). The Edinburgh Clinical Research Facility, University of Edinburgh, performed DNA extractions and the Sanger Institute performed whole-genome sequencing. The Viking Health StudyShetland (VIKING) was supported by the MRC Human Genetics Unit quinquennial programme grant QTL in Health and Disease. DNA extractions were performed at the Edinburgh Clinical Research Facility, University of Edinburgh. Whole genome sequencing was supported by the Scottish Genomes Partnership award from the Chief Scientist Office of the Scottish Government and the MRC (grant reference SGP/1) and the MRC Whole Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). We acknowledge Wellcome Trust funding (098051) for the ORCADES whole-genome sequencing. J.F.W. acknowledges support from the MRC Human Genetics Unit programme grant, Quantitative traits in health and disease (U. MC_UU_00007/10). We also acknowledge the invaluable contributions of the research nurses in Orkney and Shetland, the administrative team in Edinburgh, and the people of Orkney and Shetland.

Author contributions:J.F.W., G.W., H.M., M.P., C.J.E., and M.B.R. designed research; K. Dulias, M.G.B.F., P.J., M.S., G.O.-G., A.F., S.R., F.G., A.M., K. Donnelly, T.J.A., T.S.G.P., V.M., P.S., J.F.W., M.P., C.J.E., and M.B.R. performed research; P.J., R.M., and D.G.B. contributed new reagents/analytic tools; A.C., O.L., G.K., D.P., C.W., G.W., and H.M. provided sample materials and information; and K. Dulias, M.G.B.F., P.J., M.S., R.M., J.B., P.S., J.F.W., G.W., H.M., M.P., C.J.E., and M.B.R. wrote the paper.

The authors declare no competing interest.

A complete list of the Scottish Genomes Partnership can be found in the SI Appendix.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2108001119/-/DCSupplemental.

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Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney - pnas.org

Friday, February 4, 2022

Got an impossible polyploid or highly repetitive plant gene, or perhaps an enormous fungal genome or complex microbial community? Have an impossible dream of cracking pandemic, epidemic & endemic biology, or uncovering neurological disorders and rare diseases?

What was once impossible has become possible with HiFi Sequencing, scientists heard at the 2021 PacBio Global Virtual User Meeting.

The event, HiFi Sequencing: Around the World in 24 Hours, featured 32 speakers and 22 panelists from every region of the globe, covering human biomedical research, plant and animal sciences, and microbiology and infectious disease. There were also Ask the Experts sessions and panel discussions about trending topics, such as the COVID-19 pandemic.

If you missed it, it is now available for on-demand viewing, and here are some highlights:

When genomics gets tough, the tough get HiFi: more stories of HiFi enabled scienceKeynote speaker Jeremy Schmutz of HudsonAlpha and the Joint Genome Institute discussed some of the most difficult genomic challenges he and his colleagues face, including the known hard stuff like the FCGR region of the human immune system, an enormous 1.17 Gb zombie fungi, and the gigantic, super complex polyploid 10 Gb, 130 chromosome sugarcane.

Want to know how to get to the ultimate genome? Schmutzs advice: Start with good DNA. Sequence with HiFi. Add Hi-C, assembly curation, and polishing. Use RNA sequencing for annotation.

Unravelling the mysteries of sex determination in reptiles using HiFi sequencingThe bearded dragon lizard, Pogona vitticeps, is an increasingly popular model organism with a unique sex determination, shaped by both genotype and temperature. In his talk, Ira Deveson of the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research discussed how he used PacBio HiFi sequencing for genome assembly, phasing, and isoform profiling to elucidate the mechanisms of reptile sex determination.

Rapid, accurate surveillance of SARS-CoV-2 variants across the commonwealth of KentuckyAt the University of Louisville Sequencing Technology Center, Melissa Smith (@SmithLab_UofL) was able to create nearly complete genomes for several lineages of SARS-CoV-2 circulating in Kentucky at the end of 2021, including Beta, Gamma, and Delta, using an early access version of the new PacBio HiFiViral Kit. The new HiFiViral kit enables researchers to see a more comprehensive view of viral variation of all types and enables laboratories to identify viral mutations of all kids. Out of 646 samples run with the early access HiFiViral Kit, she saw 80% genome completion; previous methods had yielded complete genomes in only about 50% of cases, she said at the summit. She noted that she appreciated the protocols high multiplexing capacity (384 samples at a time in her lab), reduced hands-on time (by about 80%), and the end-to-end kitted solution, allowing her to avoid having to source reagents from multiple different vendors (especially during the pandemic, when supply chains have at times been unreliable). Melissa now intends to use the HiFiViral Kit to sequence more than 7,000 samples as part of a statewide virus surveillance effort.

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01Bettina Heidecker and Phillip Suwalski of Charit Universittsmedizin Berlin presented their research investigating HLA as a risk factor for COVID-19. Adjusting for other known confounding factors such as age, BMI, and sex, their data suggests that HLA-C* 04:01 increases susceptibility to SARS-CoV-2 and risk for severe course of COVID-19; the results were reproduced in GWAS data of 7,796 cases and 875,694 controls. HLA typing on the Sequel System also helped contribute to an improved understanding of the pathophysiology of COVID-19.

Characterization of HBV integration patterns with HiFi long readsHow does the hepatitis B virus (HBV) induce hepatocellular carcinoma (HCC), the most common type of primary liver cancer? Professor Kai Ye of Xian Jiaotong University explained how he conducted a genome-wide analysis of HBV cell lines and clinical samples and characterized novel recurrent genome rearrangement types associated with HBV integration, finding that different DNA repair mechanisms activated by virus integration were the major cause of virus-specific genome rearrangements.

A new era for marine microbial researchTaylor Priest (@taylorpriest2) of the Max Planck Institute for Marine Microbiology talked about the value of HiFi sequencing in his study on the ecology of microbial communities in arctic marine ecosystems, particularly microbial carbon degradation. One of the most important, but also the most difficult, aspects of elucidating the ecology of microbial populations is accurately linking phylogeny and function, he said. Using HiFi reads and the PacBio ultra-low input library prep protocol, Priest was able to recover a higher quantity and quality of metagenome assembled genomes (MAGs). And with several complete genes obtained per read, genes could be functionally annotated for community-level analysis without any assembly required.

Interested in learning more about PacBio technology? Visit our HiFi sequencing page or Sequel Systems page to learn more.

Read more:
When Genomics Gets Tough, the Tough Get HiFi: Users Share Stories of PacBio Enabled Science at Global Summit - PacBio - Pacific Biosciences

[94 Pages Report] Cancer Genome Sequencing Market Insights 2022 This report contains market size and forecasts of Cancer Genome Sequencing in United States, including the following market information:

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The United States Cancer Genome Sequencing market was valued at USD million in 2020 and is projected to reach USD million by 2027, at a CAGR of % during the forecast period.

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Excerpted from Origin: A Genetic History of the Americas. 2022 by Jennifer Raff. Published by Twelve Books. All rights reserved.

We are living through a revolution in the scientific study of human history. Because of recent technical developments in approaches for recovering and analyzing DNA, plus sequencing whole genomes, geneticists and archaeologists ability to ask and answer questions about the past has improved dramatically.

Scientists once thought the peopling of the Americas occurred around 13,000 years ago, following the last ice age, when a small group of people crossed the Bering Land Bridge from Northeast Asia to Northwestern Alaska. In the last 10 to 20 years, however, a mountain of new evidence has emerged, showing us that people had been in the Americas for thousands of years before then.

This is not a surprise to Indigenous peoples, many of whom have Traditional Histories that situate their origins within what is today known as the Americas. Some Indigenous people view their origin stories as literal, while some see them as metaphorical and compatible with Western science. Indeed, some Native American archaeologists have demonstrated the importance of Oral Traditions in interpreting the archaeological record and call for careful and analytical study of these traditions and the integration of any clues they might give for understanding the past.

I present this history of the last 36,000 years of migration from the perspective of a Western scientist who places genetic evidence in the forefront of the investigation and then tests the models it produces with archaeological, linguistic, and environmental evidence. For many Indigenous peoples, this is not the whole story or the only story that should be told.

As you read this genetic chronicle, please do not lose sight of the dignity of the human beings who lived this history and the rich complexity of individual existences that are lost in the telling. The story I tell here is akin to reconstructing a persons entire life by stitching together the photos they posted on Instagram. Not inaccurate, necessarily, just incomplete.

Around 36,000 years ago, a small group of people living in East Asia began to break off from the larger ancestral populations in the region. By about 25,000 years ago, the smaller group in East Asia itself split into two. One gave rise to a group referred to by geneticists as the ancient Paleo-Siberians, who stayed in Northeast Asia. The other became ancestral to Indigenous peoples in the Americas.

Twelve Books

Around 24,000 years ago, both groups independently began interacting with an entirely different group of people: the ancient Northern Siberians. Some archaeologists and geneticists argue that this meeting of the two grandparent populations of Native Americansthe group in East Asia and the ancient community in Northern Siberiaoccurred because people moved north, not south, in response to the last glacial maximum (LGM), a period in which much of northern North America was covered by massive glaciers. Thus, many geneticists look north, to Beringia, for the location of the refugia that may have allowed the ancestors of Native Americans to survive the ice age.

Central Beringia is mainly underwater today, but it was a substantial land connection between 50,000 and 11,000 years ago. The term Bering Land Bridge gives the impression that people raced across a narrow isthmus to reach what is today Alaska. But the oceanographic data clearly show that during the LGM, the land bridge was twice the size of Texas.

If the Out of Beringia model is correct, Beringia wasnt a crossing point but a homeland. It was a place where people lived for many generations, sheltering from an inhospitable climate and slowly evolving the genetic variation unique to their Native American descendants.

Either just before or shortly after the start of their period of isolation, the Beringians split into several groups: the Ancestral Native Americans, who would move south, below the ice sheets, and become ancestors of the First Peoples; the Ancient Beringians, who would stay behind in Beringia; and a mystery group (Unsampled Population A) known to us only indirectly from the traces of ancestry it contributed to some Mesoamerican populations.

About 17,000 years ago, on the western coast of present-day Alaska, the ice sheets began to melt, and the First Peoples expanded southward. This expansion left very clear imprints in the genomes of their descendants. Mitochondrial DNA lineages show us that after the LGM, people were suddenly and rapidly spreading out. Their populations were growing enormouslyabout 60-fold between about 16,000 and 13,000 years ago.

This population explosion is exactly what we expect to see in the genetic record when people move into new territories, where resources are far less limited, there is no competition from other people, and the game animals have no natural fear of humans, having never seen them before.

The story this rather dry genetic evidence reveals is breathtaking when you stop to think about it: A small group of people survived one of the deadliest climate episodes in all of human evolutionary history through a combination of luck and ingenuity. They established themselves in a homeland, from which their descendantshoping to make a new and better life for themselvesventured out to explore.

Roughly 36,000 years ago, a group living in East Asia began journeying east, eventually crossing Beringia into present-day Alaska, where some populations expanded south as the ice sheets melted around 17,000 years ago. Jennifer Raff

These descendants found new lands beyond their wildest expectations, entire continents (possibly) devoid of people, lands to which they quickly adapted and developed deep ties. These ties persisted through millennia into the present day and have not been severed despite climatic challenges and the brutality of colonialism, occupation, and genocide.

It was the nuclear genome from a small childwho himself did not have any descendantsthat gave us the greatest insight into this process.

In what is today south-central Montana 12,600 years ago, a child died. Based on the archaeological evidence, I imagine what happened at the Anzick site like this:

Like all their children, the 2-year-old boy was treasured by his people. To honor him, they buried him underneath a rock shelter with great care and love, sprinkling his body with red ochre. Everyone in the community contributed to the toolkit that he would take with him into the afterlife: Some placed carefully flaked finished toolsprojectile points, knives, and scrapers for hidesothers left the cores that he would need to make new ones. His parents placed carved elk bone rods into the grave to mark his connection to their ancestors. This burial site was honored by their descendants for generations, who paid their respects to the boy every time they passed it. Two thousand years later, when another boy was suddenly taken from his family, they derived some comfort by burying him close to their ancient ancestor for protection.

The graves of these two children were found accidentally by construction workers in 1968. Because they were found on private land, their remains were not under the purview of the law that requires consultation and repatriation (if requested) with affiliated tribes.

Nevertheless, after the genome of the 2-year-old had been sequenced, researchers consulted with Indigenous peoples in Montana, including the Blackfeet, Confederated Salish, and Kootenai tribes; the Gros Ventre Tribe; the Sioux and Assiniboine tribes; the Crow Tribe; and the Northern Cheyenne Tribe. The tribes agreed that the children should be reburied in a safe place near their original graves, and their wishes were followed shortly after the publication of the study.

The children are referred to by archaeologists as Anzick-1 (the 2-year-old) and Anzick-2 (the 7- or 8-year-old who was buried there later). Anzick-1 was special not only to his parents and relatives (both in the past and across time), but also to the scientific community across the world. His remains were dated to between 12,707 and 12,556 years ago, making him the oldest-known person in the Americasthe only person who lived during the Clovis period whose remains are known to have survived to the present day. His genome was also the first ancient Native American genome to have been completely sequenced, and it has given us important insights into the First Peoples movements into the Americas.

The radiation of dog lineages that mirrors human lineages is extremely strong evidence for this model of migration.

Anzick-1s complete nuclear genomeand those from additional ancient individuals that were sequenced in later yearsshow us that shortly after the LGM, the family tree of the First Peoples split into two major (and one minor) branches.

The minor branch, which diverged between 21,000 and 16,000 years ago, is currently represented by a single genome from a woman who lived on the Fraser Plateau in present-day British Columbiaknown as the Big Bar Lake site to archaeologistsabout 5,600 years ago. The fact that her lineage split before the two other major branches may reflect the divergence of her ancestors from other First Peoples as they were moving southward out of Alaska.

One major branch, which included Anzick-1 and his relatives, became the ancestors of many Native peoples of the present-day United States and everywhere south of that. This branch is referred to by geneticists as SNA (Southern Native Americans). The other branch, which is ancestral to populations of northern North America, including peoples who speak the Algonquian, Salishan, Tsimshian, and Na-Din language groups, is referred to by geneticists as NNA (Northern Native Americans).

This split between the NNA and SNA branches tells us a lot about the initial peopling of the Americas. For one thing, most genetic evidence indicates that the split took place south of the ice sheets, because representatives of Ancient Beringians are equally related to members of the NNA and SNA groups. If those groups had split before they left Alaska, its likely that one or both groups would have intermarried with Ancient Beringians, resulting in Ancient Beringians being more closely related to one branch or the other.

We also see confirmation of this split and its timing from the mitochondrial genomes of dogs, who would have been closely associated with human populations. Dog mitochondrial genomes rapidly diversify into the four lineages found in ancient North American dogs at nearly the exact same time as the NNA/SNA split: about 15,000 years ago.

With the caveat that these mitochondrial data show us only a small fraction of dog population histories in the Americasthe edge pieces of the puzzlethe radiation of dog lineages that mirrors human lineages is nevertheless extremely strong evidence for this model.

Following the split between the NNA and SNA branches, people belonging to the SNA clade dispersed throughout North and South America very rapidly. We can see just how rapid this movement must have been when we compare the genomes of the most ancient peoples in the Americas. Despite being on different continents, 6,000 miles apart, the genomes of the Anzick-1 child, an ancient man from Spirit Cave in Nevada (10,700 years ago), and five people from the Lagoa Santa site in Brazil (~10,400 to 9,800 years ago) are very closely related to one another.

The story their DNA tells us is that between 15,000 and 13,000 years ago, the ancestors of people in Central and South America diverged from populations in North America. There are two pieces of evidence that strongly suggest that their movement southward was along the coast, rather than by inland routes.

First, the coast was open by 16,000 years ago, whereas the ice-free corridor between the two ice sheets probably wasnt a viable route until about 12,500 years ago. Second, the pattern of population splits that the genomes reveal is so fastnearly instantaneousthat the scientists who analyzed them likened the migration process as nearly jumping over large regions of the landscape. This fits more closely with southward migration by boat along the coast than with overland migration. By the time people got to South America, via the Isthmus of Panama, they may have expanded along both the east and west coasts.

Around 15,000 years ago, the ancestors of people in Central and South America began moving south rapidly, likely traveling by boat along the coasts. Jennifer Raff

This rapid first movement was followed by population growth, settling in to different environments, and gradual expansions. It was also followed by other significant migrations. After about 9,000 years ago, a group of people from Central Americaancestral to the present-day Mixe in the Mexican state of Oaxacaspread throughout South America and mingled with all the populations there. They may also have migrated northward as well, as the genomes of people buried in the Lovelock Cave in Nevada (1,950 to 600 years ago) show us.

But as is typical in scientific research, this finding only raises more questions. What caused this movement? And how did traces of a new population in North America come to the Mixe genomes about 8,700 years ago? And finally, what is the explanation for very ancient traces of shared ancestry between people in South America and those in Australasia and Melanesia? (Genetics models suggest it was not the result of a trans-Pacific migration.) Finally, how does the new White Sands Locality II site in present-day New Mexico, which may date to the LGM, change our understanding of the genetic models?

We dont have answers for these questions yet. We are only at the beginning of understanding the complexities of these histories using genetic and archaeological evidence.

Editors Note: This excerpt has been edited for style and length.

Originally posted here:
A Genetic Chronicle of the First Peoples in the Americas - SAPIENS

The beer industry has been steadily growing in the United States over the last decade, driven largely by the increased popularity of craft breweries. It is predicted to continue this growth with an estimated market value of $146 billion by 2025. To meet the growing demand of beer enthusiasts, breweries need a steady supply of the three main beer ingredients: barley, hops and yeast.

Sarah Carey, postdoctoral fellow in the Department of Crop, Soil and Environmental Sciences in Auburn Universitys College of Agriculture, recently received a two-year, $225,000 postdoctoral fellowship from the U.S. Department of Agriculture National Institute of Food and Agriculture, or USDA NIFA, for developing genomic tools to sustainably accelerate hop breeding programs. Carey also works for the HudsonAlpha Institute for Biotechnology in the lab of Alex Harkess, assistant professor in the Department of Crop, Soil and Environmental Sciences and a faculty investigator with HudsonAlpha.

Although the U.S. is second in global hop production, most of the hops are grown in the Pacific Northwest due to the temperature and climate needs of current hop varieties. Globally, hop production in 2020 increased by more than 1,100 hectares, or roughly 2,056 American football fields. In an effort to ramp up the production of hops to satisfy all of the hoppy beer lovers out there, scientists and breeders are trying to create new varieties of hops that can grow across the U.S.

Marrying genomic technology, traditional breeding

Hops are the flowers, or cones, of a plant called Humulus lupulus. Glands within the hop cone produce bitter acids and other essential oils that are important to help to keep beer fresher longer and help beer retain its head of foam. However, one of the most popular attributes of hops is adding hoppy aroma, flavor and bitterness to beer. Hops are very sensitive to their environment and can only grow at a commercial scale in certain parts of the country.

In addition to their limited geographic footprint, growing hops is also complicated by the fact that only female plants develop economically valuable hop cones. Male plants are necessary for breeding purposes but must be separated from females in the fields so that they do not fertilize female plants, causing unintended crosses and the production of seeds that negatively affect the beer flavor profile. Using traditional breeding methods, breeders must wait up to two years to determine if any given plant in the field is male or female.

One way to improve the hops industry is through identifying the sex-determining genes to better control the sex of the plant. However, few hop varieties have had their genome sequenced to a level and quality necessary to investigate sex chromosomes. Careys fellowship project aims to create high-quality reference genomes, fully assembled into chromosomes for all five H. lupulus varieties.

The reference genomes and other genomic tools developed during Careys fellowship will help identify genetic markers of sex determination, allowing breeders to identify the sex of plants earlier. Early identification of male plants would reduce water and land usage, and allow more female plants to be grown. The tools will also allow breeders to identify genetic markers of other valuable traits like drought tolerance and pest resistance.

This fellowship gives me the opportunity to take the skills that I gained studying mosses and evolutionary genetics in graduate school and apply them to an agricultural crop, Carey said. By doing this work at HudsonAlpha, I will also be immersed in cutting-edge genomics that I can combine with my current skillset to create a hop breeding pipeline that is directly useful for the botanical and agricultural world.

A pipeline to create regional hops

Carey already has plans to use the genomic resources she is developing over the next three years to create an Alabama sourced hop. She and the Harkess lab have been collaborating with researchers at Auburn, like Andre da Silvas lab, to begin the process of growing hops in Alabama, a state that is outside of most hop varieties environmental comfort zone. They plan to get different varieties to make different genetic crosses, relying on the hop genomes and genetic markers from Careys project to establish hop varieties that can grow in the climate and environment here in Alabama.

Sarah has built a powerful network of collaborators and stakeholders that spans industry, academic, agronomic and biotechnology partners to come together to grow a new crop in a new place, Harkess said. Hops grow in an extremely limited geographic region, complicated by their unique reproductive biology and sex chromosomes. Sarah is approaching these problems from a different angle, leveraging the immense diversity of hop species, the evolutionary histories of those species and her unique skillset of assembling complex plant genomes and sex chromosomes.

As part of her fellowship, Carey also plans to establish the Southeastern Hop Alliance to build a community of hop scientists, breeders, brewers and other stakeholders in the hop industry. Carey hopes to organize symposiums at Alabama breweries to bring together members of the alliance and provide updates on the genome references and tutorials on using the tools she is building. From this community, Carey aims to learn the many facets of hop breeding and the hop industry to better develop genomic tools for the needs of the people actually using them.

Im so grateful for the opportunity the USDA NIFA postdoctoral fellowship is giving me, Carey said. I get to learn about hop breeding from an academic, nonprofit and industry perspective, while also learning the ins and outs of developing high-quality genomic toolkits. The end result, from the scientific perspective, will be genomic tools that will help accelerate hop breeding programs. But from a personal perspective, this fellowship will give me the skills I need to launch my career in plant genomics to new and exciting heights.

Major collaborators contributing to the hop genome project include Joshua Havill, doctoral candidate at the University of Minnesota-Twin Cities; Gary Muehlbauer, Distinguished McKnight University Professor at University of Minnesota-Twin Cities; Katherine Easterling, lead research scientist and hopsteiner; Paul Matthews, senior research scientist and hopsteiner; and da Silva.

To hear Carey talk more about her research in hops, listen to this episode of HudsonAlphas podcast Tiny Expeditions.

Originally posted here:
Auburn, HudsonAlpha researcher awarded fellowship to accelerate hop breeding programs - Office of Communications and Marketing