Is Yamnaya component in modern populations overrated?

[smd555]

Why I ask this question - there are many discrepancies in studies related to ancient DNA and modeling modern populations using ancient ones. For example, a popular model of the origin of current Europeans is a mixture of a steppe component (Yamnaya culture), Western hunters-gatherers (WHG) and Ancient Neolithic farmers (ANF). At the same time, the percent of the steppe component in the models is large, 40-60% in many European populations. Ancient DNA showed that the steppe component began to spread across Europe with the Corded Ware culture, and then the Bell-Beaker culture. And now I want to show you what the discrepancy is. I will take the calculator Eurogenes K13. In the table below, I have given as an example some populations of Yamnaya, Corded Ware and Bell-Beaker (first three rows), as well as some modern European populations. Please pay attention to the Amerindian component, which is highlighted in red. This component in Eurogenes k13 is characteristic of Eastern hunters-gatherers, as well as of Yamnaya culture (about 5%). It is also prominent in Corded Ware and Bell-Beaker cultures. Moreover, in proportion to the contribution of Yamnaya culture to them (the contribution of Yamnaya culture to Corded Ware is approximately 80%, to Bell-Beaker - approximately 60%). But in modern populations, this component is very low - on average 0.5%, that is, only 10 percent of the percentage in Yamnaya culture for this component. Genetic drift can be ignored, since after the spread of Corded Ware and Bell-Beakers, this was no longer a small group in which this Amerindian component could be reduced by genetic drift.



Is it possible that the Amerindian component is decreasing because certain allele frequencies "pick up" other components, that is, they are not additive? Or indeed the steppe component in current Europeans is not about 50%? I gave an amateur calculator as an example, in scientific works that use Admixture, the picture turns out to be similar.

[ugochaves]

Good question. Also, the pit culture had about 40-50% chg. Modern Europeans have a very low percentage of chg. About 6-11%.

[Grace O'Malley]

Both my daughter and myself have higher Amerindian than those European averages.

Daughter

Siberian 0.59 Pct
Amerindian 1.42 Pct

Myself

Siberian 0.75 Pct
Amerindian 1.37 Pct

So a bit closer to the Dutch Bell Beaker amounts.

[de Burgh II]

The thing about genetics of world populations is that it undergoes it own ecological niche and as you put it very succinctly; undergoes genetic drift and merges with the preexisting native population. A good example of positive genetic drift and gradual selective genetic alleles to survive a particular lifestyle is the polygenic selection for lactose persistence and height from the Western Steppe Herders (WSH) that is prevalent in European, Central/West Asian and South Asian dna.

A summary of several genetic studies published in Nature and Cell during the year 2015 is given by Heyd (2017):

Western Steppe Herders component "is lower in southern Europe and higher in northern Europe", where inhabitants have roughly 50% WSH ancestry on average. (Haak et al. 2015; Lazaridis et al. 2016)
It is linked to the migrations of Yamnaya populations dated to ca. 3000 BC (Allentoft et al. 2015; Haak et al. 2015);
Third-millennium Europe (and prehistoric Europe in general) was "a highly dynamic period involving large-scale population migrations and replacement" (Allentoft et al. 2015);
The Yamnaya migrations are linked to the spread of Indo-European languages (Allentoft et al. 2015; Haak et al. 2015);
The plague (Yersinia pestis) was spreaded into Europe during the third millennium BC (Rasmussen et al. 2015), and it stemmed from migrations from the Eurasian steppes;
Yamnaya peoples have the highest ever calculated genetic selection for stature (Mathieson et al. 2015). [...]

About a quarter of 5 ancient DNA samples from Yamnaya sites have an allele that is associated with lactase persistence, conferring lactose tolerance into adulthood.[45] Steppe-derived populations such as the Yamnaya are thought to have brought this trait to Europe from the Eurasian steppe, and it is hypothesized that it may have given them a biological advantage over the European populations who lacked it.[46][47][48]

Eurasian steppe populations display higher frequencies of the lactose tolerance allele than European farmers and hunter gatherers who lacked steppe admixture.[49]

https://en.wikipedia.org/wiki/Western_Steppe_Herders

Hence, WSH genes brought positive genetic traits and got positively selected for as a beneficial mutation in the gene pool that merged with the preexisting Neolithic and Hunter-Gatherer populations that existed prior.

It is no secret that Native American DNA is a hybridization between Ancient North Eurasian and Basal East Eurasian hominin.

Indigenous American populations descend from an Ancient Paleo-Siberian population, itself a combination of an Ancient East Asian lineage which diverged from other East Asian peoples prior to the Last Glacial Maximum, between 36,000 and 25,000 years ago, and subsequently migrated into Siberia, were they merged with a primarily West Eurasian (Ancient North Eurasians), deeply related to European hunter-gatherers. They later dispersed throughout the Americas after about 16,000 years ago (exceptions being the Na-Dene and Eskimo–Aleut speaking groups, which are derived partially from Siberian populations which entered the Americas at a later time).[4][5]

Analyses of genetics among Indigenous American and Siberian populations have been used to argue for early isolation of founding populations on Beringia[6] and for later, more rapid migration from Siberia through Beringia into the New World.[7] The microsatellite diversity and distributions of the Y lineage specific to South America indicates that certain Indigenous American populations have been isolated since the initial peopling of the region.[8] The Na-Dene, Inuit and Native Alaskan populations exhibit Haplogroup Q-M242; however, they are distinct from other Indigenous Americans with various mtDNA and atDNA mutations.[9][10][11] This suggests that the peoples who first settled in the northern extremes of North America and Greenland derived from later migrant populations than those who penetrated farther south in the Americas.[12][13] Linguists and biologists have reached a similar conclusion based on analysis of Indigenous American language groups and ABO blood group system distributions.[14][15][16][17] [...]

https://en.wikipedia.org/wiki/Geneti...f_the_Americas

A good example of very isolated genetic drift are the Tarim Mummies which were a mix between ANE (Ancient North Eurasian and AEE (Ancient East Eurasian) hominins before they hybridized with more East Eurasian hominins (Turkic tribes) that created the present day Uyghurs.

The Tarim mummies are a series of mummies discovered in the Tarim Basin in present-day Xinjiang, China, which date from 1800 BC to the first centuries BC,[1][2][3] with a new group of individuals recently dated to between c. 2100 and 1700 BC.[4][5] The Tarim population to which the earliest mummies belonged was agropastoral, and they lived circa 2000 BC in what was formerly a freshwater environment, which has now become desertified.[6]

A genomic study published in 2021 found that these early mummies (dating from 2,135 to 1,623 BC) had high levels of Ancient North Eurasian ancestry (ANE, about 72%), with smaller admixture from Ancient Northeast Asians (ANA, about 28%), but no detectable Western Steppe-related ancestry.[7][8] They formed a genetically isolated local population that "adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert."[9] These mummified individuals were long suspected to have been "Proto-Tocharian-speaking pastoralists", ancestors of the Tocharians, but this has now been largely discredited by their absence of a genetic connection with Indo-European-speaking migrants, particularly the Afanasievo or BMAC cultures.[10] [...]

https://en.wikipedia.org/wiki/Tarim_mummies

[ugochaves]

The thing about genetics of world populations is that it undergoes it own ecological niche and as you put it very succinctly; undergoes genetic drift and merges with the preexisting native population. A good example of positive genetic drift and gradual selective genetic alleles to survive a particular lifestyle is the polygenic selection for lactose persistence and height from the Western Steppe Herders (WSH) that is prevalent in European, Central/West Asian and South Asian dna.



https://en.wikipedia.org/wiki/Western_Steppe_Herders

Hence, WSH genes brought positive genetic traits and got positively selected for as a beneficial mutation in the gene pool that merged with the preexisting Neolithic and Hunter-Gatherer populations that existed prior.

It is no secret that Native American DNA is a hybridization between Ancient North Eurasian and Basal East Eurasian hominin.



https://en.wikipedia.org/wiki/Geneti...f_the_Americas

A good example of very isolated genetic drift are the Tarim Mummies which were a mix between ANE (Ancient North Eurasian and AEE (Ancient East Eurasian) hominins before they hybridized with more East Eurasian hominins (Turkic tribes) that created the present day Uyghurs.



https://en.wikipedia.org/wiki/Tarim_mummies

If the steppe dwellers are modeled as 50% ehg and 50% chg. Where has the chg gone from modern Europeans? Can the disappearance of chg be explained by gene drift and selection?
Target: Swedish
Distance: 6.2768% / 0.06276754
42.8 Barcin_N
40.2 EHG
9.8 WHG
7.2 CHG

[de Burgh II]

If the steppe dwellers are modeled as 50% ehg and 50% chg. Where has the chg gone from modern Europeans? Can the disappearance of chg be explained by gene drift and selection?
Target: Swedish
Distance: 6.2768% / 0.06276754
42.8 Barcin_N
40.2 EHG
9.8 WHG
7.2 CHG

Thats the thing about natural selection and positive sexual selection; it is a continuous generational cycle of polygenic alleles constantly mutating on a molecular level that effects one's genotype and phenotype to survive a particular ecological niche that has strong external selective pressures to survive in a particular environment that takes hundreds if not; thousands of years to adapt. Throughout this time, every hominin population are genetically replacing a previous population that merges into a new genetic population that becomes genetically distinctive over time. As reiterated here:

Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within lineages.[1][2][3] Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book On the Origin of Species.[4] He also identified sexual selection as a likely mechanism, but found it problematic.

There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments.[citation needed] Whether genetic drift is a minor or major contributor to speciation is the subject of much ongoing discussion.

Rapid sympatric speciation can take place through polyploidy, such as by doubling of chromosome number; the result is progeny which are immediately reproductively isolated from the parent population. New species can also be created through hybridization, followed by reproductive isolation, if the hybrid is favoured by natural selection. [...]

https://en.wikipedia.org/wiki/Speciation

A genetic isolate is a population of organisms with little genetic mixing with other organisms within the same species due to geographic isolation or other factors that prevent reproduction. Genetic isolates form new species through an evolutionary process known as speciation. All modern species diversity is a product of genetic isolates and evolution.

The current distribution of genetic differences and isolation within and among populations is also influenced by genetic processes, which can give significant input into evolution's basic principles. The resulting genetic diversity within a species' distribution range is frequently unequally distributed, and significant disparities can occur in the series of fields when population dispersion and isolation are critical for species survival.[1]

The interrelationship of genetic drift, gene flow, and natural selection determines the level and dispersion of genetic differences between populations and among species assemblages.[2] Geographic and natural elements may likewise add to these cycles and further impact species' advanced examples of hereditary variety, such as genetic differences that cause genetic isolation.[3] Genetic variations are often unequally distributed over a species' geographic distribution, with differences between populations at the geographic center and the range's extremities.[4]

Significant gene flow occurs in core populations, resulting in genetic uniformity. In contrast, low gene flow, severe genetic drift, and diverse selection conditions occur in range periphery populations, enhancing genetic isolation and heterogeneity among people.[5] Genetic differentiation resulting from genetic isolation occurs as significant alterations in genetic variations, such as fluctuations in allelic frequencies, that accumulate over time with geographic regional boundaries.

Significant genetic diversity can be detected toward the limits of a species range, where population fragmentation and isolation are more likely to affect genetic processes. Fragmentation is the division of a large population into smaller, geographically separated habitats, resulting in genetic differences within and across groups.[6] Regional splitting is produced by a variety of factors, including environmental processes that regularly change a species' indigenous distribution.[7] Additionally, human-caused environmental changes such as deforestation and land degradation can result in rapid changes in a species' distribution, leading to population decrease, segmentation, and regional isolation.[8]

https://en.wikipedia.org/wiki/Genetic_isolate

Over time, genetic divergence and distinctiveness take a hold on every hominin species that makes them genetically divergent around the planet. It is a highly instinctive and genetic process that happens over time that people/animals can instinctively perceive and differentiate close kin from foreign intruders (Genetic Similarity Theory) that bees intuitively perceive:

It is known that there is a genetic basis to the labelling of individuals for kin recognition in the honey bee, Apis mellifera. This study shows that individual workers reared in total isolation are able to discriminate between their full sisters and maternal half sisters. When individuals were reared with a half sister, recognition of their own patritype persisted, together with a comparable awareness of the patritype of their half sisters. Workers, when reared in mixed patritype groups of 10, showed no tendency to discriminate between full and half sisters, i.e. they appeared to learn both nestmate patritypes equally well. However, the labelling phenotypes of individuals reared together became more uniform, possibly through the transfer of substances during trophallaxis and mutual grooming. Workers exposed to 10 patritypes from their full sister patriline were more likely to accept an unfamiliar full sister than workers exposed to only five. Finally, workers reared in the hive appeared to retain an ability to discriminate their own patritype; i.e., even though the hive consisted of two worker patritypes, they discriminated between unfamiliar full and half sisters that had been reared under the same controlled conditions in an incubator. [...]

https://www.sciencedirect.com/scienc...03347286802500

Nevertheless, it is known that hybridization in Wildebeest and Dingo populations is always disastrous between two highly divergent populations that are genetically adapted towards a certain ecological niche that may result in cranial and skeletal deformations:

Genetics and hybrids

The diploid number of chromosomes in the wildebeest is 58.[24] Chromosomes were studied in a male and a female wildebeest. In the female, all except a pair of very large submetacentric chromosomes were found to be acrocentric. Metaphases were studied in the male's chromosomes, and very large submetacentric chromosomes were found there, as well, similar to those in the female both in size and morphology. Other chromosomes were acrocentric. The X chromosome is a large acrocentric and the Y chromosome a minute one.[15][25]

The two species of the wildebeest are known to hybridise. Male black wildebeest have been reported to mate with female blue wildebeest and vice versa.[26] The differences in social behaviour and habitats have historically prevented interspecific hybridisation between the species, but hybridisation may occur when they are both confined within the same area. The resulting offspring are usually fertile. A study of these hybrid animals at Spioenkop Dam Nature Reserve in South Africa revealed that many had disadvantageous abnormalities relating to their teeth, horns, and the wormian bones in the skull.[27] Another study reported an increase in the size of the hybrid as compared to either of its parents. In some animals, the tympanic part of the temporal bone is highly deformed, and in others, the radius and ulna are fused.[28]

https://en.wikipedia.org/wiki/Wildebeest

In 2023, a study of 402 wild and captive dingoes using 195,000 points across the dingo genome indicates that past studies of hybridisation were over-estimated and that pure dingoes are more common than they were originally thought to be.[158][159]

In 2021, DNA testing of over 5,000 wild-living canines from across Australia found that 31 were feral domestic dogs and 27 were first generation hybrids. This finding challenges the perception that dingoes are nearly extinct and have been replaced by feral domestic dogs.[160]

Coat colour cannot be used to distinguish hybrids.[64] Dingo-like domestic dogs and dingo-hybrids can be generally distinguished by the more dog-typical kind of barking that exists among the hybrids, and differences in the breeding cycle,[161] certain skull characteristics,[162] and genetic analyses[163] can be used for differentiation. Despite all the characteristics that can be used for distinguishing between dingoes and other domestic dogs, there are two problems that should not be underestimated. First, there is no real clarity regarding at what point a dog is regarded as a "pure" dingo,[136] and, secondly, no distinguishing feature is completely reliable — it is not known which characteristics permanently remain under the conditions of natural selection.

There are two main opinions regarding this process of interbreeding. The first, and likely most common, position states that the "pure" dingo should be preserved via strong controls of the wild dog populations, and only "pure" or "nearly-pure" dingoes should be protected.[164] The second position is relatively new and is of the opinion that people must accept that the dingo has changed and that it is impossible to bring the "pure" dingo back. Conservation of these dogs should therefore be based on where and how they live, as well as their cultural and ecological role, instead of concentrating on precise definitions or concerns about "genetic purity".[165] Both positions are controversially discussed.

Due to this interbreeding, there is a wider range of fur colours, skull shapes and body size in the modern-day wild dog population than in the time before the arrival of the Europeans. Over the course of the last 40 years,[when?] there has been an increase of about 20% in the average wild dog body size.[166] It is currently unknown whether, in the case of the disappearance of "pure" dingoes, remaining hybrids would alter the predation pressure on other animals. It is also unclear what kind of role these hybrids would play in the Australian ecosystems. However, it is unlikely that the dynamics of the various ecosystems will be excessively disturbed by this process.[86]

In 2011, a total of 3,941 samples were included in the first continent-wide DNA study of wild dogs. The study found that 46% were pure dingoes which exhibited no dog alleles (gene expressions). There was evidence of hybridisation in every region sampled. In Central Australia only 13% were hybrids; however, in southeastern Australia 99% were hybrids or feral dogs. Pure dingo distribution was 88% in the Northern Territory, intermediate numbers in Western Australia, South Australia and Queensland, and 1% in New South Wales and Victoria. Almost all wild dogs showed some dingo ancestry,[167][168] with only 3% of dogs showing less than 80% dingo ancestry. This indicates that domestic dogs have a low survival rate in the wild or that most hybridisation is the result of roaming dogs that return to their owners. No populations of feral dogs have been found in Australia.[167]

In 2016, a three dimensional geometric morphometric analysis of the skulls of dingoes, dogs and their hybrids found that dingo-dog hybrids exhibit morphology closer to the dingo than to the parent group dog. Hybridisation did not push the unique Canis dingo cranial morphology towards the wolf phenotype, therefore hybrids cannot be distinguished from dingoes based on cranial measures. The study suggests that the wild dingo morphology is dominant when compared with the recessive dog breed morphology, and concludes that although hybridisation introduces dog DNA into the dingo population, the native cranial morphology remains resistant to change.

https://en.wikipedia.org/wiki/Dingo

In other words, in the case for hybrids; there are two outcomes: it is either genetically incompatible with either parental populations or it reverted to one out of the two parental populations such as the Dingo cranial morphology is more dominant over the domestic dogs genetics.

Take the global irradance (solar radiation) levels that hit planet Earth on a daily basis:



These strong selective, external pressures influence one's skin pigmentation and tanning ability to adapt to certain continents around the world. That is why in certain areas around the world that recessive genetic mutations such as red heads, blond hair/blue eyes and light skin is prevalent since there isn't a strong selective environmental factor against said neutral mutations. Light features have strong positive selection to continue in the gene pool since it is highly attractive in some hominin populations in certain geographical hospots around the world. Namely, blonde hair and blue eyes in Germanic, Baltic, Oceanian and Slavic populations. Red hair in Insular Celtic, Steppic, Central Asian and East Asian populations, etc.

[ugochaves]

Thats the thing about natural selection and positive sexual selection; it is a continuous generational cycle of polygenic alleles constantly mutating on a molecular level that effects one's genotype and phenotype to survive a particular ecological niche that has strong external selective pressures to survive in a particular environment that takes hundreds if not; thousands of years to adapt. Throughout this time, every hominin population are genetically replacing a previous population that merges into a new genetic population that becomes genetically distinctive over time. As reiterated here:



https://en.wikipedia.org/wiki/Speciation



https://en.wikipedia.org/wiki/Genetic_isolate

Over time, genetic divergence and distinctiveness take a hold on every hominin species that makes them genetically divergent around the planet. It is a highly instinctive and genetic process that happens over time that people/animals can instinctively perceive and differentiate close kin from foreign intruders (Genetic Similarity Theory) that bees intuitively perceive:



https://www.sciencedirect.com/scienc...03347286802500

Nevertheless, it is known that hybridization in Wildebeest and Dingo populations is always disastrous between two highly divergent populations that are genetically adapted towards a certain ecological niche that may result in cranial and skeletal deformations:



https://en.wikipedia.org/wiki/Wildebeest



https://en.wikipedia.org/wiki/Dingo

In other words, in the case for hybrids; there are two outcomes: it is either genetically incompatible with either parental populations or it reverted to one out of the two parental populations such as the Dingo cranial morphology is more dominant over the domestic dogs genetics.

Take the global irradance (solar radiation) levels that hit planet Earth on a daily basis:



These strong selective, external pressures influence one's skin pigmentation and tanning ability to adapt to certain continents around the world. That is why in certain areas around the world that recessive genetic mutations such as red heads, blond hair/blue eyes and light skin is prevalent since there isn't a strong selective environmental factor against said neutral mutations. Light features have strong positive selection to continue in the gene pool since it is highly attractive in some hominin populations in certain geographical hospots around the world. Namely, blonde hair and blue eyes in Germanic, Baltic, Oceanian and Slavic populations. Red hair in Insular Celtic, Steppic, Central Asian and East Asian populations, etc.

For Spaniards, chg and ehg are declining evenly, as many farmers have joined them. Among the Germans, Balts and Slavs, only chg disappears. Perhaps genetics is going the wrong way today? I think that the source of Indo-Europeans among the peoples of Europe was different initially. Sredny stog is not suitable as a common ancestor for all modern Indo-Europeans of Europe. Eastern Indo-Europeans had more ehg. Western Indo-Europeans had the equivalent ehg and chg.

[Voskos]

Whatever the reason for their demise on the steppe itself, the Yamnaya-descended R-Z2103 patrilineages survived in Armenia, down to the present-day where this clade is present in appreciable frequencies in all studied Armenian groups (38), despite the substantial dilution of autosomal steppe ancestry inferred in our study. The persistent and lasting presence of Yamnaya patrilineal descendants in Armenia contrasts with mainland Europe and South Asia where steppe ancestry was introduced by people who were not patrilineal descendants of the dominant R-M12149 lineage of the Yamnaya population. Instead, they belonged to different descent groups that had received autosomal steppe admixture while carring different predominant Y-chromosome lineages.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064553/

[ugochaves]

Whatever the reason for their demise on the steppe itself, the Yamnaya-descended R-Z2103 patrilineages survived in Armenia, down to the present-day where this clade is present in appreciable frequencies in all studied Armenian groups (38), despite the substantial dilution of autosomal steppe ancestry inferred in our study. The persistent and lasting presence of Yamnaya patrilineal descendants in Armenia contrasts with mainland Europe and South Asia where steppe ancestry was introduced by people who were not patrilineal descendants of the dominant R-M12149 lineage of the Yamnaya population. Instead, they belonged to different descent groups that had received autosomal steppe admixture while carring different predominant Y-chromosome lineages.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064553/

Super! Armenians have about 1-5% of steppe autosomal origin. The Balts, Eastern Slavs, Finns, Scandinavians have more than 50%. They have different haplogroups and subclades, which are not found in any steppe culture. Even cord ceramics have other subclades of r1a. Question! Where the fuck are our ancestors?

[de Burgh II]

For Spaniards, chg and ehg are declining evenly, as many farmers have joined them. Among the Germans, Balts and Slavs, only chg disappears. Perhaps genetics is going the wrong way today? I think that the source of Indo-Europeans among the peoples of Europe was different initially. Sredny stog is not suitable as a common ancestor for all modern Indo-Europeans of Europe. Eastern Indo-Europeans had more ehg. Western Indo-Europeans had the equivalent ehg and chg.

It is no secret that Eastern Europeans retained their original Proto-Indo-European phenotypes and genetics since they score low Neolithic farmer autosomal DNA since that is where Indo-European dna came from. Whereas in Western Europe, the pre-Indo European Neolithic peoples found refuge in Southern and Western Europe which was "WHG' territory for a time being. Then, the Indo-European Bell-Beaker peoples came from the East and hybridized with the preexisting Western Hunter-Gatherer/Neolithic hybridized hominins.