Editing Neolithic Europe (section)

==Genetics==
{{see|Genetic history of Europe}}
[[File:Simplified model for the recent demographic history of Europeans.jpg|thumb|upright=1.3|Simplified model for the demographic history of Europeans during the [[Neolithic]] period in the [[Neolithic Revolution]]'s introduction of agriculture<ref>{{cite journal | vauthors = Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, Underhill PA, Sánchez-Quinto F, Zara I, Pitzalis M, Sidore C, Busonero F, Maschio A, Angius A, Jones C, Mendoza-Revilla J, Nekhrizov G, Dimitrova D, Theodossiev N, Harkins TT, Keller A, Maixner F, Zink A, Abecasis G, Sanna S, Cucca F, Bustamante CD | display-authors = 6 | title = Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe | journal = PLOS Genetics | volume = 10 | issue = 5 | pages = e1004353 | date = May 2014 | pmid = 24809476 | pmc = 4014435 | doi = 10.1371/journal.pgen.1004353 | doi-access = free }}</ref>]]
Genetic studies since the 2010s have identified the genetic contribution of Neolithic farmers to modern European populations, providing quantitative results relevant to the long-standing "replacement model" vs. "demic diffusion" dispute in archaeology.

The earlier population of Europe were the Mesolithic hunter-gatherers, called the "[[Western Hunter-Gatherers]]" (WHG). Along with the [[Scandinavian Hunter-Gatherer]]s (SHG) and [[Eastern Hunter-Gatherer]]s (EHG), the WHGs constituted one of the three main genetic groups in the postglacial period of early [[Holocene]] Europe. Later, the Neolithic farmers expanded from the Aegean and Near East; in various studies, they are described as the [[Early European Farmers]] (EEF); Aegean Neolithic Farmers (ANF),<ref name="BraceDiekmann2019" /> First European Farmers (FEF), or also as the Early Neolithic Farmers (ENF).

A seminal 2014 study first identified the contribution of three main components to modern European lineages (the third being "[[Ancient North Eurasians]]", associated with the later [[Indo-European expansion]]). The EEF component was identified based on the genome of a woman buried c. 7,000 years ago in a [[Linear Pottery culture]] grave in [[Stuttgart]], Germany.<ref>Lazaridis et al., "Ancient human genomes suggest three ancestral populations for present-day Europeans", ''Nature'', 513(7518), 18 September 2014, 409–413, doi: 10.1038/nature13673.</ref>

This 2014 study found evidence for genetic mixing between WHG and EEF throughout Europe, with the largest contribution of EEF in Mediterranean Europe (especially in Sardinia, Sicily, Malta and among Ashkenazi Jews), and the largest contribution of WHG in Northern Europe and among Basque people.<ref>Lazaridis et al. (2014), [https://www.biorxiv.org/content/biorxiv/suppl/2014/04/05/001552.DC4/001552-3.pdf Supplementary Information], p. 113.</ref>

Nevertheless, DNA studies show that when the Neolithic farmers arrived in Britain, these two groups did not seem to mix much. Instead, there was a substantial population replacement.<ref name="bbc.com"/><ref name="BraceDiekmann2019" />

Since 2014, further studies have refined the picture of interbreeding between EEF and WHG. In a 2017 analysis of 180 ancient DNA datasets of the Chalcolithic and Neolithic periods from Hungary, Germany and Spain, evidence was found of a prolonged period of interbreeding. Admixture took place regionally, from local hunter-gatherer populations, so that populations from the three regions (Germany, Iberia and Hungary) were genetically distinguishable at all stages of the Neolithic period, with a gradually increasing ratio of WHG ancestry of farming populations over time. This suggests that after the initial expansion of early farmers, there were no further long-range migrations substantial enough to homogenize the farming population, and that farming and hunter-gatherer populations existed side by side for many centuries, with ongoing gradual admixture throughout the 5th to 4th millennia BC (rather than a single admixture event on initial contact).<ref>Lipson et al., "Parallel palaeogenomic transects reveal complex genetic history of early European farmers", ''Nature'' 551, 368–372 (16 November 2017) doi:10.1038/nature24476.</ref> Admixture rates varied geographically; in the late Neolithic, WHG ancestry in farmers in Hungary was at around 10%, in Germany around 25% and in Iberia as high as 50%.<ref>Lipson et al. (2017), [https://www.researchgate.net/publication/320948082_Parallel_palaeogenomic_transects_reveal_complex_genetic_history_of_early_European_farmers Fig 2.]</ref>

During late Neolithic and early [[Bronze Age]], the EEF-derived cultures of Europe were overwhelmed by successive invasions of [[Western Steppe Herders]] (WSHs) from the [[Pontic–Caspian steppe]].<ref>{{cite journal |last1=Goldberg |first1=Amy |last2=Günther |first2=Torsten |display-authors=1 |date=March 7, 2017 |title=Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations |journal=[[Proceedings of the National Academy of Sciences of the United States of America]] |publisher=[[National Academy of Sciences]] |volume=114 |issue=10 |pages=2657–2662 |doi=10.1073/pnas.1616392114 |pmc=5347611 |pmid=28223527 |bibcode=2017PNAS..114.2657G |ref={{harvid|Goldberg et al.|2017}}|doi-access=free }}</ref> These invasions led to EEF [[paternal]] DNA lineages in Europe being almost entirely replaced with WSH paternal DNA (mainly [[Haplogroup R1b|R1b]] and [[Haplogroup R1a|R1a]]). EEF mtDNA however remained frequent, suggesting admixture between WSH males and EEF females.<ref>{{cite journal |last1=Juras |first1=Anna |last2=Chyleński |first2=Maciej |display-authors=1 |date=August 2, 2018 |title=Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations |url= |journal=[[Scientific Reports]] |publisher=[[Nature Research]] |volume=8 |issue=11603 |page=11603 |doi=10.1038/s41598-018-29914-5 |pmc=6072757 |pmid=30072694 |bibcode=2018NatSR...811603J |ref={{harvid|Juras et al.|2018}}}}</ref><ref>{{cite journal |last1=Olalde |first1=Iñigo |last2=Mallick |first2=Swapan |display-authors=1 |date=March 15, 2019 |title=The genomic history of the Iberian Peninsula over the past 8000 years |url= |journal=[[Science (journal)|Science]] |publisher=[[American Association for the Advancement of Science]] |volume=363 |issue=6432 |pages=1230–1234 |doi=10.1126/science.aav4040  |pmc=6436108 |pmid=30872528 |bibcode=2019Sci...363.1230O |ref={{harvid|Olalde et al.|2019}}}}</ref> 
<!--belongs on [[Genetic history of Europe]], [[WP:UNDUE]] for the article about Neolithic Europe.

=== Y-chromosomal haplogroups ===
[[File:Cardial map.png|thumb|450px|Ancient DNA of early Neolithic men of the [[Cardium pottery|Cardial]] Pottery culture, found in cave burials, have been found to be mainly of Y-DNA haplogroup G2a.{{sfn|Lacan|Keyser|Ricaut|Brucato|2011}}]]

Later Y-DNA based studies, exploiting an increased understanding of the phylogenetic relationships, performing micro-regional haplogroup frequency analysis, revealed a more complicated demographic history.{{sfn|Di Giacomo|Luca|Popa|Akar|2004}} The studies suggest that "the large-scale clinal patterns of Hg E and Hg J reflect a mosaic of numerous small-scale, more regional population movements, replacements, and subsequent expansions overlying previous ranges".{{sfn|Semino|Magri|Benuzzi|Lin|2004}} Rather than a single, large-scale 'wave of advance' from the Near East, the apparent Hg J2 cline is produced by distinct populations movements emanating from different part of the Aegean and Near East, over a period stretching from the Neolithic to the Classical Period. Similarly, haplogroup E1b1b was also thought to have been introduced into the Balkans by Near Eastern agriculturalists.{{sfn|Semino|Passarino|Oefner|Lin|2000}} However, {{Harvcoltxt|Cruciani et al.|2007}} discovered that the large majority of haplogroup E1b1b lineages in Europe are represented by the sub-clade [[Haplogroup E1b1b (Y-DNA)|E1b1b1a2- V13]], which is rare outside Europe. Cruciani, Battaglia and King all predict that V13 expanded from the Balkans. However, there has been no consensus as to exact timing of this expansion (King and Battalia favour a neolithic expansion, possibly coinciding with the adoption of farming by indigenous Balkaners, whilst Cruciani favours a Bronze Age expansion), nor as to where V13 actually arose (but point to somewhere in the southern Balkans or Anatolia){{sfn|Battaglia|Fornarino|Al-Zahery|Olivieri|2008}} Overall, Y-chromosome data seems to support the "Pioneer model", whereby heterogeneous groups of Neolithic farmers colonized selected areas of southern Europe via a primarily maritime route. Subsequent expansion of agriculture was facilitated by the adoption of its methods by indigenous Europeans, a process especially prominent in the Balkans.{{sfn|Di Giacomo|Luca|Popa|Akar|2004}}

A 2010 study of modern genetic diversity suggested that the lineage [[Haplogroup R1b (Y-DNA)|R1b1b2 (R-M269)]], like [[Haplogroup E1b1b (Y-DNA)|E1b1b]] or [[Haplogroup J (Y-DNA)|J]] lineages, spread together with farming from the Near East. Prior [[Archaeology|archaeological]]{{sfn|Zvelebil|2009a}}{{sfn|Zvelebil|2009b}}{{sfn|Bellwood|2004|}}{{page needed|date=October 2013}}{{sfn|Dokládal|Brožek|1961}}{{sfn|Bar-Yosef|1998}}{{sfn|Zvelebil|1989}} and [[Metrology|metrological]]{{sfn|Brace|Seguchi|Quintyn|Fox|2005}}{{sfn|Ricaut|Waelkens|2008}} studies had arrived at similar conclusions in support of the ''migrationist'' model. By this model, 80% of European Y chromosomes descend from incoming farmers, and most mtDNA from hunter-gatherers.{{sfn|Balaresque|Bowden|Adams|Leung|2010}}

In 2011, a study{{sfn|Busby|Brisighelli|Sánchez-Diz|Ramos-Luis|2011}} argued that the above migrationist model was flawed because of over-generalization in the studies of Baleresque 2010. Furthermore, Busby et al. 2012 point out "''For this haplogroup to be so ubiquitous, the population carrying R1b-S127 would have displaced most of the populations present in western Europe after the Neolithic agricultural transition''". Clearly common sense dictates that this did not happen. Also they go on to show that within the European specific R1b-M269 sub-lineage, defined by SNP S127, there exists distinct sub-haplogroups and at this level there exists several "''geographically localized pockets, with individual R1b-M269 sub- haplogroups dominating''". Their conclusions were that it is likely that R1b-S127 was already present in native European populations and grew into several geographically distinct sub-lineages across Europe before Neolithic expansion occurred.

In 2015, a study by Haak et al.about ancient DNA, concluded, however, that both R1a and R1b very likely spread into Europe from the [[Pontic-Caspian steppe]] after 3,000 BCE. They found there was a paucity of haplogroup R1b (or any other variant of R1) in the limited number of European population y-chromosome samples predating the Bronze Age, with only one of 70 individuals from Mesolithic and Neolithic Europe belonging to haplogroup R1. Among the analyzed male samples taken from [[Yamna culture]] sites, however, all possessed haplogroup R1b. Analysis of modern Europeans' autosomal DNA also gives support to a large [[Demic diffusion|population displacement]] from the steppe into Europe.<ref>« R1a and R1b are the most common haplogroups in many European populations today, and our results suggest that they spread into Europe from the East after 3,000 BCE. » in {{cite journal | author = Haak | year= 2015| title = Massive migration from the steppe was a source for Indo-European languages in Europe | doi = 10.1038/nature14317 | volume=522 | issue= 7555| journal=Nature | pages=207–211|display-authors=etal| bibcode= 2015Natur.522..207H | pmid=25731166 | pmc=5048219}}</ref>

In the 2016 Nature article 'The genetic history of Ice Age Europe', an individual from the [[Epigravettian]] cultural context in Italy (Villabruna) is mentioned, who lived circa 12,000 BCE and reportedly belonged to Y-DNA group R1b1a (L754).

===Mitochondrial haplogroups===
The data from [[Human mitochondrial DNA haplogroup|mtDNA]] is also interesting. European mtDNA haplogroup frequencies show little, if any, geographic patterning,{{sfn|Rosser|Zerjal|Hurles|Adojaan|2000}}{{sfn|Cavalli-Sforza|1997}} a result attributed to different molecular properties of mtDNA, as well as different migratory practices between females and males (Semino 2000). The vast majority of mtDNA lineages (60–70%) have been dated to have emerged either in the Mesolithic or Palaeolithic.{{sfn|Rosser|Zerjal|Hurles|Adojaan|2000}}{{sfn|Richards|Côrte-Real|Forster|MacAulay|1996}} whereas only 20% of mitochondrial lineages are "Neolithic". However, this conclusion has been questioned. Any undetected heterogeneity in the founder population would result in an overestimation in the age of the current population's molecular age. If this is true, then Europe could have been populated far more recently, e.g. during the Neolithic, by a more diverse founding population.{{sfn|Barbujani|Bertorelle|Chikhi|1998}}

As Chikhi states: "We argue that many mitochondrial lineages whose origin has been traced back to the Palaeolithic period probably reached Europe at a later time". However, Richards et al. (2000) maintain these findings even when founding population heterogeneity is considered. In one such study, Wolfgang Haak extracted [[ancient DNA|ancient]] mtDNA from what they present as early European farmers from the [[Linear Pottery Culture]] in central Europe. The bodies contained a 25% frequency of [[Haplogroup N1a (mtDNA)|mtDNA N1a]], a haplogroup which they assumed to be linked to the Neolithic. Today the frequency of this haplogroup is a mere 0.2%. Haak presented this as supportive evidence for a Palaeolithic European ancestry.{{sfn|Vandermeer|1975}}

A study of Neolithic skeletons in the [[Great Hungarian Plain]] in 2012 found a high frequency of eastern Asian maternal (mtDNA) haplogroups.{{sfn|Derenko|Malyarchuk|Denisova|Perkova|2012}}

===History of research [pre-2010]===
{{update}}
Perhaps the first scholar to posit a large-scale Neolithic migration, based on genetic evidence, was [[Luigi Luca Cavalli-Sforza]]. By applying [[principal component analysis]] to data from "classical genetic markers" (protein [[Polymorphism (biology)|polymorphisms]] from ABO blood groups, HLA loci, immunoglobulins, etc.), Cavalli-Sforza discovered interesting clues about the genetic makeup of Europeans. Although being very genetically homogeneous, several patterns did exist.{{sfn|Cavalli-Sforza|1997}} The most important one was a north-western to south-eastern [[cline (biology)|cline]] with a Near Eastern focus. Accounting for 28% of the overall genetic diversity in the European samples in his study, he attributed the cline to the spread of agriculture from the Middle East c. 10,000 to 6,000 years ago.{{sfn|Cavalli-Sforza|1997}}

Cavalli-Sforza's explanation of demic diffusions stipulated that the clines were due to the population expansion of neolithic farmers into a scarcely populated, hunter-gathering Europe, with little initial admixture between agriculturalists and foragers. The predicted route for this spread would have been from Anatolia to central Europe via the Balkans. However, given that the time depths of such patterns are not known, "associating them with particular demographic events is usually speculative".{{sfn|Rosser|Zerjal|Hurles|Adojaan|2000}} Apart from a demic Neolithic migration, the clines may also be compatible with other demographic scenarios (Barbujani and Bartorelle 2001), such as the initial Palaeolithic expansion, the Mesolithic (post-glacial) re-expansions{{sfn|Rosser|Zerjal|Hurles|Adojaan|2000}} or later (historic) colonizations.{{sfn|Di Giacomo|Luca|Popa|Akar|2004}}

Studies using direct DNA evidence have produced varying results. A notable proponent of Cavalli-Sforza's demic diffusion scenario is Chikhi. In his 1998 study, utilising polymorphic loci from seven hypervariable [[autosomal DNA]] loci, an autocorrelation analysis produced a clinal pattern closely matching that in Cavalli-Sforza's study. He calculated that the separation times were no older than 10,000 years. "The simplest interpretation of these results is that the current nuclear gene pool largely reflects the westward and northward expansion of a Neolithic group".{{sfn|Chikhi|Destro-Bisol|Bertorelle|Pascali|1998}}

Although the above studies propounded a 'significant' Neolithic genetic contribution, they did not quantify the exact magnitude of the genetic contribution. Dupanloup performed an admixture analysis based on several autosomal loci, mtDNA and NRY haplogroup frequencies. The study was based on the assumption that Basques were modern representatives of Palaeolithic hunter-gatherers' gene pool, and Near Eastern peoples were a proxy population for Neolithic farmers. Subsequently, they used admixture analysis to estimate the likely components of the contemporary European gene pool contributed by the two parental populations whose members hybridized at a certain moment in the past. The study suggested that the greatest Near Eastern admixture occurs in the Balkans (~80%) and Southern Italy (~60%), whilst it is least in peoples of the British Isles (estimating only a 20% contribution). The authors concluded that the Neolithic shift to agriculture entailed major population dispersal from the Near East.{{sfn|Dupanloup|Bertorelle|Chikhi|Barbujani|2004}}

Results derived from analysis of the non-recombining portion of the Y- chromosomes (NRY) produced, at least initially, similar gradients to the classic demic diffusion hypothesis. Two significant studies were Semino 2000 and Rosser 2000, which identified [[Haplogroup J2 (Y-DNA)|haplogroups J2]] and [[Haplogroup E1b1b (Y-DNA)|E1b1b (formerly E3b)]] as the putative genetic signatures of migrating Neolithic farmers from Anatolia,{{sfn|Rosser|Zerjal|Hurles|Adojaan|2000}} and therefore represent the Y-chromosomal components of a Neolithic demic diffusion.{{sfn|Semino|Passarino|Oefner|Lin|2000}}

This association was strengthened when King and Underhill (2002) found that there was a significant correlation between the distribution of Hg J2 and Neolithic painted pottery in European and Mediterranean sites. However, studies of the ancient Y-DNA from the earlier Neolithic cave burials of Cardium pottery culture shows they were mainly [[haplogroup G2]]a.{{sfn|Lacan|Keyser|Ricaut|Brucato|2011}} These 'Neolithic lineages' accounted for 22% of the total European Y chromosome gene pool, and were predominantly found in Mediterranean regions of Europe (Greece, Italy, southeastern Bulgaria, southeastern Iberia).
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