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

Shared ancestry of ancient Eurasian hepatitis B virus diversity linked to Bronze Age steppe

hepatitis-b-world

Ancient hepatitis B viruses from the Bronze Age to the Medieval period, by Mühlemann et al., Science (2018) 557:418–423.

NOTE. You can read the PDF at Dalia Pokutta’s Academia.edu account.

Abstract (emphasis):

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10−6–1.51 × 10−5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

hbv-genotypes-eurasia
Geographical distribution of analysed samples and modern genotypes. a (featured image), Distribution of modern human HBV genotypes. Genotypes relevant to this Letter are shown in colour. Coloured shapes indicate the locations of the HBV-positive samples included for further analysis. b (above this text), Locations of analysed Bronze Age samples are shown as circles and Iron Age and later samples are shown as triangles. Coloured markers indicate HBV-positive samples. Ancient genotype A samples are found in regions in which genotype D predominates today, and HBV-DA27 is of subgenotype D5 which today is found almost exclusively in India.

Interesting excerpts:

We find genotype A in south-western Russia by 4.3 ka (in samples RISE386 and RISE387) in individuals belonging to the Sintashta culture, and in a Hungarian sample (DA195) from the Scythian culture. The western Scythians are related to the Bronze Age cultures of western steppe populations2 and their shared ancestry suggests that the modern genotype A may descend from this ancient Eurasian diversity and not, as previously hypothesized, from African ancestors29,30. This is also consistent with the phylogeny (Fig. 2), as well as the fact that the three oldest ancient genotype A sequences (HBV-DA195, HBV-RISE386 and HBV-RISE387) lack the six-nucleotide insertion found in the youngest (HBV-DA119) and in all modern genotype A sequences. The ancestors of subgenotypes A1 and A3 could have been carried into Africa subsequently, via migration from western Eurasia31.

The ancient HBV genotype D sequences were all found in Central Asia. HBV-DA27, found in Kazakhstan and dated to 1.6 ka, falls basal to the modern subgenotype D5 sequences that today are found in the Paharia tribe from eastern India32. DA27 and the Paharia people in India are linked by their East Asian ancestry2,33.

hbv-genotype-tree
Dated maximum clade credibility tree of HBV. A log-normal relaxed clock and coalescent exponential population prior were used. Grey horizontal bars indicate the 95% HPD interval of the age of the node. Larger numbers on the nodes indicate the median age and 95% HPD interval of the age (in parentheses) under a strict clock and Bayesian skyline tree prior. Clades of genotypes C (except clade C4), E, F, G and H are collapsed and shown as dots. The figure includes a possible tenth genotype, J, based on a single human isolate. Taxon names for ancient samples indicate era (BA, Bronze Age; IA, Iron Age or later), sample name, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin. Taxon names for modern samples indicate human genotype or subgenotype or host species if non-human, GenBank accession number, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin.

(…)Despite the age of the samples and the imperfect diagnostic test, our dataset contained a high proportion of HBV-positive individuals. The actual ancient prevalence during the Bronze Age and thereafter might have been higher, reaching or exceeding the prevalence typically found in contemporary indigenous populations5. This clearly establishes the potential of HBV as powerful proxy tool for research into human spread and interactions. The data from ancient genomes reveal aspects of complexity in HBV evolution that are not apparent when only modern sequences are considered. They show the existence of ancient HBV genotypes in locations incongruent with their present-day distribution, contradicting previously suggested geographical or temporal origins of genotypes or sub-genotypes; evidence for the creation of genotype A via recombination and the emergence of the genotype outside Africa; at least one now-extinct human genotype; ancient genotype-level localized diversity; and demonstrate that the viral substitution rate obtained from modern heterochronously sampled sequences is probably misleading. Together, these findings suggest that the difficulty in formulating a coherent theory for the origin and spread of HBV may be due to genetic evidence of an earlier evolutionary scenario being overwritten by relatively recent alterations, as has previously been suggested in the context of recombination24

See also:

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:

Mitochondrial DNA unsuitable to test for IBD, and undersampling genomes show biased time and rate estimates

Two interesting papers questioning previous methods have been published.

Open access Mitochondrial DNA is unsuitable to test for isolation by distance, by Teske et al. Scientific Reports (2018) 8:8448.

Abstract (emphasis mine):

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species’ true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.

ibd-plot
Plots of geographic distances vs. F-statistics for the following species (plots on the left show mtDNA data, those on the right SNP or microsatellite data): (a) Sardinops sagax; (b) Psammogobius knysnaensis; (c) Nerita atramentosa; (d) Siphonaria diemenensis. The density of data points is indicated by colours.

Behind paywall, Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life, by Julie Marin and S. Blair Hedges, Mol Biol Evol (2018), msy103.

Abstract (emphasis mine):

Genomic data drive evolutionary research on the relationships and timescale of life but the genomes of most species remain poorly sampled. Phylogenetic trees can be reconstructed reliably using small data sets and the same has been assumed for the estimation of divergence time with molecular clocks. However, we show here that undersampling of molecular data results in a bias expressed as disproportionately shorter branch lengths and underestimated divergence times in the youngest nodes and branches, termed the small sample artifact. In turn, this leads to increasing speciation and diversification rates towards the present. Any evolutionary analyses derived from these biased branch lengths and speciation rates will be similarly biased. The widely used timetrees of the major species-rich studies of amphibians, birds, mammals, and squamate reptiles are all data-poor and show upswings in diversification rate, suggesting that their results were biased by undersampling. Our results show that greater sampling of genomes is needed for accurate time and rate estimation, which are basic data used in ecological and evolutionary research.

speciation-rate
Potential biases on speciation rate estimation. The black line represents constant speciation rate as expected if there are no artifacts or other factors affecting the rate. The small sample artifact (an insufficient number of variable sites) may impact all of the tree and diversification plot, resulting in a rate increase towards the present. The taxonomic artifact (incomplete sampling of taxa or lineages) also may impact all of the tree and diversification plot and results in a speciation rate decrease towards the present. The sparse nodes artifact (stochastic effect of a limited number of nodes) may impact the beginning of the diversification plot, causing decreases or increases in rate.

Do you remember the male-biased expansion from the Pontic-Caspian steppe, that was later contested in its methods by Lazaridis and Reich, but that is today again accepted by Reich and Lazaridis (probably for different reasons, namely Y-DNA evidence)?

Every time I read this kind of studies rejecting previous methods – which get written and published only because there is a future interest in them, not because they are (or may cause) retractions of previous results and interpretations – I remember these people inventing migration models based on genomic studies and saying “genetics is a science, linguistics/archaeology/anthropology is not”…

NOTE. Even if papers eventually receive a correction, journalists and blogs will keep echoing whatever gets published (see the famous Dennis/Denise will become dentists); there is no end to that. Believe it or not, we still see Underhill et al. (2014) being cited against the most recent papers, and even against the author’s own rejection of his paper’s results

Especially right now, it must cause some kind of dissociated reasoning among those naysayers, when they need to resort to anthropological disciplines to discuss the latest interpretations of a potential Caucasus origin or North Iranian homeland of Proto-Indo-European…

EDIT (5 JUN 2018): Also, check out the recent review From genome-wide associations to candidate causal variants by statistical fine-mapping, by Schaid, Chen, and Larson.

Related:

On Latin, Turkic, and Celtic – likely stories of mixed societies and little genetic impact

celtic-europe-national-geographic

Recent article on The Conversation, The Roman dead: new techniques are revealing just how diverse Roman Britain was, about the paper (behind paywall) A Novel Investigation into Migrant and Local Health-Statuses in the Past: A Case Study from Roman Britain, by Redfern et al. Bioarchaeology International (2018), among others.

Interesting excerpts about Roman London:

We have discovered, for example, that one middle-aged woman from the southern Mediterranean has black African ancestry. She was buried in Southwark with pottery from Kent and a fourth century local coin – her burial expresses British connections, reflecting how people’s communities and lives can be remade by migration. The people burying her may have decided to reflect her life in the city by choosing local objects, but we can’t dismiss the possibility that she may have come to London as a slave.

The evidence for Roman Britain having a diverse population only continues to grow. Bioarchaeology offers a unique and independent perspective, one based upon the people themselves. It allows us to understand more about their life stories than ever before, but requires us to be increasingly nuanced in our understanding, recognising and respecting these people’s complexities.

We already have a more or less clear idea about how little the Roman conquest may have shaped the genetic map of Europe, Africa, or the Middle East, in contrast to other previous or later migrations or conquests.

Also, on the Turkic expansion, the recent paper of Damgaard et al. (Nature 2018) stated:

In the sixth century AD, the Hunnic Empire had been broken up and dispersed as the Turkic Khaganate assumed the military and political domination of the steppes22,23. Khaganates were steppe nomad political organizations that varied in size and became dominant during this period; they can be contrasted to the previous stateless organizations of the Iron Age24. The Turkic Khaganate was eventually replaced by a number of short-lived steppe cultures25 (…).

We find evidence that elite soldiers associated with the Turkic Khaganate are genetically closer to East Asians than are the preceding Huns of the Tian Shan mountains (Supplementary Information section 3.7). We also find that one Turkic Khaganate-period nomad was a genetic outlier with pronounced European ancestries, indicating the presence of ongoing contact with Europe (…).

turk-medieval-populations
Analyses of Turk- and Medieval-period population clusters. a, PCA of Tian Shan Hun, Turk, Kimak, Kipchack, Karakhanid and Golden Horde, including 28 individuals analysed at 242,406 autosomal SNP positions. b, Results for model-based clustering analysis at K = 7. Here we illustrate the admixture analyses with K = 7 as it approximately identifies the major component of relevance (Anatolian/ European farmer component, Caucasian ancestry, EHG-related ancestry and East Asian ancestry).”

These results suggest that Turkic cultural customs were imposed by an East Asian minority elite onto central steppe nomad populations, resulting in a small detectable increase in East Asian ancestry. However, we also find that steppe nomad ancestry in this period was extremely heterogeneous, with several individuals being genetically distributed at the extremes of the first principal component (Fig. 2) separating Eastern and Western descent. On the basis of this notable heterogeneity, we suggest that during the Medieval period steppe populations were exposed to gradual admixture from the east, while interacting with incoming West Eurasians. The strong variation is a direct window into ongoing admixture processes and the multi-ethnic cultural organization of this period.

We already knew that the expansion of the La Tène culture, associated with the expansion of Celtic languages throughout Europe, was probably not accompanied by massive migrations (from the IEDM, 3rd ed.):

The Mainz research project of bio-archaeometric identification of mobility has not proven to date a mass migration of Celtic peoples in central Europe ca. 4th-3rd centuries BC, i.e. precisely in a period where textual evidence informs of large migratory movements (Scheeres 2014). La Tène material culture points to far-reaching inter-regional contacts and cultural transfers (Burmeister 2016).

Also, from the latest paper on Y-chromosome bottleneck:

[The hypothesis of patrilineal kin group competition] has an added benefit in that it could explain the temporal placement of the bottleneck if competition between patrilineal kin groups was the main form of intergroup competition for a limited episode of time after the Neolithic transition. Anthropologists have repeatedly noted that the political salience of unilineal descent groups is greatest in societies of ‘intermediate social scale’ (Korotayev47 and its citations on p. 2), which tend to be post-Neolithic small-scale societies that are acephalous, i.e. without hierarchical institutions48. Corporate kin groups tend to be absent altogether among mobile hunter gatherers with few defensible resource sites or little property (Kelly49 pp. 64–73), or in societies utilizing relatively unoccupied and under-exploited resource landscapes (Earle and Johnson50 pp. 157–171). Once they emerge, complex societies, such as chiefdoms and states, tend to supervene the patrilineal kin group as the unit of intergroup competition, and while they may not eradicate them altogether as sub-polity-level social identities, warfare between such kin groups is suppressed very effectively51,52.These factors restrict the social phenomena responsible for the bottleneck to the period after the initial Neolithic but before the emergence of complex societies, which would place the bottleneck-generating mechanisms in the right period of time for each region of the Old World.

chalcolithic_late_Europe_Bell_Beaker
Diachronic map of Late Copper Age migrations including Classical Bell Beaker (east group) expansion from central Europe ca. 2600-2250 BC

However, I recently read in a forum for linguists that the expansion of East Bell Beakers overwhelmingly of R1b-L21 subclades in the British Isles “poses a problem”, in that it should be identified with a Celtic expansion earlier than traditionally assumed…

That interpretation would be in line with the simplistic maps we are seeing right now for Bell Beakers (see below for the Copenhagen group).

If anything, the results of Bell Beaker expansions (taken alone) would seem to support a model similar to Cunliffe & Koch‘s hypotheses of a rather early Celtic expansion into Great Britain and Iberia from the Atlantic.

invasion-from-the-steppe-yamnaya
Spread of Indo-European languages (by the Copenhagen group).

But it doesn’t. Mallory already explained why in Cunliffe & Koch’s series Celtic from the West: the Bell Beaker expansion is too early for that; even for Italo-Celtic. It should correspond to North-West Indo-European speakers.

Not every population movement that is genetically very significant needs to be significant for the languages attested much later in the region.

This should be obvious to everyone with the many examples we already have. One of the least controversial now would probably be the expansion of R1b-DF27, widespread in Iberia probably at roughly the same time as R1b-L21 was in Great Britain, and still pre-Roman Iberians showed a mix of non-Indo-European languages, non-Celtic languages (at least Galaico-Lusitanian), and also some (certain) Celtic languages. And modern Iberians speak Romance languages, without much genetic impact from the Romans, either…

It is well-established in Academia that the expansion of La Tène is culturally associated with the spread of Celtic languages in Europe, including the British Isles and Iberia. While modern maps of U152 distribution may correspond to the migration of early Celts (or Italo-Celtic speakers) with Urnfield/Hallstatt, the great Celtic expansion across Europe need not show a genetic influence greater than or even equal to that of previous prehistoric migrations.

post-bell-beaker-europe
Post-Bell-Beaker Europe, after ca. 2200 BC.

You can see in these de novo models the same kind of invented theoretical ‘problem’ (as Iosif Lazaridis puts it) that we have seen with the Corded Ware showing steppe ancestry, with Old Hittite samples not showing EHG ancestry, or with CHG ancestry appearing north of the Caucasus but no EHG to the south.

However you may want to explain all these errors in scientific terms (selection bias, under-coverage, over-coverage, faulty statistical methods, etc.), these interpretations were simply fruit of the lack of knowledge of the anthropological disciplines at play.

Let’s hope the future paper on Celtic expansion takes this into consideration.

Related:

The fast spread of Neolithic farmers in the western Mediterranean

Recent open access Symbols in motion: Flexible cultural boundaries and the fast spread of the Neolithic in the western Mediterranean, by Rigaud, Manen, García-Martínez de Lagrán, PLOS One (2018).

Abstract (emphasis mine):

The rapid diffusion of farming technologies in the western Mediterranean raises questions about the mechanisms that drove the development of intensive contact networks and circulation routes between incoming Neolithic communities. Using a statistical method to analyze a brand-new set of cultural and chronological data, we document the large-scale processes that led to variations between Mediterranean archaeological cultures, and micro-scale processes responsible for the transmission of cultural practices within farming communities. The analysis of two symbolic productions, pottery decorations and personal ornaments, shed light on the complex interactions developed by Early Neolithic farmers in the western Mediterranean area. Pottery decoration diversity correlates with local processes of circulation and exchange, resulting in the emergence and the persistence of stylistic and symbolic boundaries between groups, while personal ornaments reflect extensive networks and the high level of mobility of Early Neolithic farmers. The two symbolic productions express different degrees of cultural interaction that may have facilitated the successful and rapid expansion of early farming societies in the western Mediterranean.

neolithisation-mediterranean
Mean Inverse Distance Weighting (IDW) interpolation of the first two axes of the Principal Coordinates Analysis (Figure D in S1 File). Diversity of the pottery attributes (A) and bead-type associations (B) express two different cultural geographies. Maps were made by S. R. using the software QGIS 2.6.1 and Etopo1 Digital Elevation Model [110]. https://doi.org/10.1371/journal.pone.0196488.g002.
The maps of interpolated pottery decorative techniques and bead-type diversities throughout the western Mediterranean show the highest interpolated values in southern Italy (Fig B). Hotspots restricted to the east of the Rhône Valley in southern France and eastern Iberia are also visible on the map of bead-type association diversity. Conversely, southern France and eastern Iberia are characterized by lower interpolated values on the map of pottery decorative techniques diversity (Fig A).

Conclusions:

Our results shed light on the cultural mechanisms responsible for the complex cultural geography of the western Mediterranean during the transition to farming. Pottery decorations participated in restrained networks in which geographical proximity and local processes of transmission played an influential role. Bead-type associations were used to tell multiple stories about social identities, were especially resistant to change and are characterized by a greater stability through time and space. The high level of cultural connection between the early farming communities favored movement, interaction and exploration and likely represented a successful strategy for their rapid expansion in the western Mediterranean. Cultural boundaries persisted despite a flow of individuals and symbolic transfer across them.

Genetic studies indicate that the last foragers and the first farmers developed social and cultural relationships more closely tied than previously indicated through components of the material culture [139]. Biological data and chronological models support a pattern of diffusion implying geographically discontinuous contacts between local foragers and incoming farmers, but repeated in time [9,140,141]. This process of diffusion conjointly occurred with changes in material culture, including pottery decorations and personal ornaments. Pottery production represents a technological innovation mostly associated with the Neolithic way of life in the western Mediterranean. Pottery decorations were likely particularly sensitive to interactions, leading to their high variability in time and space in order to reinforce group membership. Conversely, personal ornaments were less inclined to change in space and time. Their production by both local foragers and incoming farmers implies different cultural readjustments that led to a completely different pattern of variation in time and space. The preservation of the foragers’ personal ornament styles (and likely also meanings) within emerging farming communities [20,58] has probably contributed to the maintenance of their stability through time and space.

The two symbolic productions appear as a polythetic set of cultural behaviors dedicated to mediating early farmer identities in many ways, and personal ornaments likely reflected the most entrenched and lasting facets of farmers’ ethnicity.

This research is similar to the recent one by Kılınç et al. (2018) studying the same processes initially in Anatolia and the Aegean. With this one it may also be concluded that Archaeology is necessary to assess meaningful cultural (and thus potential ethnolinguistic) change, beyond gross genetic inflows, even in the case of the Near Eastern farmer expansion waves.

Related:

Pre-Roman and Roman mitogenomes from Southern Italy

vagnari-cemetery-haplogroups-superimposed

Ph.D. thesis Assessing Migration and Demographic Change in pre-Roman and Roman Period Southern Italy Using Whole-Mitochondrial DNA and Stable Isotope Analysis, or The Biogeographic Origins of Iron Age Peucetians and Working-Class Romans From Southern Italy, by Matthew Emery, McMaster University (2018).

Abstract (emphasis mine):

Assessing population diversity in southern Italy has traditionally relied on archaeological and historic evidence. Although informative, these lines of evidence do not establish specific instances of within lifetime mobility, nor track population diversity over time. In order to investigate the population structure of ancient South Italy I sequenced the mitochondrial DNA (mtDNA) from 15 Iron Age (7th – 4th c. BCE) and 30 Roman period (1st – 4th c. BCE) individuals buried at Iron Age Botromagno and Roman period Vagnari, in southern Italy, and analyzed δ18O and 87Sr/86Sr values from a subset of the Vagnari skeletal assemblage.

Phylogenetic analysis of 15 Iron Age mtDNAs together with 231 mtDNAs spanning European prehistory suggest that southern Italian Iapygians share close genetic affinities to Neolithic populations from eastern Europe and the Near East. Population pairwise analysis of Iron Age, Roman, and mtDNA datasets spanning the pan-Mediterranean region (n=357), indicate that Roman maternal genetic diversity is more similar to Neolithic and Bronze Age populations from central Europe and the eastern Mediterranean, respectively, than to Iron Age Italians. Genetic distance between population age categories imply moderate mtDNA turnover and constant population size during the Roman conquest of South Italy in the 3rd century BCE.

In order to determine the local versus non-local demographic at Vagnari, I measured the 87Sr/86Sr and 18O/16O of composition of 43 molars, and the 87Sr/86Sr composition of an additional 13 molars, and constructed a preliminary 87Sr/86Sr variation map of the Italian peninsula using disparate 87Sr/86Sr datasets. The relationship between 87Sr/86Sr and previously published δ18O data suggest a relatively low proportion of migrants lived at Vagnari (7%).

This research is the first to generate whole-mitochondrial DNA sequences from Iron Age and Roman period necropoleis, and demonstrates the ability to gain valuable information from the integration of aDNA, stable isotope, archaeological and historic evidence.

italy-iron-age-mtdna
mtDNA haplogroup composition between Botromagno (7th – 4th century BCE; n=15) and Vagnari (1st – 4th century CE; n=30) skeletal assemblages.

Interesting excerpts:

Taken together, population pairwise ΦST, and the distribution of mtDNA haplotypes in relation to the comparative mtDNA data set show that the Iron Age southern Italians likely descended from early to late Neolithic farmers from Anatolia and possibly as far East as the Caucasus, and from migrants arriving from eastern Europe around the late Neolithic/early Bronze Age. These findings support previous hypotheses that the ancestors of the Iapygians may have originated in the eastern Balkan region, or derive shared ancestry with a common source population from eastern Europe. Alternatively, southern Italian Iron Age mtDNA variation might also reflect LGM gene flow between southwestern European, Mediterranean, and Carpathian basin refugia, which was suggested for haplogroup subclusters of U5 and J (Malyarchuk et al., 2010; Pala et al., 2012). Future mtDNA (and nuclear DNA) analysis comprised of a larger Iron Age data set from southern Italy is necessary to answer Theodor Mommsen’s initial hypothesis that the Iapygians were the oldest immigrants to the southern Italian region.

Our investigation provides the first mtDNA evidence for the maternal ancestral affiliations of a subset of the Iapygian individuals recovered from southern Italy, and suggests a closer genetic link to European Neolithic and Iron Age Armenians, than to Bronze Age Aegeans. Future comparative ancient DNA data using whole-genome SNP, mtDNA, and NRY-chromosome analysis of pre-Roman populations will provide complementary evidence for the ancestral roots of understudied Iron Age individuals from Italy.

Illyrian_colonies_in_Italy_550_BC
Simplistic map of Illyrian colonies in Italy 550 BCE, from Wikipedia

Archaeological evidence indicates that the Iapygians traded and incorporated Hellenistic elements into their material and cultural traditions (Small, 1992; Peruzzi, 2016). These changes are most apparent in burial custom and ceramic production, and become increasingly prominent by 2400 BP (Peruzzi, 2016). Further evidence shows that Iron Age communities across South Italy retracted in size amidst ongoing conflict between colonies in Magna Graecia, and Rome and Carthage (Small, 1992). This apparent change was interpreted as a decline in local populations throughout the region. However, Bayesian Skygrid analysis using the mtDNA profiles of 15 Iapygians and 30 Roman period individuals suggest that female effective population size was comparable between the two populations. In Chapter 4, population distance (measured as population pairwise ΦST values) across a range of mtDNAs obtained from the pan-Mediterranean, European, and western Asian regions suggest closer maternal affinities to Neolithic and Bronze Age populations from the eastern Mediterranean as a cohort, than with Iron Age Italians. This finding points to moderate mtDNA turnover, and is likely the consequence of Roman gene flow stemming from central and northern Italy via the migration and subsequent occupation by Roman colonies after 2250 BP.

Roman Imperial pursuits peaked by ~2050 BP. This extension of power, coupled with an increase in food and materials procurement, was driven by a substantial labour force comprised of both low status Romans and slaves (Harris, 1980; Bradley, 1987, 1994, 2000). Although several attempts have been made to quantify the number of slaves required to maintain the Roman economy, it is unknown what fraction of the Roman population was slave-owned (~approximately 1 to 3 million by 2050 BP) (Scheidel, 2005). Rome’s slave acquisition during the early centuries of the Republic was likely maintained through military campaigns and conquest, a trend that is well documented in Italy (Scheidel, 1997, 1999, 2005; Harris, 1999; Small, 2002). However, once territory was secured, local slave populations were likely maintained through one or a combination of the following: i) the importation of slaves from non-local regions, ii) were born to slave-owned parents, or iii) were voluntarily self-enslaved to acquire subsistence (Harris, 1999). The importation of foreign slaves was likely more costly than maintaining a self-reproducing slave population, especially in rural areas. As such, rural Roman necropoleis, such Vagnari, provide an opportune case to determine the local versus non-local demographic. Archaeological evidence suggests that Vagnari was involved in agriculture and industrial procurement, and was likely staffed by low-class individuals possibly including slaves (Small et al., 2000). However, without direct archaeological or epigraphic evidence, it is impossible to identify the proportion of slaves at rural sites.

italy-iron-age-roman-plot
Multi-dimensional scaling plots showing pairwise ΦST values by a) age and b) country. We removed age and geographic categories with less than 5 mtDNA sequence representation to reduce scaling stress, which decreased the sample size from 402 mtDNAs to n = 378 by age, and n= 382 by country. a) MDS plot of the mtDNA categorized by country of origin; b) MDS of mtDNA dataset by age spanning the Upper Paleolithic (pre-LGM) to the Roman period. IronAge 1 = Italian Iron Age samples; IronAge 2 = Armenian Iron Age samples; Roman 1 = Italian Roman samples; Roman 2 = Egyptian Roman samples; TIP = Third Intermediary Period (Egypt); LP = Late Period (Egypt); PP = Ptolemaic Period (Egypt).

(…) The isotope values presented in Chapter 3 obtained from 56 Roman individuals buried at Vagnari suggest that over half (58%) were born directly at Vagnari, with a further 34% originating from South Italy. Only 7% (3/43 with both δ18O and 87Sr/86Sr values) of the individuals sampled resulted in isotope values non-local to the southern peninsula. Two of these individuals originated from either northern Italy or, more broadly, from central Europe, while one individual likely originated from North Africa. Overall, the isotope data suggest a low number of immigrants at Vagnari, which conforms with the population pairwise (ΦST) data for the Iron Age and Roman mtDNAs, and suggests that as the Romans occupied the region, they populated their Imperial properties with people from central Italy (possible the region of Latium, and the surrounding environs of Rome). These results also integrate with the historical evidence concerning the Roman slave economy during the Imperial period. Future research using a larger comparative dataset comprised of pre-Roman and Roman period mtDNAs, δ18O and, 87Sr/86Sr results will refine the interpretations outlined here.

A paper from this thesis is already published in a peer-review journal, Mapping the origins of Imperial Roman workers (1st–4th century CE) at Vagnari, Southern Italy, using 87Sr/86Sr and δ18O variability, Am J Phys Anthropol (2018).

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How an empire of steppe nomads coped with environmental stress

uyghur-empire

Recent paper (behind paywall), Environmental Stress and Steppe Nomads: Rethinking the History of the Uyghur Empire (744–840) with Paleoclimate Data, by Di Cosmo et al. JINH (2018) XLVIII(4):439-463.

Abstract (emphasis mine):

Newly available paleoclimate data and a re-evaluation of the historical and archaeological evidence regarding the Uyghur Empire (744–840)—one of several nomadic empires to emerge on the Inner Asian steppe—suggests that the assumption of a direct causal link between drought and the stability of nomadic societies is not always justified. The fact that a severe drought lasting nearly seven decades did not cause the Uyghur Empire to collapse, to wage war, or to disintegrate gives rise to speculations about which of its characteristics enabled it to withstand unfavorable climatic conditions and environmental change. More broadly, it raises questions about the complex suite of strategies and responses that may have been available to steppe societies in the face of environmental stress.

Interesting excerpts:

The heart of the matter is whether the apparent capacity to withstand adverse climatic conditions was due to a set of cultural and/or political choices, unrelated to climate, or to a modification of their nomadic ways toward a greater reliance on agriculture and trade. In support of the first alternative, the Uyghur Empire’s initial military rise and expansion (c. 744 to 780) may have been aided by conditions of high moisture that would have made the grasslands especially productive. The alliance with China, the conversion to Manichaeism, and the growing incorporation of Sogdian elites in their empire that took place during this period may have aided the Uyghurs, serendipitously, to withstand the climatic crisis. In the long run, however, some areas of society most likely suffered adverse effects, which might explain the internal splits and the final defeat at the hands of the Kirgiz. These developments owe as much to the sedentary habits of the Uyghur elites and their ineffective leadership as to the erosion of the pastoral resources that constituted the main support of a nomadic army.

uyghur-climate
The findings are based on scPDSI reconstructions at 0.5-degree grid derived from tree
ring records across Asia.

The evidence from tree-ring data points to environmental conditions that alter the historical narrative of the rise and fall of the Uyghur Empire. Although several studies have focused on how climatic extremes affected agricultural societies, the fate of complex nomadic societies did not necessarily follow the same path. Steppe empires, at least from the first Türk Empire (established in the sixth century C.E.), and possibly earlier, were based on expansive geographical networks, diversified economies, and a degree of co-dependency with merchant classes. Even though these elements varied greatly between empires, they probably reacted to climatic variability in ways radically different from the ways in which agricultural and urban polities did. Once we account for socio-economic complexity, the case of the Uyghur Empire belies the general assumption that nomadic peoples are more vulnerable to climatic stress. The severe and protracted drought did not trigger migration, pillaging, or conquest. Sudden shocks, however, could have had a devastating effect on an economy already weakened.

The catastrophic event of the winter of 839/40, which appears to be a dzud (a weather condition of extreme cold and heavy snowfall that causes high animal mortality) was likely the coup de grâce to an already compromised pastoral production. Contemporary studies of the dzud emphasize that the degree of calamity of the winter disaster is closely related to the drought conditions that preceded it. Thus, the collapse of the Uyghur Empire, generally understood as a rapidly evolving political crisis compounded by a catastrophic weather event, is also connected to multidecadal climatic change, dependency mechanisms, and geopolitical constraints.

I found it interesting mainly because of the potential application of this kind of studies to other previous steppe societies.

Discovered via news on Sapiens.org, posted by Spencer Wells.

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Homo sapiens in Arabia by 85,000 years ago

Homo sapiens in Arabia by 85,000 years ago, by Groucutt et al. Nat Ecol. Evol. (2018).

Abstract (emphasis mine):

Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130–90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60–50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95–86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.

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Distribution of Southern Iberian haplogroup H indicates exchanges in the western Mediterranean

Recent open access paper The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean, by Hernández, Dugoujon, Novelletto, Rodríguez, Cuesta and Calderón, BMC Genetics (2017).

Abstract (emphasis mine):

Background
The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature.

Results
Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean.

Conclusions
Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.

mtdna-h1-h3-europe-frequency
a, b, c. Interpolated frequency surfaces of clade H and its main sub-clades (H1 and H3). Frequencies (%) are showed in a colour scale. See information about the populations used in Additional files 4 and 5. Map templates were taken from Natural Earth free map repository (http://www.naturalearthdata.com/)

I usually find mtDNA data, especially studies like this one based on modern populations, very difficult to interpret for anthropological purposes. It is well-known that there are important differences in the pattern of Y-DNA and mtDNA expansion and distribution.

A paragraph in this respect caught my attention:

The patterns of variation in the Y-chromosome between western and eastern Andalusians, based on 416 males, have also been investigated for a set of Y-Short Tandem Repeats (Y-STRs) and Y-SNPs [53, 54, 55], Calderón et al., unpublished data] in combination to mtDNA analyses ([18, 19] and present study). In general, for both uniparental makers, Andalusians exhibit a typical western European genetic background, with peak frequencies of mtDNA Hg H and Y-chromosome Hg R1b1b2-M269 (45% and 60%, respectively). Interestingly, our results have further revealed that the influence of African female input is far more significant when compared to male influence in contemporary Andalusians. The lack of correspondence between the maternal and paternal genetic profiles of human populations reflects intrinsic differences in migratory behavior related to sex-biased processes and admixture, as well as differences in male and female effective population sizes related to the variance in reproductive success affected, for example, by polygyny [56, 57].

I think that the greater reduction in patrilineal lineages compared to maternal lineages we usually see during and after prehistoric or historic migrations have more to do with the renown Uí Néill family case and with war-related casualties (since combatants were usually men) than with other more popular explanations, such as enslavement of women or polygyny.

The most successful paternal lines (anywhere in the world) were probably those who remained in power for a long time (be it a patriarchal society based on families, clans, or more complex organizational units), who were richer and thus more capable of having healthy offspring, who in turn were able to survive longer and have more children who inherited power, etc.

In case of recent migrations or population movements that disrupt the previously established organization, after a certain number of generations, successful patrilocal families (usually from incoming lineages) might slowly dominate over a whole region, with poorer families (usually of ‘indigenous’ lineages) suffering a greater – especially perinatal and child – mortality, without any obvious (pre)historic event associated to these gradual changes.

This gradual replacement of paternal lineages is compatible with the adoption of the native language by newcomers. If the number of migrants is greater that the native population, and especially if their technology is more advanced, then a more radical change including ethnolinguistic identification is more likely.

I don’t deny the (pre)historic existence of radical replacement of male populations with continuity of female lineages due to massacres of men, female slavery, or polygyny, but they are probably not the main explanation for most regional differences seen in paternal lineages, and should thus be used with caution.

Gradual replacement and founder effects are also the most logical explanation for why autochthonous continuity myths (that the modern regional prevalence of few successful lineages tended to create in the 2000s) haven’t been corroborated by ancient DNA; e.g. R1b-DF27 in Basques, N1c-M178 in Finnic populations, R1a-Z283 in Slavs, etc. There is nothing different in those areas from other recent founder effects and internal migratory flows seen everywhere in Europe in the past millennia.

Paper discovered via a link by Alberto Gonzalez on Facebook group Iberia ADN

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