Agricultural origins on the Anatolian plateau

anatolia-neolithic-agriculture

New paper (behind paywall) Agricultural origins on the Anatolian plateau, by Baird et al. PNAS (2018), published ahead of print (March 19).

Abstract (emphasis mine):

This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the mid ninth millennium cal BC, but also demonstrate that uptake was not uniform, and that some communities chose to actively disregard cultivation. Adoption of cultivation was accompanied by experimentation with sheep/goat herding in a system of low-level food production that was integrated into foraging practices rather than used to replace them. Furthermore, rather than being a short-lived transitional state, low-level food production formed part of a subsistence strategy that lasted for several centuries, although its adoption had significant long-term social consequences for the adopting community at Boncuklu. Material continuities suggest that Boncuklu’s community was ancestral to that seen at the much larger settlement of Çatalhöyük East from 7100 cal BC, by which time a modest involvement with food production had been transformed into a major commitment to mixed farming, allowing the sustenance of a very large sedentary community. This evidence from Central Anatolia illustrates that polarized positions explaining the early spread of farming, opposing indigenous adoption to farmer colonization, are unsuited to understanding local sequences of subsistence and related social change. We go beyond identifying the mechanisms for the spread of farming by investigating the shorter- and longer-term implications of rejecting or adopting farming practices.

anatolia-neolithic
Map of central Anatolia showing the principal sites mentioned in the text.

Interesting excerpts:

The persistence of foraging and rejection of farming at Pınarbaşı is also worthy of further consideration. Pınarbaşı’s longevity as a settlement locale in the early Holocene appears to have been based on hunting of wild mammals, wetland exploitation, and significant focus on nut exploitation, all afforded by its ecotonal setting between the hills, plain, and wetland. Perhaps this existing diversity, including nutritious storable plant resources, was a key factor in a lack of interest in adopting cultivation. Another factor may have been a conscious desire to maintain traditional identities and long-standing distinctions with other communities, in part reflected in its particular way of life and its specific connections with particular elements in landscape, for example the almond and terebinth woodlands whose harvests underwrote the continuity of the Pınarbaşı settlement.

The variability in response to the possibilities of early food production in a relatively small geographical area demonstrated here is notable and provides an example useful in evaluating the spread of farming in other regions. It shows the possible role of indigenous foragers, the potential patchwork and diffuse nature of the spread of farming, the lack of homogeneity likely in the communities caught up in the process, the probability of significant continuities in local cultural traditions within the process, and the potentially long-term stable adaptation offered by lowlevel food production. The strength of identities linked to exploitation of particular foods and particular parts of the landscape may have been a major factor contributing to rejection or adoption of food production by indigenous foragers.

The results are also relevant for understanding the processes that underpinned the initial development of farming within the Fertile Crescent itself: that is, the region in which the wild progenitors of the Old World founder crops and stock animals are found. Recent research has rejected the notion of a core area for farming’s first appearance in southwest Asia and demonstrated that farming developed in diverse ways over the Fertile Crescent zone from the southern Levant to the Zagros, very analogous to the situation just described for Central Anatolia (2). Cultivation, herding, and domestication developed in that region, and it seems inescapable that exchange of crops and herded animals occurred between communities (2), involving a spread of farming within the Fertile Crescent, leading eventually to the Neolithic farming package that was so similar across the region and which spread into Europe (5). Central Anatolia was clearly linked to the Fertile Crescent, with significant evidence of exchange and some shared cultural traditions from at least the Epipaleolithic (22). The evidence presented here demonstrates very clearly the movement of crops between settlements and regions in early phases of the Neolithic through exchange, and thus allows us to identify episodes of crop exchange that were probably taking place within the Fertile Crescent itself, but are difficult, if not impossible, to distinguish due to the presence of crop progenitors across much of the region.

A very interesting read in combination with 14C-radiometric data and climatic conditions showing potential triggers of dispersal of Neolithic lifeways from Turkey to Southeast Europe, e.g. Dispersal of Neolithic Lifeways: Absolute Chronology and Rapid Climate Change in Central and West Anatolia, by Lee Clare & Bernhard Weninger, in The Neolithic in Turkey, Vol.6 (2014), Edited by Mehmet Özdogan, Nezih Basgelen, Peter Kuniholm.

anatolian-neolithic-aegean
The Late Neolithic (6600-6000 cal. BC) witnesses the rapid westward dispersal of Neolithic communities, apparently reaching the Aegean in the space of a very short time (ca. 6600 cal. BC). This process is linked to the demand of individuals, groups, and communities for less vulnerable conditions in the face of climate fluctuation associated with RCC. Coastal areas not only offered respite from more frequently occurring physical impacts (extreme winters and high drought risk) in inner Anatolia, they may also have provided refuge for weaker (more vulnerable) social groups (…).

Featured image, from the latter: “In the Early Pottery Neolithic (7000-6600 cal. BC) there occurs a clear break with precedeing (PPN) traditions, attested by abandonment and decreasing size of settlements, albeit that evidence for migration of groups westwards towards the Aegean is still ambiguous (black arrows: human migrations; white arrows: Anatolian obsidian)”

See also:

Reconstructing the genetic history of late Neanderthals

neanderthal-late-europe

New paper (behind paywall) Reconstructing the genetic history of late Neanderthals, by Mateja Hajdinjak, Qiaomei Fu, Alexander Hübner, et al. Nature (2018).

Abstract (edited):

Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

neanderthal-denisova-modern-humans-dna
Phylogenetic relationships of late Neanderthals. a, Bayesian phylogenetic tree of mitochondrial genomes of 23 Neanderthals, 3 Denisovans, 64 modern humans and a hominin from Sima de los Huesos. The posterior probabilities for the branches are shown. b, Neighbour-joining tree of Y chromosome sequences of Mezmaiskaya 2, Spy 94a, 175 present-day humans21 and two present-day humans carrying the A00 haplogroup30. The number of substitutions is shown above the branches. c, Neighbour-joining tree of nuclear genomes based on autosomal transversions among late Neanderthals, Vindija 33.19, Mezmaiskaya 1, Altai Neanderthal, Denisovan and 12 present-day humans. Bootstrap support values after 1,000 replications are shown.

Interesting excerpts (edited):

(…) Mezmaiskaya 2 shared more derived alleles with the other late Neanderthals than with Mezmaiskaya 1 (− 2.13 ≤ Z ≤ − 9.56; Supplementary Information 9), suggesting that there was a population turnover towards the end of Neanderthal history. This turnover may have been the result of a population related to western Neanderthals replacing earlier Neanderthals in the Caucasus, or the replacement of Neanderthals in western Europe by a population related to Mezmaiskaya 2. The timing of this turnover coincides with pronounced climatic fluctuations during Marine Isotope Stage 3 between 60 and 24 ka, when extreme cold periods in northern Europe may have triggered the local extinction of Neanderthal populations and subsequent re-colonization from refugia in southern Europe or western Asia.

(…) the majority of gene flow into early modern humans appears to have originated from one or more Neanderthal populations that diverged from other late Neanderthals after their split from the Altai Neanderthal about 150 ka, but before the split from Mezmaiskaya 1 at least 90 ka. Owing to the scarcity of overlapping genetic data from Oase 1, whose genome revealed an unusually high percentage of Neanderthal ancestry11, we were unable to resolve whether one of these late Neanderthals was significantly closer than others to the introgressing Neanderthal in Oase 1.

Interbreeding between Neanderthals and early modern humans is likely to have occurred intermittently, presumably resulting in gene flow in both directions. However, when we applied an approach that uses the extended length of haplotypes expected from recent introgression into the analysed late Neanderthals, we did not find any indications of recent gene flow from early modern humans to the late Neanderthals. We caution that given the small number of analysed Neanderthals we cannot exclude that such gene flow occurred. However, it is striking that Oase 1, one of two early modern humans that overlapped in time with late Neanderthals, showed evidence for recent additional Neanderthal introgression whereas none of the late Neanderthals analysed here do. This may indicate that gene flow affected the ancestry of modern human populations more than it did Neanderthals

Related:

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

taforalt-samples

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations, by van de Loosdrecht et al. Science (2018).

Abstract

North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.

Excerpts:

We analyzed the genetic affinities of the Taforalt individ-uals by performing principal component analysis (PCA) and model-based clustering of worldwide data (Fig. 2). When pro-jected onto the top PCs of African and West Eurasian popu-lations, the Taforalt individuals form a distinct cluster in an intermediate position between present-day North Africans (e.g., Amazighes (Berbers), Mozabite and Saharawi) and East Africans (e.g., Afar, Oromo and Somali) (Fig. 2A). Consist-ently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (18). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleolithic Natufians and Pre-Pottery Neolithic Levantines (“Levant_N”) (16). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maximized in early Holocene Levantines, East African hunter-gatherer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2B). In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2B).

Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool.

Mitochondrial consensus sequences of the Taforalt indi-viduals belong to the U6a (n = 6) and M1b (n = 1) haplogroups (15), which are mostly confined to present-day populations in North and East Africa (7). U6 and M1 have been proposed as markers for autochthonous Maghreb ancestry, which might have been originally introduced into this region by a back-to-Africa migration from West Asia (6, 7). The occurrence of both haplogroups in the Taforalt individuals proves their pre-Holocene presence in the Maghreb.
(…) the diversification of haplogroup U6a and M1 found for Taforalt is dated to ~24,000 yBP (fig. S23), which is close in time to the earliest known appearance of the Iberomaurusian in Northwest Africa (25,845-25,270 cal. yBP at Tamar Hat (26)).

taforalt-admixture
A summary of the genetic profile of the Taforalt individuals. (A) The top two PCs calculated from present-day African, Near Eastern and South European individuals from 72 populations. The Taforalt individuals are projected thereon (red-colored circles). Selected present-day populations are marked by colored symbols. Labels for other populations (marked by small grey circles) are provided in fig. S8. (B) ADMIXTURE results of chosen African and Middle Eastern populations (K = 10). Ancient individuals are labeled in red color. Major ancestry components in Taforalt are maximized in early Holocene Levantines (green), West Africans (purple) and East African Hadza (brown). The ancestry component prevalent in pre-Neolithic Europeans (beige) is absent in Taforalt.

The relationships of the Iberomaurusian culture with the preceding MSA, including the local backed bladelet technologies in Northeast Africa, and the Epigravettian in southern Europe have been questioned (13). The genetic profile of Taforalt suggests substantial Natufian-related and sub-Saharan African-related ancestries (63.5% and 36.5%, respec-tively), but not additional ancestry from Epigravettian or other Upper Paleolithic European populations. Therefore, we provide genomic evidence for a Late Pleistocene connection between North Africa and the Near East, predating the Neolithic transition by at least four millennia, while rejecting a potential Epigravettian gene flow from southern Europe into northern Africa within the resolution of our data.

It seems that the Taforalt gene pool (ca. 13000-12000 BC) cannot be explained by a connection with Upper Palaeolithic Europeans, but a more archaic admixture, so the authors cannot prove a migration through the Strait of Gibraltar or Sicily.

Nevertheless, these results apparently suggest:

  • That there is no contact before ca. 12000 BC through the Strait of Gibraltar; therefore the Sicilian route I support for the migration of R1b-V88 lineages is still the most likely one.
  • That the North African connection with Natufians is quite old – for which we already had modern Y-DNA investigation – , and therefore unlikely to be related to the Afroasiatic expansion.

I am glad I had some more time this week to read at least some interesting parts of the published papers, because the information to process is becoming insanely huge…

Related:

Two sources of archaic Denisovan ancestry in East Asia, one possibly after the isolation of Native Americans

east-asian-ancestry

Open access paper Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, by Sharon L. Browning, Brian L. Browning, Zhou, Tucci, & Akey, Cell (2018).

Summary:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

neanderthal-denisovan-admixture
Mean detected archaic sequence per individual (Mb)

The discussion on the potential implication of the paper:

Featured image, from the article: Contour Density Plots of Match Proportion of Introgressed Segments to the Altai Neanderthal and Altai Denisovan Genomes.

Related:

Genetic ancestry of Hadza and Sandawe peoples reveals ancient population structure in Africa

Open access paper Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa, by Shriner, Tekola-Ayele, Adeyemo, & Rotimi, GBE (2018).

Abstract (emphasis mine):

The Hadza and Sandawe populations in present-day Tanzania speak languages containing click sounds and therefore thought to be distantly related to southern African Khoisan languages. We analyzed genome-wide genotype data for individuals sampled from the Hadza and Sandawe populations in the context of a global data set of 3,528 individuals from 163 ethno-linguistic groups. We found that Hadza and Sandawe individuals share ancestry distinct from and most closely related to Omotic ancestry; share Khoisan ancestry with populations such as ≠Khomani, Karretjie, and Ju/’hoansi in southern Africa; share Niger-Congo ancestry with populations such as Yoruba from Nigeria and Luhya from Kenya, consistent with migration associated with the Bantu Expansion; and share Cushitic ancestry with Somali, multiple Ethiopian populations, the Maasai population in Kenya, and the Nama population in Namibia. We detected evidence for low levels of Arabian, Nilo-Saharan, and Pygmy ancestries in a minority of individuals. Our results indicate that west Eurasian ancestry in eastern Africa is more precisely the Arabian parent of Cushitic ancestry. Relative to the Out-of-Africa migrations, Hadza ancestry emerged early whereas Sandawe ancestry emerged late.

Excerpts:

Introduction
In the Hadza population, the distribution of Y chromosomes includes mostly B2 haplogroups, with a smaller number of E1b1a haplogroups, which are common in Niger-Congo-speaking populations, and E1b1b haplogroups, which are common in Cushitic populations (Tishkoff, et al. 2007). In the Sandawe population, E1b1a and E1b1b haplogroups are more common, with lower frequencies of B2 and A3b2 haplogroups (Tishkoff, et al. 2007).

Conclusion
We found that Hadza ancestry diverged early, rather than late. We found evidence for contributions of Cushitic and Niger-Congo ancestries in Tanzania, consistent with the movements of herding and cultivating Cushitic speakers ~4,000 years ago and agricultural Niger-Congo speakers ~2,500 years ago (Newman 1995). However, we did not find evidence of a substantial contribution of Nilo-Saharan ancestry that might have resulted from movement of pastoralist Nilo-Saharan speakers (Newman 1995). We also identified west Eurasian ancestry in eastern and southern African populations more precisely as the Arabian parent of Cushitic ancestry. Finally, our ancestry analyses support the hypothesis that Omotic, Hadza, and Sandawe languages group together, rather than Omotic languages belonging to the Afroasiatic family and Hadza and Sandawe languages belonging to the Khoisan family.

I don’t like linguistic assumptions from admixture analysis; especially from scarce modern samples, as in this case.

Nevertheless, these papers may help clarify the different nature of Omotic and Cushitic among Afroasiatic languages, and thus leave the origin of Afroasiatic either:

a) To the east, with the traditionalist Afroasiatic – Semitic/Hamitic homeland association.

afroasiatic-homeland
Expansion of Afroasiatic

b) To the west, near modern Chadic languages (associated with the expansion of R1b-V88 subclades through a Green Sahara), as I suggested.

Related:

On the potential origin of Caucasus hunter-gatherer ancestry in Eneolithic steppe cultures

An interesting open genomic question is the origin and spread of Caucasus hunter-gatherer (CHG) ancestry in steppe populations during the Eneolithic.

My broad theory regarding the appearance of this ancestral component is based on:

Two recently published papers ivestigating the Don Region may shed some light on this issue:

Plant food subsistence in the human diet of the Bronze Age Caspian and Low Don steppe pastoralists: archaeobotanical, isotope and 14C data, by Shishlina, Bobrov, Simakova, et al. Veget Hist Archaeobot (2018).

EDIT (16/3/2018): You can now read or download the paper at Academia.edu.

Abstract:

The paper presents the result of analysis of charred food on the interior part of the vessels from the graves of the East Manych and West Manych Catacomb archaeological cultures (2500–2350 cal bc). The phytolith and pollen analyses identified pollen of wild steppe plants and phytoliths of domesticated gramineous plants determined as barley phytoliths. Direct 14С dating of one of the samples demonstrates that barley spikelets and stems were used in funeral rites by local steppe communities. However, there are no data suggesting that steppe inhabitants of the Lower Don Region were engaged in agriculture in the mid-3000 bc. Supposedly, barley could have reached the steppes through seasonal migrations of mobile pastoralists to the south, use of North Caucasus grasslands in the economic system of seasonal moves and exchange with local people. Nevertheless, presence of carbonized barley seeds in the occupation layers at North Caucasus settlements of 4000–3000 bc requires confirmation by direct 14С dating of such samples.

catacomb-sites-peschany
Location of sites. 1: Ulan IV; 2: Peschany IV and V; 3: Shakhaevskaya 1; 4: Zunda-Tolga 2; 5: Lesnoye; 6: Chidgom; 7: Meshoko; 8: Chishkho; 9: Svobodnoye

Dynamics of Chemical and Microbiological Soil Properties in the Desert–Steppe Zone of the Southeast Russian Plain during the Second Part of the Holocene (4000 BC–XIII century AC), Kashirskaya, Khomutova, Kuznetsova, et al. Arid Ecosyst (2018) 8(1):38-46.

Abstract:

The results of studies of the chemical and microbiological properties of the soils buried under the barrows of the Eneolithic, Bronze, and Middle Ages periods of the southeast of the Russian Plain are presented. It was shown that the climate of the region in the Eneolithic period (4200–4100 BC) and in the Middle Ages (700 years ago) was more humid in comparison to the present time. The third millennium BC was characterized by a gradual increase of the climate aridity. Its peak was at the end of the III millennium BC. The number and biomass of microbial cells was maximal in soils buried in periods of high atmospheric humidity (4200–4100 and 3000–2800 BC) and sharply decreased during the aridization period in the second half of the III millennium BC. In general, the variability of indicators of microbocenosis conditions of desert–steppe buried soils of all ages from the burial mounds correlated with the centuries-old dynamics of the climate.

steppe-humidity-periods
Number of microbial cells in buried soils of different ages and modern background soil.

It is well known that access to more food – as in favorable crops and cattle feeding – may cause demographic explosions, and the second article – together with recent genomic data – may be yet another proof of that.

Until now, pastoralism seemed to be the main subsistence economy for most steppe groups. It seems that earlier Eneolithic contacts of certain steppe groups with settlements of the Northern Caucasus might have been not just to obtain prestige goods though, but – if proper radiocarbon dating confirms it – also implied essential goods, and maybe more stable seasonal exchange systems.

Such stable economic exchanges might have therefore included bidirectional exogamy practices, justifying the sizeable genomic contribution from the Caucasus.

At this point this is just another good theory to take into account.

Related:

Quantitative analysis of population-scale family trees with millions of relatives

genealogy-demographic-data

The paper Quantitative analysis of population-scale family trees with millions of relatives, by Kaplanis, Gordon, Shor, et al. Science (2018) 359(6379), based on a study of genealogical information at Geni, is today news worldwide.

Abstract:

Family trees have vast applications in multiple fields from genetics to anthropology and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. Here, we collected 86 million profiles from publicly-available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of longevity by inspecting millions of relative pairs and to provide insights into the geographical dispersion of families. We also report a simple digital procedure to overlay other datasets with our resource in order to empower studies with population-scale genealogical data.

While the article is behind a paywall, you can still read its preprint at bioRxiv.

Excerpts interesting for genetic genealogy(emphasis mine):

Assessment of theories of familial dispersion

Familial dispersion is a major driving force of various genetic, economical, and demographic processes (…)

First, we analyzed sex-specific migration patterns (21) to resolve conflicting results regarding sex bias in human migration (52). Our results indicate that females migrate more than males in Western societies but over shorter distances. The median mother-child distances were significantly larger (Wilcox, one-tailed, p < 10−90) by a factor of 1.6x than father-child distances (Fig. 4A). This trend appeared throughout the 300 years of our analysis window, including in the most recent birth cohort, and was observed both in North American (Wilcox, one-tailed, p < 10−23) and European duos (Wilcox, one-tailed, p < 10−87). On the other hand, we found that the average mother-child distances (fig. S17) were significantly shorter than the father-child distances (t-test, p < 10−90), suggesting that long-range migration events are biased toward males. Consistent with this pattern, fathers displayed a significantly (p < 10−83) higher frequency than mothers to be born in a different country than their offspring (Fig. 4B). Again, this pattern was evident when restricting the data to North American or European duos. Taken together, males and females in Western societies show different migration distributions in which patrilocality occurs only in relatively local migration events and large-scale events that usually involve a change of country are more common in males than females.

genealogical-tree-generations
An example of the genealogical and demographic information available on the website, with a real pedigree of ~6000 individuals. Green: profiles, red: marriages. The family tree spans about 7 generations

Next, we inspected the marital radius (the distance be-tween mates’ places of birth) and its effect on the genetic relatedness of couples (21). The isolation by distance theory of Malécot predicts that increases in the marital radius should exponentially decrease the genetic relatedness of individuals (53). But the magnitude of these forces is also a function of factors such as taboos against cousin marriages (54).

We started by analyzing temporal changes in the birth locations of couples in our cohort. Prior to the Industrial Revolution (<1750), most marriages occurred between peo-ple born only 10km from each other (Fig. 4A [black line]). Similar patterns were found when analyzing European-born individuals (fig. S18) or North American-born individuals (fig. S19). After the beginning of the second Industrial Revolution (1870), the marital radius rapidly increased and reached ~100km for most marriages in the birth cohort in 1950. Next, we analyzed the genetic relatedness (IBD) of couples as measured by tracing their genealogical ties (Fig. 4C). Between 1650 and 1850, the average IBD of couples was relatively stable and on the order of ~4th cousins, whereas IBD exhibited a rapid decrease post-1850. Overall, the medi-an marital radius for each year showed a strong correlation (R2 = 72%) with the expected IBD between couples. Every 70km increase in the marital radius correlated with a decrease in the genetic relatedness of couples by one meiosis event (Fig. 4D). This correlation matches previous isolation by distance forces in continental regions (55). However, this trend was not consistent over time and exhibits three phases. For the pre-1800 birth cohorts, the correlation between marital distance and IBD was insignificant (p > 0.2) and weak (R2 = 0.7%) (fig. S20A). Couples born around 1800-1850 showed a two-fold increase in their marital distance from 8km in 1800 to 19km in 1850. Marriages are usually about 20-25 years after birth and around this time (1820-1875) rapid transportation changes took place, such as the advent of railroad travel in most of Europe and the United States. However, the increase in marital distance was significantly (p < 10−13) coupled with an increase in genetic relat-edness, contrary to the isolation by distance theory (fig. S20B). Only for the cohorts born after 1850, did the data match (R2 = 80%) the theoretical model of isolation by distance (fig. S20C). Taken together, the data shows a 50-year lag between the advent of increased familial dispersion and the decline of genetic relatedness between couples. During this time, individuals continued to marry relatives despite the increased distance. From these results, we hypothesize that changes in 19th century transportation were not the primary cause for decreased consanguinity. Rather, our results suggest that shifting cultural factors played a more important role in the recent reduction of genetic relatedness of couples in Western societies.

EDIT 3/2/2018: Added details of the article.

See also:

Earliest modern humans outside Africa and ancient genomic history

palaeolithic

Interesting new paper at Science, The earliest modern humans outside Africa, by Hershkovitz et al., Science (2018) Vol. 359, Issue 6374, pp. 456-459

Introduction:

Recent paleoanthropological studies have suggested that modern humans migrated from Africa as early as the beginning of the Late Pleistocene, 120,000 years ago. Hershkovitz et al. now suggest that early modern humans were already present outside of Africa more than 55,000 years earlier (see the Perspective by Stringer and Galway-Witham). During excavations of sediments at Mount Carmel, Israel, they found a fossil of a mouth part, a left hemimaxilla, with almost complete dentition.

The sediments contain a series of well-defined hearths and a rich stone-based industry, as well as abundant animal remains. Analysis of the human remains, and dating of the site and the fossil itself, indicate a likely age of at least 177,000 years for the fossil—making it the oldest member of the Homo sapiens clade found outside Africa.

Abstract

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Beautifully complementing this anthropological research, the open access review Insights into Modern Human Prehistory Using Ancient Genomes, by Melinda A. Yang and Qiaomei Fu, Trends in Genetics (2018), depicts potential later migrations:

eurasia-americas-populations
Key Figure: Schematic of Populations in Eurasia and the Americas (Bottom Right) during Ancient Modern A (AMA, ∼45–35 ka), Ancient Modern B (AMB, ∼34–15 ka), and Ancient Modern C (AMC, ∼14–7.5 ka).

Abbreviations: AMER, ancestry related to present-day Native Americans and Anzick 1; ANE, ancestry related to ancient North Eurasians represented by Mal’ta 1; EAS, ancestry related to present-day East Asians and the Tianyuan and Devil’s Gate individuals; EUR, ancestry related to ancient Europeans and found partially in present-day Europeans; NE, ancestry related to an unsampled population known as Basal Eurasian and found in partial amounts in ancient and present-day populations of the Near East and in present-day Europeans. Broken lines indicate no ancient genetic samples have been found for a population with the inferred ancestry. Colors loosely indicate genetic groupings between or within a region, with color gradients showing the connections (i.e., gene flow) that may exist between different ancient populations. A summary of major events in each of the time periods is on the left.

Summary:

Eurasia ∼45–35 ka shows the presence of at least four distinct populations: early Asians and Europeans, as well as populations with ancestry found hardly or not at all in present-day populations.

Europeans from around 34–15 ka show high internal population structure.

Approximately 14–7.5 ka, populations across Eurasia shared genetic similarities, suggesting greater interactions between geographically distant populations.

Ancient modern human genomes support at least two Neanderthal admixture events, one ∼60–50 ka in early ancestors of non-African populations and a second >37 ka related to the Oase 1 individual.

A gradual decline in archaic ancestry in Europeans dating from ∼37 to 14 ka suggests that purifying selection lowered the amount of Neanderthal ancestry first introduced into ancient modern humans.

The genetic relationship of past modern humans to today’s populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45 000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa.

(Both articles discovered via Iosif Lazaridis Twitter account).

See also:

Review article about Ancient Genomics, by Pontus Skoglund and Iain Mathieson

ancient-genomics-holocene-migrations

A preprint article by two of the most prolific researchers in Human Ancestry is out, and they request feedback: Ancient genomics: a new view into human prehistory and evolution, by Skoglund and Mathieson (2017). Right now, it is downloadable on Dropbox.

Abstract:

The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on ancient genomic data, including greatly increased resolution of the timing and structure of the out-of-Africa event, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document patterns of population continuity and change on every inhabited continent–in particular the effect of agricultural expansions in Africa, Europe and Oceania–and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia–the most populous continent, and Africa–the continent that contains the most genetic diversity. Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.

The paper may be highly recommended as an introduction for anyone interested in the field of Human Ancestry in general.

However, its short summary of steppe ancestry expansion (where the Corded Ware culture predominates) is still reminiscent of the infamous “Yamnaya -> Corded Ware -> Bell Beaker” model set forth by the 2015 Nature articles on the subject, and Kristiansen’s Indo-European Corded Ware theory.

Here is an excerpt (emphasis mine):

The next substantial change is closely related to ancestry that by around 5000 BP extended over a region of more than 2000 miles of the Eurasian steppe, including in individuals associated with the Yamnaya Cultural Complex in far-eastern Europe (1; 38) and with the Afanasievo culture in the central Asian Altai mountains (1). This “steppe” ancestry is itself a mixture between ancestry that is related to Mesolithic hunter-gatherers of eastern Europe and ancestry that is related to both present-day populations (38) and Mesolithic hunter-gatherers (46) from the Caucasus mountains, and also to the populations of Neolithic (11), and Copper Age (56) Iran. Steppe ancestry appeared in southeastern Europe by 6000 BP (72), northeastern Europe around 5000 BP (47) and central Europe at the time of the Corded Ware Complex around 4600 BP (1; 38). These dates are reasonably tight constraints, because in each case there is no evidence of steppe ancestry in individuals immediately preceding these dates (47; 72). Gene flow on the steppe was extensive and bidirectional, as shown by the eastward flow of Anatolian Neolithic ancestry– reaching well into central Eurasia by the time of the Andronovo culture ~3500 BP (1)–and the westward flow of East Asian ancestry–found in individuals associated with the Iron Age Scythian culture close to the Black Sea ~2500 BP (143).

Copper and Bronze Age population movements (14; 78 Martiniano, 2017 #8761; 85; 112), as well as later movements in the Iron Age and Historical period (70; 119) further distributed steppe ancestry around Europe. Present-day western European populations can be modeled as mixtures of these three ancestry components (Mesolithic hunter-gatherer, Anatolian Neolithic and Steppe) (38; 57). In eastern Europe, further shifts in ancestry are the result of additional or distinct gene flow from Anatolia throughout the Neolithic and Bronze Age in the Aegean (42; 51; 55; 72; 87), and gene flow from Siberian-related populations in Finland and the Baltic region (38). East-west gene flow also brought new ancestry–related to populations from 265 Copper Age Iran–to the Levant during the Copper and Bronze ages (39; 56).

The geographic structure of these population transformations gave rise to population structure of present-day Europe. For example Anatolian Neolithic ancestry is highest in southern European populations like Sardinians, and lowest in northern European populations (38). Steppe ancestry is at high frequency in north-central Europeans and low in the south. Isolation-by-distance may have contributed to these patterns to some extent, but the contribution must have been small. In much of Europe, extreme population discontinuity was the norm.

Featured image: from the article, “Major Holocene population movements and expansions that have been demonstrated using ancient DNA.”

Related:

Before steppe ancestry: Europe’s genetic diversity shaped mainly by local processes, with varied sources and proportions of hunter-gatherer ancestry

neolithic-mesolithic-europe

The definitive publication of a BioRxiv preprint article, in Nature: Parallel palaeogenomic transects reveal complex genetic history of early European farmers, by Lipson et al. (2017).

The dataset with all new samples is available at the Reich Lab’s website. You can try my drafts on how to do your own PCA and ADMIXTURE analysis with some of their new datasets.

Abstract:

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 BC, n = 100), Germany (5500–3000 BC, n = 42) and Spain (5500–2200 BC, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

There were some interesting finds on a regional level, with some late survival of hunter-gatherer ancestry (and Y-DNA haplogroups) in certain specific sites, but nothing especially surprising. This survival of HG ancestry and lineages in Iberia and other regions may be used to revive (yet again) the controversy over the origin of non-Indo-European languages of Europe attested in historical times, such as the only (non-Uralic) one surviving to this day, the Basque language.

This study kept confirming the absence of Y-DNA R1b-M269 subclades in Central Europe before the arrival of Yamna migrants, though, which offers strong reasons to reject the Indo-European from the west hypothesis.

Here are first the PCA of samples included in this paper, and then the PCA of ancient Eurasians (Mathieson et al. 2017) and modern populations (Lazaridis et al. 2014) for comparison of similar clusters:

mesolithic-neolithic-PCA
First two principal components from the PCA. We computed the principal components (PCs) for a set of 782 present-day western Eurasian individuals genotyped on the Affymetrix Human Origins array (background grey points) and then projected ancient individuals onto these axes. A close-up omitting the present-day Bedouin population is shown. From Lipton et al. (2017(
pca-south-east-europe
PCA of South-East European and other European samples from Mathieson et al. (2017)
pca-ancient-modern-europe
Ancient and modern samples on Lazaridis et al. (2014)

Related: