User:Tewdar/sandbox/BeakerGenetics

BeakerGenetics

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The mechanism behind the spread of the Bell Beaker cultural complex has been the subject of considerable debate amongst archaeologists and geneticists, with evidence for both demic migration and trans-cultural diffusion. Recent archaeogenetics studies indicate that both processes had a central function, but with regional variations in their relative importance. Ancient DNA data suggest that the Bell Beaker complex did not spread from Iberia to Central and Northern Europe through the migration of people; instead, genetic evidence indicates that populations associated with the Corded Ware culture in Central Europe adopted the Bell Beaker package without significant population movement or gene flow. Subsequently, the Beaker complex was further spread by the expansion of Central and Northern European Bell Beaker-associated populations to other parts of Europe.

Individuals associated with the Bell Beaker culture are genetically heterogeneous, residing on a cline of variation defined by two distinct populations; at one extreme, Yamnaya pastoralists from the Eurasian steppe; and at the other extreme, Middle Neolithic and Copper Age European farmers. Very variable proportions of these ancestral components may be detected in Bell Beaker individuals at all levels of granularity, at Pan-European, regional, and even individual site scale.

Significant regional differences are found in the autosomal DNA and uniparental haplogroups of Beaker populations. In Northern and Central Europe, high levels (c. 50%) of Yamnaya related ancestry are found in Beaker-associated individuals, usually in conjunction with Y-chromosome haplogroup R1b-M269, especially its subclade, R1b-P312 (which is the most common male haplogroup in Western Europe today), along with a wide variety of mtDNA haplogroups. In southern Europe (Iberia, southern France, Italy, and the islands of the Mediterranean), the Yamnaya related ancestry contribution was substantially lower and later.

In Bell Beaker contexts, for early Iberian individuals and all Sardinian and Sicilian individuals, there is no evidence for Yamnaya related ancestry. These individuals are genetically very similar to the local Middle Neolithic and Copper Age populations that preceded them, and can be modelled as mainly Anatolian Farmer ancestry with some Western Hunter-Gatherer admixture. Males from these regions typically carry Y-DNA haplogroups characteristic of preceding local Neolithic populations, such as I2, G2, H, and E1, and not subclades of R1b-M269.

Early Bell Beaker individuals in northern and central Europe are genetically heterogeneous, consistent with recent admixture between migrants carrying steppe-like ancestry and local Neolithic populations. The proportion of Caucasus Hunter-Gatherer and Eastern European Hunter-Gatherer ancestry in the 'steppe' component in these groups is roughly equal, consistent with transmission of these components through a Yamnaya-like population. These individuals carry levels of Yamnaya-related ancestry that varied from as little as zero to as much as 75%, which is as high as Corded Ware individuals. These groups became more homogeneous over time, with levels of Yamnaya related ancestry in these populations becoming more equal. North and central European Beaker groups have very little, or zero, Iberian ancestry. Their Neolithic farmer ancestry was mostly similar to preceding local populations, who carried comparatively high levels of hunter-gatherer ancestry.

From northern and central Europe, Bell Beaker populations carrying Yamnaya related ancestry expanded to other areas of Europe. In Britain, c. 90% of autosomal and Y-DNA haplogroups were replaced by migrants carrying Yamnaya related ancestry between c. 2500 BCE and c. 2000 BCE. British Bell Beaker populations derive most of their ancestry from Central European Bell Beakers, and are most similar to Beaker individuals from Oostwoud, Netherlands, with almost identical proportions of Yamnaya related ancestry. British and Dutch Beaker groups are likely both derived from same ancestral population, who may originate from somewhere in the region that includes southern Britain, the Netherlands, northern France, Belgium, or north Germany. It has been suggested that the R1b-P312 haplogroup carried by the majority of Bell Beaker males may perhaps also have originated somewhere near the Rhine, before expanding northwest and east.

In later Iberian Bell Beaker associated individuals, Yamnaya related ancestry is found in outliers by c. 2500 BCE. By 2000 BCE, Yamnaya related ancestry becomes ubiquitous in Iberia, and local Neolithic YDNA haplogroups are almost completely replaced by subclades of R1b-M269 (predominantly R1b-P312). Admixture between groups carrying steppe-like ancestry and local Iberian Chalcolithic populations resulted in the formation of early 2nd millennium Iberian Bronze Age populations, which are best modelled as 60% German Bell Beaker and 40% Iberian Chalcolithic. Early Bronze Age individuals carrying Yamnaya related ancestry from Sicily and Mallorca are genetically similar to Iberian Bronze Age individuals, and most likely shared ancestry from an Iberian Bell Beaker source carrying Yamnaya related ancestry.

In France, steppe like ancestry is found in Bell Beaker associated individuals from c. 2500, with high variation. In northern France one individual, c. 2500 BCE 'CBV95' carrying ydna R1b-M269 and mtDNA J2a1a2, was modelled in one study as entirely Yamnaya ancestry with no additional admixture from other sources. Another individual from southwestern France, 'PEI2', was found to be similar to local Neolithic populations, but carried around 28% Yamnaya related ancestry.

In Poland, the Bell Beaker complex arrived c. 2400 BCE. Bell Beaker individuals remained genetically distinct from earlier Polish Corded Ware groups, even when these groups were near each other. Bell Beaker individuals from southern Poland are broadly similar genetically to other Central European Bell Beakers from Germany, Czechia, and Hungary.

In Italy, steppe related ancestry arrived in the north in Bell Beaker associated individuals c. 2000 BCE, and in central Italy around 400 years later. Autosomal and Y-DNA suggests that this ancestry could have arrived from north of the Alps, perhaps through a Central European Bell Beaker group.

Unlike Y-DNA haplogroups, mitochondrial DNA haplogroups in Northern and Central European Bell Beaker associated individuals are very diverse. A study of mtDNA haplogroups at Bell Beaker sites in France found that no two individuals at the same site had the same mtDNA haplotype. A study of two Bell Beaker sites in South Germany identified 23 different mtDNA haplotypes among 34 individuals. In Britain, new mtDNA haplogroups associated with Eastern migrants including I, R1a, and U4 were introduced. However in Iberia, no major turnover in mtDNA haplotypes occurred between the Neolithic and the Early Bronze Age.

The extent to which the transmission of steppe ancestry in Bell Beaker populations was driven by males is uncertain. Mittnik et al. (2019) detect male bias in Corded Ware but not Bell Beaker population movements. Scorrano et al. (2021) suggest that transmission of steppe ancestry was male biased in Bell Beakers, but less so than in the Corded Ware culture. Olalde et al 2019 and Liu et al 2021 state that, because most Y-DNA was replaced by lineages from the Eastern European steppe in the British Isles and Iberia, this suggests that the spread of the (high steppe ancestry) Bell Beaker complex was male-driven. Olalde et al. 2019 further state that the lower proportion of non-local ancestry on the X chromosome in Iberian individuals suggests a male-biased contribution. Overall there is a possible male-biased expansion, but not male-exclusive, at least in some areas such as Britain where new mtDNA haplogroups were introduced, demonstrating that females also migrated.

ToDo

 * Switzerland

3 bb indivs c. 2470–1985 BCE, Sion-Petit-Chasseur (from Furtwängler et al., supp dat 4)

WHG/ANAT_NEO/YAM_SAM

I5755 (0.125,0.553,0.323)

I5757 (-0.003,0.555,0.448)

I5759 (0.164,0.621,0.215)


 * More France


 * More Bohemia


 * More Netherlands


 * Hungary


 * Jutland


 * phenotypes, genetic disorders? (Estimating the age of p.(Phe508del) with family studies of geographically distinct European populations and the early spread of cystic fibrosis)

(In Britain,) "Derived alleles at rs16891982 in SLC45A2 and rs12913832 in HERC2/OCA2,which contribute to reduced skin and eye pigmentation in Europeans, considerably increased in frequency between the Neolithic period and the Beaker and Bronze Age periods...The arrival of migrants associated with the Beaker complex therefore markedly altered the pigmentation phenotypes of British populations. However, the lactase persistence allele at SNP rs4988235 in LCT remained at very low frequencies across this transition, both in Britain and continental Europe" (Olalde et al 2018)

Dubious
Chintalapati et al. 2022 infer admixture between Yamnaya related and c and w euro neo pops in bb c9mplex assoc indivs c. 2700bce, with earliest dates in Netherlands (est. c 3000- 2500bce) followed by Germany (est. 2900-2700bce) and France. Admix into ancestors of brit bell beakers est. c. 2770-2550, earlier than attested date of arrival this ancestry to brit. suggest this admix occ. mainland Europe.

Genomic perspectives on human dispersals during the Holocene (Stoneking et al.|2023)

 * BBAIs have "remarkable regional variation in ancestry"


 * CEuro BBs 50% steppe ancestry


 * Brit bbs "largely central European ancestry, which replaced the existing Neolithic ancestry by up to 90%"


 * Iberian early bbs almost completely lack YAM, later bbais "showing only a modest amount of steppe-related ancestry"


 * indicate that the spread of bb complex "was not mediated by a single migrating population but was also adopted by local groups by cultural diffusion"


 * the (genetic) impact of steppe migration was "substantially smaller in southern Europe"

The return of the Beaker folk? Rethinking migration and population change in British prehistory (Armit & Reich|2021)

 * BBs in Iberia ancestry mostly from local Neo farmer pops


 * unlike BBs in c Europe...


 * between c. 3000&2600bce, pops w ancestry mostly from eba (c. 3400–2600 BC)  YAM pastoralists from Eurasian steppe migrated to n and c europe


 * By final Neo, pops in c &n europe(= CW culture) have substantial YAM ancestry but w large local variation


 * CWC pops adopted BB culture in c Europe


 * contrast in Iberian and C Eur BB complex (autosomal and YDNA)


 * Iberian BBs have YDNA commonly found since begin of Neo,


 * C Euro BBs dominated by haplogroup R1b-M269 < Eurasian Steppe


 * BB culture did not spread from Iberia to c Europe by migration of people


 * Brit Neolithic have no YAM


 * BUT BB assoc indivs in eba&mba have high props YAM


 * > 90 % of BB (and later) males are haplog  R1b, not found in Brit Neo


 * R1b "a definitive indicator of the Steppe ancestry common in Central Europe...demonstrating the arrival of substantial numbers of men from the Continent."


 * also prev. absent mtDNA haplos I, R1a and U4 demonstrate that female migration also took place


 * maybe some male bias, but YAM migration to Britain was not only men


 * 93% of gene pool replaced, suggesting "massive turnover of population" associated w arrival of BB complex in Britain


 * British BBs genetically closest to contemporaneous indivs from lower Rhine, esp. Oostwoud, NL (AOC beakers dominate in both Brit and NL)


 * suggests major source population in this area


 * Brit Neolithic farmers made only small genetic contrib to british bronze age pops


 * genetic turnover > 90 % from c. 2500 to 2000bce

who we are and how we got here (Reich|2018)
p115


 * Iberian BBs genetically indistinguishable from preceding non beaker pops


 * But BBs in central Europe were very different, mostly YAM ancestry, very little or zero ancestry shared w iberian BBs


 * BB culture did not spread to c europe via migration of people


 * after BB culture reached c. Europe it spread through migration


 * before BB culture spread to Brit, no individual had any YAM ancesyry


 * after c. 2500bce, large amounts pf steppe ancestry in brit and no particular relationship to Iberian BBs


 * brit BBs similar props of steppe ancestry to BBs across channel


 * BA britain pops only 10% neolithic farmer ancestry and 90% from pop similar to BBs in Netherlands

p116


 * at one Hungarian BB site YAM ancestry ranged from 0% to 75 % (75% is as high as CW indivs)

The genetic history of the Southern Arc a bridge between West Asia and Europe (Lazaridis et al.|2022)

 * YAM c. 50% ancestry from CHG (higher than BA Europeans from c. n. europe, italy, or balkans, but CHG/EHG in equal proportions, like c. and n. european CW and BBs

The genomic history of southeastern Europe (Mathieson et al.|2018)
CW c. 75% YAM, BB c. 50% YAM (YAM==a pop w similar ancestry to Yamnaya individuals who prob moved from pc steppe in 3rd millennium bce

Insights into human history from the first decade of ancient human genomics (Liu et al.|2021)
c.2600bce indivs w/ YAM arrived in B Isles w BB complex, replacing 90% of gene pool


 * mostly driven by male migration : in b isles&iberia, majority of Late neo YDNA replaced by EEuro steppe YDNA

Population genomics of Bronze Age Eurasia (Allentoft et al.|2015)

 * Late Neolithic and Bronze Age Corded Ware, Bell Beaker, Unetice, and Scandinavian cultures genetically very similar, forming a cline of genetic affinity with Yamnaya, highest in Corded Ware, lowest in Hungary, Bell Beakers from c Europe intermediate

The Beaker phenomenon and the genomic transformation of northwest Europe (Olalde et al.|2018)

 * "A major debate in archaeology has revolved around the question of whether the spread of the Beaker complex was mediated by the movement of people, culture or a combination of both [...] Our results support a model in which cultural transmission and human migration both had important roles, with the relative balance of these two processes depending on the region"


 * only limited genetic affinity between Iberian and c euro BBs, therefore migration excluded as important mechanism of spread of BB culture from Iberia to c Euro


 * however migration was important for later spread of BB complex was


 * intro of BBC to brit brought high levels of YAM, 90% of brit gene pool replaced in few hundred years, continuing a migration from east to west that previously brought YAM to cent and n Europe


 * CWC indivs. most of their ancestry from pops related to EBA YAM from Eurasian steppe


 * high levels of YAM in German and Czech BBs, who are an admixture of steppe pops and Euro Neo farmers


 * BB males outside Iberia dominated by R1b-M269 (assoc. w steppe migrants in c euro > 3000bce) Of the M269s, most were P312 (the dominant haplogroup in W Euro today)


 * BBs in Iberia had higher props of Y haplogroups common in Neolithic Europe (mainly I, also G2)


 * In Iberia, M269 found in some indivs. assoc. w YAM ancestry, incl. 2 w P312


 * Widespread P312 in BBs in c and w Euro suggests BB indivs key part spreading this lineage to mosts arras where found today


 * BBs are heterogeneous, differentiated by variable levels of steppe YAM vs Middle Neo/CopperAge Euro ancestry ('European cline')


 * BBs three main ancestral components:Euro Meso HGs, Neolithic Levant&Anatolia, and Neolithic Iran (found admixed in steppe pops)


 * In areas outside Iberia and Sicily, majority BBs had signif. props of YAM ancestry


 * Iberian BBs only minority (c. 25%) carry YAM, these are earliest representative of YAM ancestry in Iberia


 * BB complex individuals: variations in ancestry at pan european, regional, and site level


 * at Szigetszentmiklós, Hungary, BB YAM ancestry ranged from 0% to 75%


 * this genetic heterogeneity is "consistent with early stages of mixture between previously established European Neolithic populations and migrants with steppe-related ancestry"


 * Iberian BBs best modelled as local Middle Neo and CA pops as source of Neolithic ancestry (c and n Euro Neo pops excluded as source of Neo ancestry)


 * Neo ancestry in non-Iberian BBs mostly related to c and n Euro Neo pops w comparatively high HG admix, (Iberian pops excluded as source for Neo ancestry)


 * BbS had different origins


 * No detectable Iberian ancestry outside Iberia


 * "Nearly complete turnover of ancestry in Britain"


 * Brit BBs similar to c Euro BBs, in both AOC-associated(c Euro) and M associated(Iberia) pottery types


 * prev neo indivs in Brit no YAM affinity, cluster w Euro Middle Neo and CA indivs.


 * YAM arrived in Ireland by BA, Brit by CA


 * Most s Brit BBs are most similar to individuals from Oostwoud, NL (near identical YAM, highest shared genetic drift, symetric relations to most ancient pops) and so prob derived from same ancestral pop


 * Oostwoud BBs not necessarily direct ancestors of Brit BBs, but closely related to source pop that migrated from European mainland to Brit


 * between c. 2450 and 2000bce BB ancestry props variable, consistent w migrants mixing w local Brit Neo pop


 * >2000bce more homogeneous, less varied, higher Neolithic related ancestry


 * c. 90% pop turnover by mba(1500-1000bce)


 * R1b absent in brit Neo, but >90% in Ca/BA brit


 * new mtdna haplos (I, R1a,U4) not found in neo brit (but found in European BBs) suggests females also migrated


 * Increase in freq. of derived alleles rs16891982 (SLC45A2) and rs12913832 (HERC2/OCA2), (contrib. reduced skin/eye pigmentation in Euros) between neo and BB/Bronze Age periods


 * pigmentation phenotypes of brit pops changed w migration of BBs


 * lactase persistence allele still very low levels


 * In Iberia majority of BBs lack YAM affinity, were most similar to prev local Iberian pops


 * in c euro, YAM ancestry widespread, no substantial contrib. from Iberian BBs


 * YAM in some Iberian BBs shows gene flow to Iberia

Dynamic changes in genomic and social structures in third millennium BCE central Europe (Papac et al.|2021)

 * earliest bohemian BBs similar position in PCA to CWs, suggesting genetic continuity


 * late bohemian BBs individuals harbour signif. more middle Eneolithic ancestry cf. early bohemian BBs


 * bohemian bb late modelled as 2way bohem BB early and local middle eneol.


 * bohem_bb_late have additional c. 20% middle eneol ancestry cf bb early


 * closer relat. between YDNA lineages in CW early and BB than late CW/BB and YAM/BB


 * R1b-L151 is most common (55%) among CW early males, w/ 1 ancestral to P312 ( dominant Y-lineage in BB).


 * most Bohemian BBs belong to R1b-L2


 * several BB males from England belong to R1b-L21, ie neither Brit or Bohem BB males can be descended from the other


 * "A scenario of R1b-P312 originating somewhere between Bohemia and England, possibly in the vicinity of the Rhine, followed by an expansion northwest and east is compatible with our current understanding of the phylogeography of ancient R1b-L151–derived lineages"

Ancient genomes from present-day France unveil 7,000 years of its demographic history (Brunel et al.|2020)

 * French BB individuals diverse props of YAM proportions eg:


 * CBV95 (northern France, R1b, 2500bce) shares most alleles with YAM, earliest ex of this haplogroup in France (outlier modelled as 100% YAM)


 * (r1b assoc. w/ LNeo steppe migrants to c Europe, found in other areas in Europe and BBs from S France, but near-absent in Iberia)


 * PEI2, (SW France) genetically similar to Neolithic Farmers. 3way model(AN, WHG, YAM_SAM) still gives 28.3% YAM though


 * YAM ancestry introduced later and with less genetic turnover in Sw europe than other parts of Europe

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome (Cassidy et al.|2016)

 * beaker culture "most probable vector" of YAM into Ireland from Europe

The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age(Szécsényi-Nagy et al.|2017)

 * "In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character"


 * no evidence for direct genetic link between Iberia chalco and contemporaneous c Europe


 * no evidence for e to w influx: no chalco indivs have steppe ancestry (found in contemp. c euro CW and BBs), suggesting YAM did not reach Iberia until later

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia (Villalba-Mouco et al.|2021)

 * south Iberian CA indivs do not have steppe related ancestry


 * El Argar sites at La Bastida and La Almoloya do have steppe ancestry


 * DATES estimated admix of c. 2550 BCE c. 1642 BCE

NOT FINISHED YET

The Spread of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean (Fernandes et al.|2020)

 * After c. 3000 BCE, people with YAM migrated west, admixing with local c. European Neo farmers at up to 75:25 in CW culture, and to w Europe (BB "complex")


 * outlier YAMs in Iberia by 2500bce, mixed into pop by 2000bce


 * Mallorca EBA modelled as a clade with the small number of Iberian BBs w YAM, rejecting models without an Iberian source


 * related pop movements brought YAM to Iberia and Balearic Islands. (on basis of 1 indiv.)


 * Neolithic Sardinians - no evidence of YAM, not even in BB archaeo. context, like BB burials in Sicily and (most of) Iberia,


 * in contrast w/ c and n Europe, where BBs have signif. YAM ancestry

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia (Marcus et al.|2020)

 * absence of YAM suggests genetic isolation from many BA Euro pops on mainland, incl. Iberian BBs, R1bM269 absent through to 1000bce

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula (Saupe et al.|2021)

 * with 2 source pops, all target BA pops from n and c italy support scenario chalcolithic like pop receive stepp related ancestry, perhaps through pops from North eg BB Germany, Middle neo France , Italy chalcolithic


 * YAM ancestry main diff between BA Italian and Sardinian/sicilian indivs


 * YAM ancestry absent in neo and chalco Italians, appears in early italian BA (ie Italian BB), (C.2200-2000Bc) and increases over time


 * YDNA, and autosomal affinity of m and c italian pos w late neo Germany indicates a "possibly Northern-, trans-alpine-, and potentially Bell-Beaker-associated source of the Italian Steppe-related ancestry"

Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition (García-Fernández et al.|2022)

 * BB complex major culture coincident w transition to BA, predominant in W and SW EURope


 * spread of bb cult was "a complex process involving cultural diffusion and demographic migrations with a variable balance."


 * BBs were "genetically heterogeneous, with a cline of ancestries related to the Eastern Steppe, European Middle Neolithic, and Copper Age groups"


 * BB YDNA more homogeneous, M269 predominates


 * R1b-M269 still most frequent haplogroup in w euro, specifically subclade P312


 * spread of bb complex had important role in spread of M269


 * In BA, 40% of Iberian ancestry was related to c euro BB groups


 * almost complete ydna replacement of various CA lineages w M269 in BA Iberia

Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries (Sjögren et al.|2020)
(Alburg and Irlbach BB cemeteries, germany)


 * All BB males YDNA R1b-M269 (major haplogroup assoc w YAM ancestry in W Europe > 2500bce)


 * all who could be subtyped were derived for P312 subtype dominant in contemporary w and c europeans


 * This represents "an extraordinary uniformity along the male line, practically linking all men in both cemeteries and in fact the vast majority of Central European Bell Beaker culture men who are also R1b-S116/P312 positive" (this does not nec. imply close paternal relat. between males at these two cemeteries or in c euro BBs in general, as p312 mutation dates from several hundred years earlier


 * mtdna diversity: in contrast to y haplos, there are 14 different mtdna haplotypes at Irlbach(n=18) and 9 diff mtdna haplotypes at Alburg (n=16)


 * this suggests poss. of widespread (institutionalized?) exogamy


 * none of the mtdna haplotypes is shared between the two cemeteries


 * at later Augsburg site 200 km away, there are 16 different htypes ( n= 19)


 * individuals from both cemeteries are on a cline, with some indivs close to steppe/CW, and others closer to Early and Middle Neo Euro farmers (similar to Augsburg)

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France (Seguin-Orlando et al.|2021)

 * "No individuals from the same archaeological site carried iden-tical mitochondrial haplotypes, indicating no maternal related-ness"