Scythians in Ukraine, Natufian and sub-Saharan ancestry in North Africa (ISBA 8, 21st Sep)

jena-isba8

Interesting information from ISBA 8 sesions today, as seen on Twitter (see programme in PDF, and sessions from the 19th and the 20th september).

Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

Scythian population genetics and settlement patterns

Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.

The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP1. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

However, the transition from the Scythian to the Chernyakhov culture between 2,100 and 1,700 cal BP does mark a shift in the Ponto-Caspian genetic landscape, with various analyses showing that Chernyakhov culture samples share more drift and derived alleles with Bronze/Iron Age and modern Europeans, while the Scythians position outside modern European variation. Our results agree well with the Ostrogothic origins of the Chernyakhov culture and support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

Detail of the slide with admixture of Scythian groups in Ukraine:

scythians-admixture

Interesting to read in combination with yesterday’s re-evaluation of Scythian mobility and settlement patterns in the west (showing adaptation to the different regional cultures), The Steppe was Sown – multi-isotopic research changes our understandings of Scythian diet and mobility, by Ventresca Miller et al.

Nomadic pastoralists conventionally known as the Scythians occupied the Pontic steppe during the Iron Age, c. 700-200 BC, a period of unprecedented pan-regional interaction. Popular science accounts of the Scythians promote narratives of roving bands of nomadic warriors traversing the steppe from the Altai Mountains to the Black Sea coastline. The quantity and scale of mobility in the region is usually emphasized based on the wide distribution of material culture and the characterization of Iron Age subsistence economies in the Pontic steppe and forest-steppe as mobile pastoralism. Yet, there remains a lack of systematic, direct analysis of the mobility of individuals and their animals. Here, we present a multi-isotopic analysis of humans from Iron Age Scythian sites in Ukraine. Mobility and dietary intake were documented through strontium, carbon and oxygen isotope analyses of tooth enamel. Our results provide direct evidence for mobility among populations in the steppe and forest-steppe zones, demonstrating a range of localized mobility strategies. However, we found that very few individuals came from outside of the broader vicinity of each site, often staying within a 90 km radius. Dietary intake varied at the intrasite level and was based in agro-pastoralism.

While terrestrial protein did form a portion of the diet for some individuals, there were also high levels of a 13C-enriched food source among many individuals, which has been interpreted as millet consumption. Individuals exhibiting 87Sr/86Sr ratios that fell outside the local range were more likely to have lower rates of millet consumption than those that fell within the local range. This suggests that individuals moving to the site later in life had different economic pursuits and consumed less millet. There is also strong evidence that children and infants moved at the pan-regional scale. Contrary to the popular narrative, the majority of Scythians engaged in localized mobility as part of agricultural lifeways while pan-regional movements included family groups.

North-Africans show ancestry from the ancient Near East and sub-Saharan Africa

Pleistocene North Africans show dual genetic ancestry from the ancient Near East and sub-Saharan Africa, by van de Loosdrecht et al.

North Africa, connecting sub-Saharan Africa and Eurasia, is important for understanding human history. However, the genetic history of modern humans in this region is largely unknown before the introduction of agriculture. After the Last Glacial Maximum modern humans, associated with the Iberomaurusian culture, inhabited a wide area spanning from Morocco to Libya. The Iberomaurusian is part of the early Later Stone Age and characterized by a distinct microlithic bladelet technology, complex hunter-gathering and tooth evulsion.

Here we present genomic data from seven individuals, directly dated to ~15,000-year-ago, from Grotte des Pigeons, Taforalt in Morocco. Uni-parental marker analyses show mitochondrial haplogroup U6a for six individuals and M1b for one individual, and Y-chromosome haplogroup E-M78 (E1b1b1a1) for males. We find a strong genetic affinity of the Taforalt individuals with ancient Near Easterners, best represented by ~12,000 year old Levantine Natufians, that made the transition from complex hunter-gathering to more sedentary food production. This suggests that genetic connections between Africa and the Near East predate the introduction of agriculture in North Africa by several millennia. Notably, we do not find evidence for gene flow from Paleolithic Europeans into the ~15,000 year old North Africans as previously suggested based on archaeological similarities. Finally, 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 Africans (Yoruba, Mende) and Africans from Tanzania (Hadza). In contrast, modern North Africans have a much smaller sub-Saharan African component with no apparent link to Hadza. Our results provide the earliest direct evidence for genetic interactions between modern humans across Africa and Eurasia.

A detail of the cultures involved in these population movements:

north-africa-natufian-saharan

So, most likely, Natufian-related ancestry – as sub-Saharan ancestry – not related to the Afroasiatic expansion.

NOTE. This now probably outdated already by the new preprint on Dzudzuana samples, from the Caucasus.

Impact of colonization in north-eastern Siberia

Exploring the genomic impact of colonization in north-eastern Siberia by Seguin-Orlando et al.

Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

Also interesting to read Balanovsky’s session, and a previous paper on the expansion of Yakuts.

Expansion of haplogroup G2a in Anatolia possibly associated with the Mature Aceramic period

anatolian-hunter-gatherer-sampling

Preprint Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, by Feldman et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

Anatolian hunter-gatherers experienced climatic changes during the last glaciation and inhabited a region that connects Europe to the Near East. However, interactions between Anatolia and Southeastern Europe in the later Upper Palaeolithic/Epipalaeolithic are so far not well documented archaeologically. Interestingly, a previous genomic study showed that present-day Near-Easterners share more alleles with European hunter-gatherers younger than 14,000 BP (‘Later European HG’) than with earlier ones (‘Earlier European HG’). With ancient genomic data available, we could directly compare the Near-Eastern hunter-gatherers (AHG and Natufian) with the European ones. As is the case for present-day Near-Easterners, the Near-Eastern hunter-gatherers share more alleles with the Later European HG than with the Earlier European HG, shown by the significantly positive statistic D(Later European HG, Earlier European HG; AHG/Natufian, Mbuti). Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’), are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna and Ranchot respectively) as the next two European hunter-gatherers genetically closest to AHG. Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component.

anatolian-hunter-gatherer-pca
Ancient genomes (marked with color-filled symbols) projected onto the principal components 5 computed from present-day west Eurasians (grey circles) (fig. S4). The geographic location of each ancient group is marked in (A). Ancient individuals newly reported in this study are additionally marked with a black dot inside the symbol

We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry 5 component (α), which is prevalent in the Near East but undetectable in European hunter-gatherers. Following a published approach, we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians, consistent with previous estimates for the latter. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %, suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

near-eastern-european-hg
Basal Eurasian ancestry proportions (α) as a marker for Near-Eastern gene flow. Mixture proportions inferred by qpAdm for AHG and the Iron Gates HG are schematically represented. The lower schematic shows the expected α in Iron Gates HG under 10 assumption of unidirectional gene flow, inferred from α in the AHG source population. The observed α for Iron Gates HG is considerably smaller than expected thus, the unidirectional gene flow from the Near East to Europe is not sufficient to explain the above affinity.

While ancestry is not always relevant to distinguish certain population movements (see here), especially – as in this case – when there are few samples (thus neither geographically nor chronologically representative) and no previous model to test, it seems that ancestry and Y-DNA show a great degree of continuity in Anatolia since the Palaeolithic until the Neolithic, at least in the sampled regions. C1a2 appears in Europe since ca. 40,000 years ago (viz. Kostenki, Goyet, Vestonice, etc., and later emerges again in the Balkans after the Anatolian Neolithic expansion, probably a resurge of European groups).

The potential transition of a G2a-dominated agricultural society – that is later prevalent in Anatolian and European farmers – may have therefore happened during the Aceramic III period (ca. 8000 BC), a process of haplogroup expansion probably continuing through the early part of the Pottery Neolithic, as the society based on kinship appeared (Rosenberg and Erim-Özdoğan 2011). There is still much to know about the spread of ceramic technology and southwestern Asia domesticate complex, though.

anatolian-palaeolithic-hg

Without a proper geographical sampling, representative of previous and posterior populations, it is impossible to say. But the expansion of R1b-L754 through Anatolia to form part of the Villabruna cluster (and also the Iron Gates HG) seems perfectly possible with this data, although this paper does not help clarify the when or how. We have seen significant changes in ancestry happen within centuries with expanding populations admixing with locals. Palaeolithic sampling – like this one – shows few individuals scattered geographically over thousands of km and chronologically over thousands of years…

Related

Modelling of prehistoric dispersal of rice varieties in India point to a north-western origin

rice-dispersal

New paper (behind paywall), A tale of two rice varieties: Modelling the prehistoric dispersals of japonica and proto-indica rices, by Silva et al., The Holocene (2018).

Interesting excerpts (emphasis mine):

Materials

Our empirical evidence comes from the Rice Archaeological Database (RAD). The first version of this database was used for a synthesis of rice dispersal by Fuller et al. (2010), a slightly expanded dataset (version 1.1) was used to model the dispersal of rice, land area under wet rice cultivation and associated methane emissions from 5000–1000 BP (Fuller et al., 2011). The present dataset (version 2) was used in a previous analysis of the origins of rice domestication (Silva et al., 2015). The database records sites and chronological phases within sites where rice has been reported, including whether rice was identified from plant macroremains, phytoliths or impressions in ceramics. Ages are recorded as the start and end date of each phase, and a median age of the phase is then used for analysis. Dating is based on radiocarbon evidence (…)

Modelling framework

Our approach expands on previous efforts to model the geographical origins, and subsequent spread, of japonica rice (Silva et al., 2015). The methodology is based on the explicit modelling of dispersal hypotheses using the Fast Marching algorithm, which computes the cost-distance of an expanding front at each point of a discrete lattice or raster from the source(s) of diffusion (Sethian, 1996; Silva and Steele, 2012, 2014). Sites in the RAD database are then queried for their cost-distance, the distance from the source(s) of dispersal along the cost-surface that represents the hypothesis being modelled (see Connolly and Lake, 2006; Douglas, 1994; Silva et al., 2015; Silva and Steele, 2014 for more on this approach) and, together with the site’s dating, used for regression analysis. (…)

india-japonica-rice
Predicted arrival times of the non-shattering rice variety (japonica or the hybrid indica) across southern Asia based on best-fitting model H2. Included are also sites with known presence of non-shattering spikelet bases (see text).

Model and results

The ‘Inner Asia Mountain Corridor’ hypothesis (H2) therefore predicts japonica rice to arrive first in northwest India via a route that starts in the Yellow river valley, travels west via the well-known Hexi corridor, then just south of the Inner Asian Mountains and thence to India.

The results also show that the addition of the Inner Asia Mountain Corridor significantly improves the model’s fit to the data, particularly model H2 where rice is introduced to the Indian subcontinent exclusively via a trade route that circumvents the Tibetan plateau. This agrees with independent archaeological evidence that sees millets spread westwards along this corridor perhaps as early as 3000 BC (e.g. Boivin et al., 2012; Kohler-Schneider and Canepelle, 2009; Rassamakin, 1999) and certainly by 2500–2000 BC (Frachetti et al., 2010; Spengler 2015; Stevens et al., 2016), that is, in the same time frame as that predicted for rice in model H2. The arrival of western livestock (sheep, cattle) into central China, 2500–2000 BC (Fuller et al., 2011; Yuan and Campbell, 2009), and wheat, ca. 2000 BC (Betts et al., 2014; Flad et al., 2010; Stevens et al., 2016; Zhao, 2015), add evidence for the role of the Inner Asia Mountain Corridor for domesticated species dispersal in this period.

Conclusion

Through a combination of explicit spatial modelling and simulation, we have demonstrated the high likelihood that dispersal of rice via traders in Central Asia introduced japonica rice into South Asia. Only slightly less likely is a combination of introduction via two routes including a Central Asia to Pakistan/northwestern India route as well as introduction to northeastern India directly from China/Myanmar. However, there is a very low probability that current archaeological evidence for rice fits with a single introduction of japonica into India via the northeast. We have also simulated the minimum amount of archaeobotanical sampling from the Neolithic (to Bronze Age) period in the regions of northeastern India and Myanmar that will be necessary to strengthen support for the combined introduction (model H3) or a single Central Asian introduction (model H2).

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Cereal cultivation and processing in Trypillian mega-sites

eneolithic-trypillia-cucuteni-steppe

New paper (behind paywall) Where are the cereals? Contribution of phytolith analysis to the study of subsistence economy at the Trypillia site Maidanetske (ca. 3900-3650 BCE), central Ukraine, by Dal Corso et al. Journal of Arid Environments (2018).

Interesting excerpts (only introduction and conclusions, emphasis mine):

Archaeological setting at the site of Maidanetske, Ukraine

From ca. 4800 to 3350 BCE, Trypillia settlements were widespread over parts of eastern Romania, Moldova and Ukraine (Menotti and Korvin-Piotrovskiy, 2012; Müller et al., 2016; Videiko, 2004). Maidanetske (Fig. 1B) is one of the so-called “mega-sites” which developed during ca. 3900–3400 BCE in central Ukraine, in the Uman region (Cherkasy district) (Müller and Videiko, 2016; Müller et al., 2017). In this region, nine of these “mega-sites” have been found. Mega-sites are characterized by a regular plan with concentric rings of houses around a large empty central space, additional quartiers, with radial and peripheral track ways (Fig. 1B). The three mega-sites Maidanetske, Taljanky and Dobrovody, lay ca. 15 km apart from each other (Fig. 1A); other mega-sites are located within a 50 km radius around Maidanetske. Archaeologically, these mega-sites consist of the remains of buildings most of them burnt, although a minority of unburnt buildings is known of as well (Burdo and Videiko, 2016; Müller and Videiko, 2016; Ohlrau, 2015). Most of these buildings have a standardized regular size (average 6×12 m) and architecture including domestic installations and a standardized assemblage of artifacts. At Maidanetske beside normal sized houses there are few larger rectangular buildings that are located regularly along the main pathways. Further archaeological contexts include pits, pottery kilns, and peripheral ditches. A huge variety of mostly painted pottery (including many with figurative animal and plant motives), some flint artifacts, rare copper objects, querns, adzes and a broad range of anthropomorphic and zoomorphic figurines are attested within houses and mega-structures. In terms of organic remains, animal bones are fairly common, while botanical macro-remains appear to be scarce and poorly preserved (Kirleis and Dal Corso, 2016; Pashkevich and Videjko, 2006).

trypillia-maidanetske-north-pontic-steppe-forest
The location of the Chalcolithic site of Maidanetske and of other sites mentioned in the text within the map of the natural vegetation (modified after Kirleis
and Dreibrodt, 2016, graphic K. Winter, Kiel University).

Environmental setting at Maidanetske

The Trypillia sites in central Ukraine, including Maidanetske, are located in a semi-arid forest-steppe ecozone, a mosaic-like ecosystem stretched between the dry steppe grasslands in the south and temperate woodland biomes in the north (Fig. 1A). In this transitional zone the natural vegetation is supposed to be patchy and sensitive to climate and topography (Feurdean et al., 2015; Molnàr et al., 2012; Walter, 1974). Since most of the accessible plateaus are converted to agricultural land and the scarce broadleaf woodlands are managed, the natural landscape heterogeneity is difficult to trace within the current landscape (Kuzemko et al., 2014). Besides agricultural fields and villages, narrow river valleys incised into the loess plateaus are present, with riparian vegetation and artificial lakes. This western Pontic area has a humid continental climate with wet winters and warm summers (Köppen and Geiger, 1939), which corresponds to a semi-arid 0.2–0.5 aridity index value according to UNEP (1997). Nevertheless, the reconstruction of past climatic as well as environmental conditions is not straightforward, since undisturbed archives for pollen analysis are lacking in the region and published climatic reconstructions combine evidences from peripheral areas (Gerasimenko, 1997; Harper, 2017; Kirleis and Dreibrodt, 2016). In the Transylvanian forest-steppe region, palynological investigations suggest that dry grasslands have expanded since the end of the 4th millennium BCE, fostered by Bronze Age forest clearance, while before this the area was largely forested (Feurdean et al., 2015). In the Hungarian forest-steppe, the mixed oak forest on Loess almost disappeared by the end of the 18th century AD, hampered by factors such as fragmentation, slow regeneration, spread of invasive species and lowering of the water table due to increased aridity (Molnàr et al., 2012). It is clear that forest-steppe environments are very sensitive to aridity and land use practices. To understand whether similar landscape change can have occurred in central Ukraine already at the time of Chalcolithic mega-sites, an understanding of the extent of crop growing and deforestation is crucial.

The site of Maidanetske is situated on a plateau covered by Loess deposited during the Last Glaciation. This plateau is dissected by valleys of different sizes with perennial rivers present within the large valleys. One of these rivers passes the site in a distance of less than 500 m. The soils that are present nowadays are Chernozems. They show dark greyish-brown A-horizons of thicknesses between 30 and 50 cm and a texture dominated by silt. Numerous filled crotowinas indicate an intensive bioturbation during the formation of these soils. The Chernozems cover the archaeological record. The variations in thickness of the A-horizon are probably reflecting post-depositional soil erosion processes. Buried soils discovered at lower slope positions below colluvial layers show properties of Cambisols, thus pointing towards a forested past of the surrounding landscape (Kirleis and Dreibrodt, 2016).

trypillia-maidanetske-mega-city-settlement-old-europe
The reconstruction of Maidanetske based on geomagnetic survey (modern and from the 1970s by
Dudkin), with the position of the trenches mentioned in this study.

Conclusion

At the site of Maidanetske, the phytolith record from different contexts including multiple houses, was studied, which confirmed cereal cultivation as part of the subsistence economy of the site. Furthermore, phytoliths gave information about wild grasses, whereas dicotyledonous material was scarce. For the house structures cereal byproducts, chaff and straw were identified as material selected for tempering daub for the wall construction. Ash layers in a pit filled with house remains show similar pattern. Daub fragments and pit filling are the most promising archives for further phytolith work on cereals at Trypillia sites. The sediment inside four burnt houses and the areas outside two houses, where also grinding stones were sampled, showed little presence of the remains of final cereal processing, suggesting that either the surfaces were cleaned and the chaff was collected after dehusking, or the cereal processing activity took place somewhere else. Specific archaeological contexts, such as vessels and grinding stones, did not differ much from the control samples from archaeological sediment nearby, suggesting disturbance of the record.(…)

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Expansion of domesticated goat echoes expansion of early farmers

goat-neolithic

New paper (behind paywall) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, by Daly et al. Science (2018) 361(6397):85-88.

Interesting excerpts (emphasis mine):

Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).

PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.

goat-middle-east
Maximumlikelihood phylogeny and geographical distributions of ancient mtDNA haplogroups. (A) A phylogeny placing ancient whole mtDNA sequences in the context of known haplogroups. Symbols denoting individuals are colored by clade membership; shape indicates archaeological period (see key). Unlabeled nodes are modern bezoar and outgroup sequence (Nubian ibex) added for reference.We define haplogroup T as the sister branch to the West Caucasian tur (9). (B and C) Geographical distributions of haplogroups show early highly structured diversity in the Neolithic period (B) followed by collapse of structure in succeeding periods (C).We delineate the tiled maps at 7250 to 6950 BP, a period >bracketing both our earliest Chalcolithic sequence (24, Mianroud) and latest Neolithic (6, Aşağı Pınar). Numbered archaeological sites also include Direkli Cave (8), Abu Ghosh (9), ‘Ain Ghazal (10), and Hovk-1 Cave (11) (table S1) (9).

Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.

Related

Male-biased expansions and migrations also observed in Northwestern Amazonia

Open access preprint Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia, by Arias et al., bioRxiv (2018).

Abstract (emphasis mine):

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

y-dna-mtdna-amazonia
MDS plots for mtDNA and NRY. Stress values (within parentheses) are indicated in percentages.

Looking more precisely at the different groups (even with the resampling approach), there are no significant differences between matrilocal and patrilocal groups. At best, as the study proposes, “this is just one of the factors at play in structuring the observed genetic variation”.

Interesting excerpts:

(…) we found evidence that the patterns of genetic differentiation depend on the geographical scale of the study. The magnitude of between-population differentiation in the NRY compared to the mtDNA is smaller when looking at the continental scale than in NWA (Figure 6). This is in agreement with the findings of Wilkins and Marlowe (2006), who showed that the excess of between-population differentiation for the NRY in comparison to the mtDNA decreases when comparing more geographically distant populations. Heyer et al. (2012) and Wilkins and Marlowe (2006) have proposed that at a local scale the patterns of genetic diversity reflect cultural practices over a relatively small number of generations, whereas at a larger geographic scale the genetic diversity reflects old migration and/or old common ancestry patterns(Heyer et al. 2012; Wilkins and Marlowe 2006).

y-dna-mtdna-amazon
BSPs for the mtDNA and NRY sequences from NWA. The dotted lines indicate the 95% HPD intervals. Ne was corrected for generation time according to (Fenner 2005), using 26 years for mtDNA and 31 years for NRY.

The BSP plots and the diversity statistics indicate that overall the Ne of males has been smaller than that of females. One tentative explanation for this difference is that it reflects larger differences in reproductive success among males than among females. Some support for this explanation comes from the shape of the phylogenies (Supplementary Figures 1 and 6), since differences in reproductive success and the cultural transmission of fertility lead to imbalance phylogenies (Blum et al. 2006; Heyer et al. 2015). We estimated a common index of tree imbalance (Colless index) and calculated whether the mtDNA and NRY trees were more unbalanced than 1000 simulated trees generated under a Yule process (Bortolussi et al. 2006) (i.e. a simple pure birth process that assumes that the birth rate of new lineages is the same along the tree). We found that the NRY tree is more unbalanced than predicted by the Yule model (p-value=0.001), whereas the mtDNA tree is not significantly different from trees generated by the Yule model (p-value=0.628). It has been suggested that highly mobile hunter-gatherer societies, such as those typical of most of human prehistory, were polygynous bands (Dupanloup et al. 2003); similarly, nomadic horticulturalist Amazonian societies exhibit strong differences in reproductive success due to the common practice of polygyny, especially among community chiefs, whose offspring also enjoy a high fertility (Neel 1970; 1980; Neel and Weiss 1975).

Furthermore, a more recent expansion can be observed in the BSP based on the NRY, but not in the mtDNA BSP (Figure 5), indicating an expansion specifically in the paternal line. The reasons behind this recent male-biased population expansion, which starts ~3.5 kya, are as yet unclear. However, similar male-biased expansions have been observed in other studies using high-resolution NRY sequences (Batini et al. 2017; Karmin et al. 2015).

Related:

Ancient genomes from North Africa evidence Neolithic migrations to the Maghreb

BioRxiv preprint now published (behind paywall) Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe, by Fregel et al., PNAS (2018).

NOTE. I think one of the important changes in this version compared to the preprint is the addition of the recent Iberomaurusian samples.

Abstract (emphasis mine):

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

north-africa-genomes-pca
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. PCA analysis using the Human Origins panel (European, Middle Eastern, and North African populations) and LASER projection of aDNA samples.

Relevant excerpts:

FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ∼15,000-y old and ∼7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa.

Genetic analyses have revealed that the population history of modern North Africans is quite complex (11). Based on our aDNA analysis, we identify an Early Neolithic Moroccan component that is (i) restricted to North Africa in present-day populations (11); (ii) the sole ancestry in IAM samples; and (iii) similar to the one observed in Later Stone Age samples from Morocco (17). We conclude that this component, distantly related to that of Epipaleolithic communities from the Levant, represents the autochthonous Maghrebi ancestry associated with Berber populations. Our data suggests that human populations were isolated in the Maghreb since Upper Paleolithic times. Our hypothesis is in agreement with archaeological research pointing to the first stage of the Neolithic expansion in Morocco as the result of a local population that adopted some technological innovations, such as pottery production or farming, from neighboring areas.

By 3,000 BCE, a continuity in the Neolithic spread brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Other archaeological remains, such as African elephant ivory and ostrich eggs found in Iberian sites, confirm the existence of contacts and exchange networks through both sides of the Gibraltar strait at this time. Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/ Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves. Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today.

north-africa-iberia-admixture
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. (B) ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, and North African populations) for modern and ancient samples (K = 8). (D) Detail of ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, North African, and sub-Saharan African populations) for modern and ancient samples, including Taforalt.

Also, from the main author’s Twitter account:

I just realized that the paragraph with information on data availability is missing! Sequence data in the European Nucleotide Archive (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology Information (Accession Numbers MF991431-MF991448).

I find it hard to believe that this genetic continuity from Upper Palaeolithic to Late Neolithic could be representative of an autochthonous development of Afroasiatic. An important population movement – likely more than one – must be found in ancient DNA influencing North-Central and North-East Africa, probably during the time of the Green Sahara corridor.

See here:

Improving environmental conditions favoured higher local population density, which favoured domestication

agricultural-origins

New paper (behind paywall) Hindcasting global population densities reveals forces enabling the origin of agriculture, by Kavanagh et al., Nature Human Behaviour (2018)

Abstract (emphasis mine):

The development and spread of agriculture changed fundamental characteristics of human societies1,2,3. However, the degree to which environmental and social conditions enabled the origins of agriculture remains contested4,5,6. We test three hypothesized links between the environment, population density and the origins of plant and animal domestication, a prerequisite for agriculture: (1) domestication arose as environmental conditions improved and population densities increased7 (surplus hypothesis); (2) populations needed domestication to overcome deteriorating environmental conditions (necessity hypothesis)8,9; (3) factors promoting domestication were distinct in each location10 (regional uniqueness hypothesis). We overcome previous data limitations with a statistical model, in which environmental, geographic and cultural variables capture 77% of the variation in population density among 220 foraging societies worldwide. We use this model to hindcast potential population densities across the globe from 21,000 to 4,000 years before present. Despite the timing of domestication varying by thousands of years, we show that improving environmental conditions favoured higher local population densities during periods when domestication arose in every known agricultural origin centre. Our results uncover a common, global factor that facilitated one of humanity’s most significant innovations and demonstrate that modelling ancestral demographic changes can illuminate major events deep in human history.

cultural-variables-population-densities
Path diagram for piecewise-SEM exploring the effects of environmental and cultural variables on population densities of foraging societies. Measured variables are represented by the large boxes and R2 GLMM values (see Methods) are provided for response variables. n = 220. Red arrows depict negative relationships among variables, black arrows positive relationships, and dashed grey arrows depict non-significant paths (P ≥ 0.05). Standardized coefficients are presented for all paths (small boxes) and arrow widths are scaled to reflect the magnitude of path coefficients.

Interesting excerpts:

(…) our results are consistent with the surplus hypothesis, which suggests that improving environmental conditions and the potential for increased population density may have facilitated the domestication of plants and animals in agricultural origin centres4,7 (Fig. 3). Several factors may explain the links between environmental conditions, potential population density and the origin of domestication. For one, rates of innovation may scale positively with the number of potential innovators13,14. In turn, the likelihood of domestication innovations may have increased in environments that could support increasingly higher densities of foraging people.

In addition, foraging societies may have become more sedentary to take advantage of locally abundant resources, some of which were later domesticated35. Our results indicate that residential mobility scales negatively with population density in foraging societies (Fig. 1). Therefore, increasingly sedentary lifestyles may have contributed further to increases in population density and the potential for innovation. Increases in the productivity of wild progenitors of important domesticates may have also facilitated growing population densities and the viability of cultivation for food production15,16.

population-density-foragers
Predictions of potential population density for foragers. a–c, Predicted population densities at 4,000 (a), 10,000 (b) and 21,000 (c) YBP. Blue hues depict potential population densities below the median population density of observed foraging societies, and red hues depict potential population densities above the median. The second red hue and above are greater than the mean population density of observed foraging societies. Note the increase in area, through time, with potential population densities greater than the mean of observed foraging societies (number of 0.5° × 0.5° cells: 21,000 YBP = 3,027; 4,000 YBP = 4,673). For example, a notable increase in the number of red cells in the Sudanic savannah and Ganges of East India (Northeast India) between panels c and a.

It is also possible that improving environmental conditions may have resulted in a situation where necessity drove the origins of domestication. For example, population densities may have increased in foraging societies that occupied productive, coastal areas, causing an outflow of groups into regions with less ideal conditions where the cultivation of plants and animals was required to secure adequate food resources6,17,18. Our results cannot support, or refute, the possible influence the outflow of people from hospitable locations to less ideal environments may have played. A detailed understanding of the movements of ancient populations is required for more rigorous testing of the role that forced habitation of marginal environments may have played in the origins of domestication at particular sites.

See also: