Sahara’s rather pale-green and discontinuous Sahelo-Sudanian steppe corridor, and the R1b – Afroasiatic connection

palaeolakes-world

Interesting new paper (behind paywall) Megalakes in the Sahara? A Review, by Quade et al. (2018).

Abstract (emphasis mine):

The Sahara was wetter and greener during multiple interglacial periods of the Quaternary, when some have suggested it featured very large (mega) lakes, ranging in surface area from 30,000 to 350,000 km2. In this paper, we review the physical and biological evidence for these large lakes, especially during the African Humid Period (AHP) 11–5 ka. Megalake systems from around the world provide a checklist of diagnostic features, such as multiple well-defined shoreline benches, wave-rounded beach gravels where coarse material is present, landscape smoothing by lacustrine sediment, large-scale deltaic deposits, and in places, tufas encrusting shorelines. Our survey reveals no clear evidence of these features in the Sahara, except in the Chad basin. Hydrologic modeling of the proposed megalakes requires mean annual rainfall ≥1.2 m/yr and a northward displacement of tropical rainfall belts by ≥1000 km. Such a profound displacement is not supported by other paleo-climate proxies and comprehensive climate models, challenging the existence of megalakes in the Sahara. Rather than megalakes, isolated wetlands and small lakes are more consistent with the Sahelo-Sudanian paleoenvironment that prevailed in the Sahara during the AHP. A pale-green and discontinuously wet Sahara is the likelier context for human migrations out of Africa during the late Quaternary.

The whole review is an interesting read, but here are some relevant excerpts:

Various researchers have suggested that megalakes coevally covered portions of the Sahara during the AHP and previous periods, such as paleolakes Chad, Darfur, Fezzan, Ahnet-Mouydir, and Chotts (Fig. 2, Table 2). These proposed paleolakes range in size by an order of magnitude in surface area from the Caspian Sea–scale paleo-Lake Chad at 350,000 km2 to Lake Chotts at 30,000 km2. At their maximum, megalakes would have covered ~ 10% of the central and western Sahara, similar to the coverage by megalakes Victoria, Malawi, and Tanganyika in the equatorial tropics of the African Rift today. This observation alone should raise questions of the existence of megalakes in the Sahara, and especially if they developed coevally. Megalakes, because of their significant depth and area, generate large waves that become powerful modifiers of the land surface and leave conspicuous and extensive traces in the geologic record.

megalakes-sahara
ETOPO1 digital elevation model (1 arc-minute; Amante and Eakins, 2009) of proposed megalakes in the Sahara Desert during the late Quaternary. Colors denote Köppen-Geiger climate zones: blue, Aw, Af, Am (tropical); light tan, Bwk, BSh, BSk, Csa, Csb, Cwb, Cfa, Cfb (temperate); red-brown, Bwh (arid, hot desert and steppe climate). Lake area at proposed megalake high stands and present Lake Victoria are in blue, and contributing catchment areas are shown as thin solid black lines. The main tributaries of Lake Chad are denoted by blue lines (from west to east: the Komadougou-Yobe, Logone, and Chari Rivers; source: Global Runoff Data Center, Koblenz, Germany). Rainfall isohyets (50, 200, 800, 1200, and 1600) are marked in dashed gray-scale lines. Physical parameters of each basin are shown in white boxes: Abt, total basin area; AW, lake area; Vw, lake volume; and aW= AW/Abt. Black dots mark the location of the paleohydrological records from Lezine et al. (2011), also compiled in Supplementary Table S5.

Lakes, megalakes, and wetlands

Active ground-water discharge systems abound in the Sahara today, although they were much more widespread in the AHP. They range from isolated springs and wet ground in many oases scattered across the Sahara (e.g., Haynes et al., 1989) to wetlands and small lakes (Kröpelin et al., 2008). Ground water feeding these systems is dominated by fossil AHP-age and older water (e.g., Edmunds and Wright 1979; Sonntag et al., 1980), although recently recharged water (<50 yr) has been locally identified in Saharan ground water (e.g., Sultan et al., 2000; Maduapuchi et al., 2006).

Megalake Chad

In our view, Lake Chad is the only former megalake in the Sahara firmly documented by sedimentologic and geomorphic evidence. Mega-Lake Chad is thought to have covered ~ 345,000 km2, stretching for nearly 8° (10–18°N) of latitude (Ghienne et al., 2002) (Fig. 2). The presence of paleo- Lake Chad was at one point challenged, but several—and in our view very robust—lines of evidence have been presented to support its development during the AHP. These include: (1) clear paleo-shorelines at various elevations, visible on the ground (Abafoni et al., 2014) and in radar and satellite images (Schuster et al., 2005; Drake and Bristow, 2006; Bouchette et al., 2010); (2) sand spits and shoreline berms (Thiemeyer, 2000; Abafoni et al., 2014); and (3) evaporites and aquatic fauna such as fresh-water mollusks and diatoms in basin deposits (e.g., Servant, 1973; Servant and Servant, 1983). Age determinations for all but the Holocene history of mega- Lake Chad are sparse, but there is evidence for Mio-Pliocene lake (s) (Lebatard et al., 2010) and major expansion of paleo- Lake Chad during the AHP (LeBlanc et al., 2006; Schuster et al., 2005; Abafoni et al., 2014; summarized in Armitage et al., 2015) up to the basin overflow level at ~ 329m asl.

Insights from hydrologic mass balance of megalakes

sahara-annaul-rainfall
Graph of mean annual rainfall (mm/yr) versus aw (area lake/area basin, AW/AL); their modeled relationship using our Sahelo-Sudanian hydrologic model for the different lake basins are shown as solid colored lines. Superimposed on this (dashed lines) are the aw values for individual megalake basins and the mean annual rainfall required to sustain them. Mean annual paleo-rainfall estimates of 200– 400 mm/yr during the AHP from fossil pollen and mollusk evidence is shown as a tan box. The intersection of this box with the solid colored lines describes the resulting aw for Saharan paleolakes on the y-axis. The low predicted values for aw suggest that very large lakes would not form under Sahelo-Sudanian conditions where sustained by purely local rainfall and runoff. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Using these conservative conditions (i.e., erring in the direction that will support megalake formation), our hydrologic models for the two biggest central Saharan megalakes (Darfur and Fezzan) require minimum annual average rainfall amounts of ~ 1.1 m/yr to balance moisture losses from their respective basins (Supplementary Table S1). Lake Chad required a similar amount (~1 m/yr; Supplementary Table S1) during the AHP according to our calculations, but this is plausible, because even today the southern third of the Chad basin receives ≥1.2 m/yr (Fig. 2) and experiences a climate similar to Lake Victoria. A modest 5° shift in the rainfall belt would bring this moist zone northward to cover a much larger portion of the Chad basin, which spans N13° ±7°. Estimated rainfall rates for Darfur and Fezzan are slightly less than the average of ~ 1.3 m/yr for the Lake Victoria basin, because of the lower aw values, that is, smaller areas of Saharan megalakes compared with their respective drainage basins (Fig. 15).

Estimates of paleo-rainfall during the AHP

Here major contradictions develop between the model outcomes and paleo-vegetation evidence, because our Sahelo-Sudanian hydrologic model predicts wetter conditions and therefore more tropical vegetation assemblages than found around Lake Victoria today. In fact, none of the very wet rainfall scenarios required by all our model runs can be reconciled with the relatively dry conditions implied by the fossil plant and animal evidence. In short, megalakes cannot be produced in Sahelo-Sudanian conditions past or present; to form, they require a tropical or subtropical setting, and major displacements of the African monsoon or extra-desert moisture sources.

sahara-palaeoclimate
Change in mean annual precipitation over northern Africa between mid-Holocene (6 ka) and pre-industrial conditions in PMIP3 models (affiliations are provided in Supplementary Table S4). Lakes Victoria and Chad outlined in blue. (a) Ensemble mean change in mean annual precipitation and positions of the African summer (July–September) ensemble mean ITCZ during mid-Holocene (solid red line) and pre-industrial conditions (solid blue line). (b) Zonal average of change in mean annual precipitation over land (20°W–30°E) for the ensemble mean (thick black) and individual models are listed on right). The range of minimal estimated change in mean annual precipitation required to sustain steppe is shown in shaded green (Jolly et al., 1998).

Conclusions

If not megalakes, what size lakes, marshes, discharging springs, and flowing rivers in the Sahara were sustainable in Sahelo-Sudanian climatic conditions? For lakes and perennial rivers to be created and sustained, net rainfall in the basin has to exceed loss to evapotranspiration, evaporation, and infiltration, yielding runoff that then supplies a local lake or river. Our hydrologic models (see Supplementary Material) and empirical observations (Gash et al., 1991; Monteith, 1991) for the Sahel suggest that this limit is in the 200–300 mm/yr range, meaning that most of the Sahara during the AHP was probably too dry to support very large lakes or perennial rivers by means of local runoff. This does not preclude creation of local wetlands supplied by ground-water recharge focused from a very large recharge area or forced to the surface by hydrologic barriers such as faults, nor megalakes like Chad supplied by moisture from the subtropics and tropics outside the Sahel. But it does raise a key question concerning the size of paleolakes, if not megalakes, in the Sahara during the AHP. Our analysis suggests that Sahelo-Sudanian climate could perhaps support a paleolake approximately ≤5000 km2 in area in the Darfur basin and ≤10,000–20,000 km2 in the Fezzan basin. These are more than an order of magnitude smaller than the megalakes envisioned for these basins, but they are still sizable, and if enclosed in a single body of water, should have been large enough to generate clear shorelines (Enzel et al., 2015, 2017). On the other hand, if surface water was dispersed across a series of shallow and extensive but partly disconnected wetlands, as also implied by previous research (e.g., Pachur and Hoelzmann, 1991), then shorelines may not have developed.

One of the underdeveloped ideas of my Indo-European demic diffusion model was that R1b-V88 had migrated through South Italy to Northern Africa, and from it using the Sahara Green Corridor to the south, from where the “upside-down” view of Bender (2007) could have occurred, i.e. Afroasiatic expanding westwards within the Green Sahara, precisely at this time, and from a homeland near the Megalake Chad region (see here).

Whether or not R1b-V88 brought the ‘original’ lineage that expanded Afroasiatic languages may be contended, but after D’Atanasio et al. (2018) it seems that only two lineages, E-M2 and R1b-V88, fit the star-like haplogroup expansion and necessary regional distribution that could explain the spread of Afroasiatic languages within a reasonable time frame.

palaeolithic
Palaeolithic migrations

This review shows that the hypothesized Green Sahara corridor full of megalakes that some proposed had fully connected Africa from west to east was actually a strip of Sahelo-Sudanian steppe spread to the north of its current distribution, including the Chad megalake, East Africa and Arabia, apart from other discontinuous local wetlands further to the north in Africa. This would have probably allowed for the initial spread of early Afroasiatic proto-languages only from the southern part of the current Sahara Desert. This and the R1b-V88 haplogroup prevalence among Chadic speakers (probably due to later bottlenecks), but also found in West Africa, leaves still fewer possibilities for an expansion of Afroasiatic from anywhere else.

If my proposal turns out to be correct, this Afroasiatic-like language would be the one suggested by some in the vocabulary of Old European and Scandinavian local groups (viz. Kroonen for Pre-Germanic), and not Anatolian farmer ancestry or haplogroup G2, which would have been rather confined to Southern Europe, mainly south of the Loess line, where incoming Middle East farmers encountered the main difficulties spreading agriculture and herding, and where they eventually admixed with local hunter-gatherers.

If related to attested languages before the Roman expansion, Tyrsenian would be a good candidate for a descendant of the language of Anatolian farmers, given the more recent expansion of Anatolian ancestry to the Tuscan region (even if already influenced by Iran farmer ancestry), which reinforces its direct connection to the Aegean.

The fiercest opposition to this R1b-V88 – Afroasiatic connection may come from:

  • Traditional Hamito-Semitic scholars, who try to look for any parent language almost invariably in or around the Near East – the typical “here it was first attested, ergo here must be the origin, too”-assumption (coupled with the cradle of civilization memes) akin to the original reasons behind Anatolian or Out-of-India hypotheses; and of course
  • autochthonous continuity theories based on modern subclades, of (mainly Semitic) peoples of haplogroup E or J, who will root for either one or the other as the Afroasiatic source no matter what. As we have seen with the R1a – Indo-European hypothesis (see here for its history), this is never the right way to look at prehistoric migrations, though.

I proposed that it was R1a-M417 the lineage marking an expansion of Indo-Uralic from the east near Lake Baikal, then obviously connected to Yukaghir and Altaic languages marked by R1a-M17, and that haplogroup R could then be the source of a hypothetic Nostratic expansion (where R2 could mark the Dravidian expansion), with upper clades being maybe responsible for Borean.

nostratic-tree
Simple Nostratic tree by Bomhard (2008)

However, recent studies have shown early expansions of R1b-297 to East Europe (Mathieson et al. 2017 & 2018), R1b-M73 to East Eurasia probably up to Siberia and the Pacific (Jeong et al. 2018), as well as Steppe and Caucasus Eneolithic (Wang et al. 2018) samples able to explain the WHG – EHG – ANE ancestry cline seen in the Mesolithic and Neolithic Eurasia.

Also, Dravidian is now after Narasimhan et al. (2018) and Damgaard et al. (Science 2018) more and more likely to be linked to the expansion of the Indus Valley civilization and haplogroup J which is in turn linked to Iranian farmer ancestry, thus giving support to an Elamo-Dravidian group stemming from Iran Neolithic.

NOTE. This Dravidian-IVC and Iran connection has been supported for years by knowledgeable bloggers and commenters alike, see e.g. one of Razib Khan’s posts on the subject. This rather early support for what is obvious today is probably behind the reactionary views by some nationalist Hindus, who probably saw in this a potential reason for a strengthened Indo-Aryan/Dravidian divide adding to the religious patchwork that is modern India.

I am not in a good position to judge Nostratic, and I don’t think Glottochronology, Swadesh lists, or any statistical methods applied to a bunch of words are of any use, here or anywhere. The work of pioneers like Illich-Svitych or Starostin, on the other hand, seem to me solid attempts to obtain a faithful reconstruction, if rather outdated today.

NOTE. I am still struggling to learn more about Uralic and Indo-Uralic; not because it is more difficult than Indo-European, but because – in comparison to PIE comparative grammar – material about them is scarce, and the few available sources are sometimes contradictory. My knowledge of Afroasiatic is limited to Semitic (Arabic and Akkadian), and the field is not much more developed here than for Uralic…

y-haplogroup-r1b-p343
Spread of Y-haplogroup R1b-M73, according to Jeong et al. 2018.

If one wanted to support a Nostratic proto-language, though, and not being able to take into account genome-wide autosomal admixture, the only haplogroup right now which can connect the expansion of all its branches is R1b-M343:

  • R1b-L278 expanded from East Eurasia to Europe through the Iranian Plateau, since early subclades are found in Iran and the Caucasus region, thus supporting the separation of Elamo-Dravidian and Kartvelian branches;
  • From the Danube or another European region ‘near’ the Villabruna 1 sample (of haplogroup R1b-L754):
    • R1b-V88 expanding everywhere in Europe, and especially the branch expanding to the south into Africa may be linked to the initial Afroasiatic expansion through the Pale-Green Sahara corridor (and even a hypothetic expansion from the Near East with E subclades would also leave open the influence of previous R1b subclades from the Middle East in the emergence of the language there);
    • R1b-297 subclades expanding to the east may be linked to Eurasiatic, giving rise to both Indo-Uralic (M269) and Macro- or Micro-Altaic (M73) expansions.

This is shameless, simplistic speculation, of course, but not more than the Nostratic hypothesis, and it has the main advantage of offering ‘small and late’ language expansions relative to other proposals spanning thousands (or even tens of thousands) of years of language separation. On the other hand, that would leave Borean mostly out of a common group, unless the initial expansion of R1b from a community close to lake Baikal (and Mal’ta) is proposed also as the origin of the other supposedly related branches, whether linked to haplogroup R or to any other…

NOTE. If Afroasiatic and Indo-Uralic (or Eurasiatic) are not genetically related, my previous simplistic model, R1b-Afroasiatic vs. R1a-Eurasiatic, may still be supported, with R1a-M17 potentially marking the latest meaningful westward population expansion from which EHG ancestry might have developed (see here). Without detailed works on Nostratic comparative grammar and dialectalization, and especially without a lot more Palaeolithic and Mesolithic samples, all this will remain highly speculative, like proposals of the 2000s about Y-DNA-haplogroup – language relationships.

Related:

Recent Africa origin with hybridization, and back to Africa 70,000 years ago

mtdna-l-out-of-africa-expansion

Open access Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago, by Cabrera et al. BMC Evol Biol (2018) 18(98).

Abstract (emphasis mine):

Background

The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.

Results

The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.

Conclusions

These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.

homo-sapiens-neandertal-denisovan

You can also read the recent interesting open access review How did Homo sapiens evolve? by Julia Galway-Witham, Chris Stringer, Science (2018) 360:6395 1296-1298.

Related:

Reconstruction of Y-DNA phylogeny helps also reconstruct Tibeto-Burman expansion

tibeto-burman-han-chinese-population

New paper (behind paywall) Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations by Wang et al. Mol Genet Genomics (2018).

Interesting excerpts:

Archeological studies suggest that a subgroup of ancient populations of the Miaodigou culture (~ 6300–5500 BP) moved westward to the upper stream region of the Yellow River and created the Majiayao culture (~ 5400–4900 BP) (Liu et al. 2010), which was proposed to be the remains of direct ancestors of Tibeto-Burman populations (Sagart 2008). On the other hand, Han populations, the other major descendant group of the Yang-Shao culture (~ 7000–5500 BP), are composed of many other sub-lineages of Oα-F5 and extremely low frequencies of D-M174 (Additional files 1: Figure S1; Additional files 2: Table S1). Therefore, we propose that Oα-F5 may be one of the dominant paternal lineages in ancient populations of Yang-Shao culture and its successors.

In this study, we demonstrated that both sub-lineages of D-M174 and Oα-F5 are founding paternal lineages of modern Tibeto-Burman populations. The genetic patterns suggested that the ancestor group of modern Tibeto-Burman populations may be an admixture of two distinct ancient populations. One of them may be hunter–gatherer populations who survived on the plateau since the Paleolithic Age, represented by varied sub-lineages of sub-lineages of D-M174. The other one was comprised of farmers who migrated from the middle Yellow River basin, represented by sub-lineages of Oα-F5. In general, the genetic evidence in this study supports the conclusion that the appearance of the ancestor group of Tibeto-Burman populations was triggered by the Neolithic expansion from the upper-middle Yellow River basin and admixture with local populations on the Tibetan Plateau (Su et al. 2000).

tibeto-burman-phylogenetic-tree
Simplified phylogenetic tree showing sample locations. The size of the circle for each sampling location corresponds to the number of samples

Two neolithic expansion origins of Tibeto‑Burman populations

We also observed significant differences in the paternal gene pool of different subgroups of Tibeto-Burman populations. Haplogroup D-M174 contributed ~ 54% percent in a sampling of 2354 Tibetan males throughout the Tibetan Plateau (Qi et al. 2013). Previous studies have also found high frequencies of D-M174 in other populations on the Tibetan Plateau (Shi et al. 2008), including Sherpa (Lu et al. 2016) and Qiang (Wang et al. 2014). In contrast, haplogroup D-M174 is rare or absent from Tibeto-Burman populations from Northeast India and Burma (Shi et al. 2008). In populations of the Ngwi-Burmese language subgroup, the average frequencies of haplogroup D-M174 are ~ 5% (Dong et al. 2004; Peng et al. 2014). Furthermore, we found that lineage Oα1c1b-CTS5308 is mainly found in Tibeto-Burman populations from the Tibetan Plateau. In contrast, lineage Oα1c1a-Z25929 was found in Tibeto-Burman populations from Northeast India, Burma, and the Yunan and Hunan provinces of China (Additional files 1: Figure S1; Additional files 2: Table S1). In general, enrichment of lineage Oα1c1b- CTS5308 and high frequencies of D-M174 can be found in most Tibeto-Burman populations on the Tibetan Plateau and adjacent regions, whereas Tibeto-Burman populations from other regions tend to have lineage Oα1c1a-Z25929 and a little to no percentage of D-M174.

The inconsistent pattern we observed in the paternal gene pool of modern Tibeto-Burman populations suggested that there may be two distinct ancestor groups (Fig. 3). The proposed migration routes shown in Fig. 3 are somewhat different from those proposed by Su et al. (2000). According to our age estimation, most of the D1a2a-P47 samples belong to sub-lineage PH116, a young lineage that emerged ~ 2500 years ago (95% CI 1915–3188 years). On the other hand, continuous differentiation can be observed on a phylogenetic tree of lineages D1a1a1a1-PH4979 and D1a1a1a2-Z31591 since 6000 years ago. Therefore, we proposed that a group of ancient populations may have moved to the upper basin of the Yellow River and admixed intensively with local populations with high frequencies of haplogroup D-M174, including its sub-lineage D1a2a-P47 (Fig. 3). This ancestor group eventually gave birth to modern Tibeto-Burman populations on the Tibetan Plateau and adjacent regions. The other ancestor group moved toward the southwest and finally reached South East Asia (Burma and other locations) and the northeastern part of India (Fig. 3). This ancestor group may have had no or a minor admixture of D-M174 in their paternal gene pool.

tibeto-burman-migrations
Two proposed ancestor groups and migration routes for Tibeto-Burman populations

Long‑term admixture before expansion to a high‑altitude region

It is interesting to investigate the time gap between the appearance of Neolithic cultures in the northeastern part of the Tibetan Plateau and the final phase of human expansion across the Tibetan Plateau. The Majiayao culture (~ 5400–4900 BP) is the earliest Neolithic culture in the northeastern part of the Tibetan Plateau (Liu et al. 2010). However, previous archeological study has suggested that the final phase of diffusion into the high-altitude area of the Tibetan Plateau occurred at approximately 3.6 kya (Chen et al. 2015). Our genetic evidence in this study is consistent with this scenario based on archeological evidence. Based on Y-chromosome analysis in this study, many unique lineages of Tibeto-Burman populations emerged between 6000 years ago and 2500 years ago (Additional files 3: Table S2). The most recent common age of D1a2-PH116, a sub-lineage that spread throughout the Tibetan Plateau, is only 2500 years ago.

We propose that there may be two important factors for the observed age gap. First, living in a high-altitude environment may require some crucial physical characteristics that were lacking from Neolithic immigrants from the middle Yellow River Basin. Intense genetic admixture with local people who had survived on the Tibetan Plateau since the Paleolithic Age may have actually guaranteed the expansion of humans across the Tibetan Plateau. Therefore, a long period of admixture, lasting from 5.4 to 3.6 kya, may be necessary for the appearance of a population with beneficial genetic variants that was genetically adapted to the high-altitude environment. Second, technological innovations, such as the domestication of wheat and highland barley (Chen et al. 2015), establishment of yak pastoralism (Rhode et al. 2007), and introduction of other culture elements in the Bronze Age (Ma et al. 2016), are also important factors that facilitated permanent settlements with large population sizes in the high-altitude area of the Tibetan Plateau.

Related:

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

turko-mongol-indo-iranian

Open access Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy, by Marchi et al. Scientific Reports (2018) 8:9397.

Abstract (emphasis mine):

When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.

Interesting excerpts:

Two cultural groups, which matrimonial systems are reported to differ, coexist in Inner Asia: Turko-Mongols are described as mainly exogamous while Indo-Iranians are thought to be mainly endogamous45. However, it is not always clear if exogamy refers to clan (ethnic) or village (geographical) exogamy. Here, we used a dataset of 16 populations representing 11 different ethnic groups from both cultural groups and we quantified geographical exogamy rates and distances in each population. Using an empirical threshold of 4 km, we confirmed that matrimonial behaviours differ as described in the literature, even though we found some exceptions: three Turko-Mongol populations (out of 14) have less than 50% exogamy, whereas one Indo-Iranian population (out of four) has more than 50% exogamy.(…).

geographic-distance-turko-mongols-indo-iranian
Geographical distances between the birth places of couples in Turko-Mongols and Indo-Iranians. The geographical distances are plotted in log scale (km). Their densities are represented by population (dashed lines) or for the Indo-Iranian and Turko-Mongol groups (solid lines). We represented the average distances within couples per population using a Kernel’s density estimate implemented in R with a smoothing bandwidth of 0.2. See Supplementary Table 1B for population codes.

An additional important result of our study is that geographical distances are not negatively correlated with inbreeding, as could have been expected under an isolation-by-distance model65. Interestingly, a recent study based on a large genealogical dataset, collected across Western Europe and North America, and including birth places information, similarly found an absence of correlation between relatedness and the distance between couples, for the cohorts born before 185066. Our analyses within present-day Turko-Mongols reveal more specifically that the structure of the relationship between geographical distance and mating choice inbreeding is not linear, but rather tends to be bell-shaped, and thus cannot be correctly assessed with a single correlation test. Indeed, descendants from parents born 4 to 40 km apart are more inbred than descendants from endogamous couples (≤4 km) or from long-range exogamous ones (>40 km). As a consequence, close inbreeding exists despite geographical exogamy, and about a third of descendants from exogamous couples are inbred.

These results, in addition to those obtained by [Kaplanis et al. 2018]66, highlight the importance of using geographic distances rather than exogamy rates to characterize the impact of exogamy on inbreeding, as already described when studying patrilocality67. Indeed, when we compare mating choice inbreeding patterns for descendants from exogamous and endogamous couples defined for thresholds of 4, 10, 20 and 30 km, we find no significant differences (for number and total length of class C-ROHs and F-Median coefficient: MWU test p-values > 0.1). We only detect significantly lower values in descendants from exogamous couples for larger distances above 40 and 50 km (p-values < 0.03).

genetic-diversity-turko-mongol-indo-iranian
Genetic diversity (A) and inbreeding patterns (B,C) within populations. Grey lines in (B) represent inbreeding values corresponding to second-cousins and first-cousins. The grey line in (C) represents the homozygosity population baseline expected under panmixia. The number of samples per population is indicated between parentheses. See Supplementary Table 1B for population codes.

Our results also challenge the intuition that exogamy necessarily increases the genetic diversity within a population and therefore reduces drift inbreeding. Indeed, we found that Turko-Mongol populations have a lower genetic diversity (as measured by the mean haplotypic heterozygosity) and more intermediate ROHs associated with drift inbreeding than those of Indo-Iranians despite higher exogamous rates. (…)

Overall, this research sheds light on mating choice preferences: we showed that two thirds of partners that have not dispersed did mate with unrelated individuals, and that drift and mating choice inbreeding is variable, even among close-by populations. We also provide new insights into the relationship between dispersal and inbreeding in humans, based on genetic data, and demonstrate that geographical exogamy is not necessarily negatively associated with mating choice inbreeding, but rather can have a more complex non-linear relationship. Contrary to the common situation in many animals, this finding suggests that Inner Asian human populations who practise exogamy at small geographical scales might be focused on alliance strategies that result in kinship endogamy. (…)

Related:

Kortlandt: West Indo-Europeans along the Danube, Germanic and Balto-Slavic share a Corded Ware substrate

copper-age-early_yamna-corded-ware

New paper (behind paywall) The Expansion of the Indo-European Languages, by Frederik Kortlandt, JIES (2018) 46(1 & 2):219-231.

Abstract:

When considering the way the Indo-Europeans took to the west, it is important to realize that mountains, forests and marshlands were prohibitive impediments. Moreover, people need fresh water, all the more so when traveling with horses. The natural way from the Russian steppe to the west is therefore along the northern bank of the river Danube. This leads to the hypothesis that the western Indo-Europeans represent successive waves of migration along the Danube and its tributaries. The Celts evidently followed the Danube all the way to southern Germany. The ancestors of the Italic tribes, including the Veneti, may have followed the river Sava towards northern Italy. The ancestors of Germanic speakers apparently moved into Moravia and Bohemia and followed the Elbe into Saxony. A part of the Veneti may have followed them into Moravia and moved along the Oder through the Moravian Gate into Silesia. The hypothetical speakers of Temematic probably moved through Slovakia along the river Orava into western Galicia. The ancestors of speakers of Balkan languages crossed the lower Danube and moved to the south. This scenario is in agreement with the generally accepted view of the earliest relations between these branches of Indo-European.

The western Indo-European vocabulary in Baltic and Slavic is the result of an Indo-European substratum which contained an older non-Indo-European layer and was part of the Corded Ware horizon. The numbers show that a considerable part of the vocabulary was borrowed after the split between Baltic and Slavic, which came about when their speakers moved westwards north and south of the Pripet marshes. These events are older than the westward movement of the Slavs which brought them into contact with Temematic speakers. One may conjecture that the Venedi occupied the Oder basin and then expanded eastwards over the larger part of present-day Poland before the western Balts came down the river Niemen and moved onwards to the lower Vistula. We may then identify the Venedic expansion with the spread of the Corded Ware horizon and the westward migration of the Balts and the Slavs with their integration into the larger cultural complex. The theory that the Venedi separated from the Veneti in the upper Sava region and moved through Moravia and Silesia to the Baltic Sea explains the “im Namenmaterial auffällige Übereinstimmung zwischen dem Baltikum und den Gebieten um den Nordteil der Adria” (Udolph 1981: 61). The Balts probably moved in two stages because the differences between West and East Baltic are considerable.

Instead of reinterpreting his views in light of the recent genetic finds, Kortlandt tries to mix in this paper his own old theories with the recent interpretations of genetic papers, using also dubious secondary sources – e.g. Iversen and Kroonen (2017) or Klejn (2017) [see here, and here] – which, in my opinion, creates a potentially dangerous circular reasoning.

For example, even though he criticizes the general stance of recent genetic papers with regard to Proto-Indo-European dialectalization and expansion as too early, and he supports the Danube expansion route, he nevertheless follows their interpretations in accepting that Corded Ware was Indo-European (which would then be in his view either pre-LPIE, or an LPIE dialect with no known descendants; but with Western IE vocabulary??).

He still follows his good old Indo-Slavonic group in the east, but at the same time maintains Kallio’s view that there were no early Uralic loanwords in Balto-Slavic, and also Kallio’s (and the general) view that there were close contacts with PIE and Pre-Proto-Indo-Iranian…

NOTE. The latest paper on Eurasian migrations by Damgaard et al. (Nature 2018), which shows mainly Proto-Iranians dominating over East Europe after the Early Bronze Age, have left still fewer space for a Proto-Balto-Slavic group emerging from the east.

Also, he asserts the following, which is a rather weird interpretation of events:

It appears that the Corded Ware horizon spread to southern Scandinavia (cf. Iversen & Kroonen 2017) but not to the Baltic region during the Neolithic.

“However, we also find indications of genetic impact from exogenous populations during the Neolithic, most likely from northern Eurasia and the Pontic Steppe. These influences are distinct from the Anatolian-farmer-related gene flow found in Central Europe during this period.”

It follows that the Indo-Europeans did not reach the Baltic region before the Late Neolithic. The influx of non-local people from northern Eurasia may be identified with the expansion of the Finno-Ugrians, who came into contact with the Indo-Europeans as a result of the eastward expansion of the latter in the fourth millennium. This was long before the split between Balto-Slavic and Indo-Iranian.

In the Late Neolithic there was “a further population movement into the regions surrounding the Baltic Sea” that was “accompanied by the first evidence of extensive animal husbandry in the Eastern Baltic”, which “suggests import of the new economy by an incoming steppe-like population independent of the agricultural societies that were already established to the south and west of the Baltic Sea.” (Mittnik & al. 2018). These may have been the ancestors of Balto-Slavic speakers. At a later stage, the Corded Ware horizon spread eastward, giving rise to farming ancestry in Eastern Baltic individuals and to a female gene-flow from the Eastern Baltic into Central Europe (ibidem).

copper-age-late-urals
Late Copper Age migrations in Asia ca. 2800-2300 BC.

He is a strong Indo-Uralic supporter, and supports a parallel Indo-European – Uralic development in Eastern Europe, and (as you can read) he misunderstands the description of population movements in the Baltic region, and thus misplaces Finno-Ugric speakers as Eurasian migrants arriving in the Baltic from the east during the Late Neolithic, before the Corded Ware expansion, which is not what the cited papers implied.

NOTE. Such an identification of westward Neolithic migrations with Uralic speakers is furthermore to be rejected following the most recent paper on Fennoscandian samples.

He has previously asserted that the substrate common to Germanic and Balto-Slavic is non-Indo-European, so I guess that this proposal of an intermediate Indo-European language of the Corded Ware culture strongly influenced by a Non-Indo-European substrate, which in turn influences (as a substrate) both Germanic and Balto-Slavic, is the best way he could put everything together, if one assumes the widespread interpretations of genetic papers.

NOTE. It is very likely that this paper was sent in late 2017. That’s the main problem with traditional publications including the most recent genetic investigation: by the time something gets eventually published, the text is already outdated.

I obviously share his opinion on precedence of disciplines in Indo-European studies:

The methodological point to be emphasized here is that the linguistic evidence takes precedence over archaeological and genetic data, which give no information about the languages spoken and can only support the linguistic evidence. The relative chronology of developments must be established on the basis of the comparative method and internal reconstruction. The location of a reconstructed language can only be established on the basis of lexical and onomastic material. On the other hand, archaeological or genetic data may supply the corresponding absolute chronology. It is therefore incorrect to attribute cultural influences in southern Scandinavia and the Baltic region in the third millennium to Germanic or Baltic speakers because these languages did not yet exist. While the Italo-Celtic branch may have separated from its Indo-European neighbors in the first half of the third millennium, Proto-Balto-Slavic and Proto-Indo-Iranian can be dated to the second millennium and Proto-Germanic to the end of the first millennium BC (cf. Kortlandt 2010: 173f., 197f., 249f.). The Indo-Europeans who moved to southern Scandinavia as part of the Corded Ware horizon were not the ancestors of Germanic speakers, who lived farther to the south, but belonged to an unknown branch that was eventually replaced by Germanic.

I hope we can see more and more anthropological papers like this, using traditional linguistics coupled with archaeology and the most recent genetic investigations.

Related:

Bantu distinguished from Khoe by uniparental markers, not genome-wide autosomal admixture

bantu-expansion

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola, by Oliveira et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

The origins of NRY diversity in SW Angola

In accordance with our previous mtDNA study9, the present NRY analysis reveals a major division between the Kx’a-speaking !Xun and the Bantu-speaking groups, whose paternal genetic ancestry does not display any old remnant lineages, or a clear link to pre-Bantu eastern African migrants introducing Khoe-Kwadi languages and pastoralism into southern Africa (cf. 15). This is especially evident in the distribution of the eastern African subhaplogroup E1b1b1b2b29, which reaches the highest frequency in the !Xun (25%) and not in the formerly Kwadi-speaking Kwepe (7%). This observation, together with recent genome-wide estimates of 9-22% of eastern African ancestry in other Kx’a and Tuu-speaking groups35, suggests that eastern African admixture was not restricted to present-day Khoe-Kwadi speakers. Alternatively, it is likely that the dispersal of pastoralism and Khoe-Kwadi languages involved a series of punctuated contacts that led to a wide variety of cultural, genetic and linguistic outcomes, including possible shifts to Khoe-Kwadi by originally Bantu-speaking peoples36.

Although traces of an ancestral pre-Bantu population may yet be found in autosomal genome-wide studies, the extant variation in both uniparental markers strongly supports a scenario in which all groups of the Angolan Namib share most of their genetic ancestry with other Bantu groups but became increasingly differentiated within the highly stratified social context of SW African pastoral societies11.

bantu-pastoralists
Y chromosome phylogeny, haplogroup distribution and map of the sampling locations. The phylogenetic tree was reconstructed in BEAST based on 2,379 SNPs and is in accordance with the known Y chromosome topology. Main haplogroup clades and their labels are shown with different colors. Age estimates are reported in italics near each node, with the TMRCA of main haplogroups shown with their corresponding color. A map of the sampling locations, re-used with permission from Oliveira et al. (2018) 9, is shown on the bottom left, and the haplogroup distribution per population is shown on the bottom right, with color-coding corresponding to the phylogenetic tree.

The influence of socio-cultural behaviors on the diversity of NRY and mtDNA

A comparison of the NRY variation with previous mtDNA results for the same groups 9 identifies three main sex-specific patterns. First, gene flow from the Bantu into the !Xun is much higher for male than for female lineages (31% NRY vs. 3% mtDNA), similar to the reported male-biased patterns of gene flow from Bantu to Khoisan-speaking groups33, and from non-Pygmies to Pygmies in Central Africa 37. A comparable trend, involving exclusive introgression of NRY eastern African lineages into the !Xun (25%) was also found. (…)

Secondly, the levels of intrapopulation diversity in the Bantu-speaking peoples from the Namib were found to be consistently higher for mtDNA than for the NRY, reflecting the marked association between the Bantu expansion and the relatively young NRY E1b1a1a1 haplogroup, which has no parallel in mtDNA25,39. (…)

In the context of the Bantu expansions, these patterns have been mostly interpreted as the result of polygyny and/or higher levels of assimilation of females from resident forager communities38,40. However, most groups from the Angolan Namib are only mildly polygynous11 and ethnographic data suggest that the actual rates of polygyny in many populations may be insufficient to significantly reduce Nem2,41. In addition, the finding of a large Nef/ Nem ratio in the Himba (Fig. S5), who have almost no Khoisan-related mtDNA lineages9, indicates that female biased introgression cannot fully explain the observed patterns.

An alternative explanation may be sought in the prevailing matrilineal descent rules, which might have created a sex-specific structuring effect, similar to that proposed for patrilineal groups from Central Asia (…)

bantu-xun-plot
Bayesian skyline plots (BSP) of effective population size change through time, based on mtDNA (red) and the NRY (black). Thick lines show the mean estimates and dashed lines show the 95% HPD intervals. The vertical line highlights the 2 ky before present mark. Effective sizes are plotted on a log scale. Generation times of 25 and 31 years were assumed for mtDNA and the NRY, respectively32.

The third important sex-specific pattern observed in this study is the much lower amount of between-group differentiation for NRY than for mtDNA among Bantu-speaking populations (4.4% NRY vs. 20.2% mtDNA), in spite of the patrilocal residence patterns of all ethnic groups (Table S5). This difference can hardly be explained by unequal levels of introgression of “Khoisan” mtDNA lineages into the Bantu, since the percentage of mtDNA variation remains high (18.8%) when the Kuvale, who have high frequencies of “Khoisan”-related mtDNA, are excluded from the comparisons. It therefore seems more plausible that differentiation is higher in the mtDNA simply because there is more ancestral mtDNA than NRY variation that can be sorted among different populations (see 45). Moreover, due to the matriclanic organization of all Bantu-speaking communities, factors enhancing inter-group differentiation, like kin-structured migration and kin-structured founder effects46, would have been restricted to mtDNA. Finally, it is also likely that the discrepancy between among-group divergence of mtDNA and NRY might have been influenced by higher migration rates in males than females. In fact, although all Bantu-speaking populations have patrilocal residence patterns, the observance of endogamy rules severely constrains the between-group mobility of females. In this context, the children from extramarital unions involving members from different populations tend to be raised in the mother’s group, effectively increasing male versus female migration rates. Moreover, it is likely that, in the highly hierarchized setting of the Namib, most intergroup extramarital unions would involve men from dominant groups and women from peripatetic communities. This hypothesis is indirectly supported by the finding that in NRY-based clusters (but not in mtDNA) pastoralist populations are grouped together with peripatetic communities that share their cultural traits (Figs. S6 and 3b), suggesting that migration of NRY lineages follows a path that is similar to horizontally transmitted cultural features.

Related:

Pasture usage by ancient pastoralists in Middle and Late Bronze Age Kazakhstan

bestamak-lisakovsk-study-area

Open access Pasture usage by ancient pastoralists in the northern Kazakh steppe informed by carbon and nitrogen isoscapes of contemporary floral biomes, by Miller et al. Archaeol Anthropol Sci (2018).

Interesting excerpts (emphasis mine):

Bronze age settlement, society, and subsistence in the northern Kazakh steppe

The Middle to Late Bronze Age (2200 to 1400 cal BCE) in the northern Kazakh steppe encompassed a major shift in settlement patterns from semi-sedentary pastoralism to more dispersed, mobile lifeways engaged in pastoral nomadism (Tkacheva 1999; Grigory’ev 2002; Koryakova and Epimakhov 2007; Kuz’mina 2007; Tkacheva and Tkachev 2008). Middle Bronze Age (2200 to 1700 cal BCE) settlements had large enclosures consisting of an earthen wall and ditch. Inside the enclosure, earthen domestic structures with shared walls (numbering from 30 to 60) housed an estimated 200 to 700 individuals (Gening et al. 1992; Grigor’yev 2002; Anthony 2007; Kohl 2007; Koryakova and Epimakhov 2007; Hanks 2009; Batanina and Hanks 2013). MBA settlements were repeatedly occupied, evidenced by successive building phases that added structures and enlarged enclosures. Aggregated MBA sites are situated between 40 and 60 km apart, and landscapes between enclosed settlements may have been territories of particular settlements (Epimakhov 2002; Zdanovich and Batanina 2002; Merrony et al. 2009; Stobbe et al. 2016). While there is currently no archeological evidence for structures such as animal corrals or walls outside of MBA settlement enclosures, open areas within settlements may have been used to house livestock. Reconstructions of landscape use in the vicinity of MBA sites determined that pastures within 4 km of the site could have supported herd sizes large enough to sustain sedentary livestock herders (Stobbe et al. 2016). During the subsequent Late Bronze Age (1800 to 1400 cal BCE) settlements were more dispersed across the landscape and significantly smaller, consisting of fewer than 20 dwellings, further lacking enclosures and building phases (Kuz’mina 2007:36–8; Zakh and Ilyushina 2010). This shift in settlement size and distribution has been interpreted to indicate the emergence of nomadic pastoralism and the intensification of long-distance mobility (Tkacheva 1999; Grigory’ev 2000; Kuz’mina 2007; Tkacheva and Tkachev 2008).

MBA communities engaged in pastoralism and supplemented their diets with wild plants and wild game (Krause and Koryakova 2013; Ventresca Miller et al. 2014a; Hanks et al. 2018). A variety of wild plants have been recovered during flotation, but so far, domesticated grains have not been recovered (Krause and Koryakova 2013; Ng 2013; Hanks et al. 2018). Carbon and nitrogen stable isotope analyses of bone collagen indicate that human dietary intake in the MBA focused on terrestrial animal protein, likely in the form of meat and milk, which was supplemented by locally available fish and wild plants (Ventresca Miller et al. 2014a; Hanks et al. 2018). While the subsequent LBA has been interpreted as a shift to nomadic pastoralism, little data is available regarding landscape use or herd management strategies for this period. Paleodietary studies suggest that human diets during the LBA focused on pastoral products and were supplemented by wild plants, fish, and wild animals (Ventresca Miller et al. 2014a, 2014b).

kazakhstan-russia-sintashta-andronovo
Location of the archeological sites of Bestamak (MBA), Kamennyi Ambar (MBA), Bolshekaragansky (MBA), and Lisakovsk (LBA)

Conclusions

A major shift in patterns of settlement occurred at the Middle to Late Bronze Age transition, from large semi-sedentary populations in enclosed settlements to smaller populations in open settlements dispersed across the landscape. Scholars have suggested that animal management strategies also changed at this time from semi-sedentary pastoralism to more mobile forms of pastoral nomadism. However, our findings suggest that livestock management practices did not shift in concert with social landscapes, demonstrating consistency in pastoral adaptations through time in the region. Similar isotopic patterning between livestock during the MBA and LBA across several sites in the CES indicates that there were no changes across time in pasture usage patterns. Among ancient livestock, differences in δ13C and δ15N values between horses and ruminants (cattle, sheep, goat) strongly suggest that livestock were grazed pastures either extensively or intensively, respectively. Horses grazed in open steppe areas or intermittently in areas with well-watered soils that lacked salinity, likely staying well outside of settlements. In contrast, cattle and sheep/goat grazed in pastures across multiple zones, both near the settlement and in non-local pastures that were grazed intensively. A wider range of δ13C and δ15N values among ruminants at Kamennyi Ambar (MBA) suggests that aggregated human populations may have had larger herds, some of which accessed non-local pastures outside of the easily accessible territories surrounding enclosed sites. Continued research on the isotopic composition of vegetation surrounding Bronze Age sites should clarify patterns of landscape use between MBA sites.

Related:

Complex history of dog origins and translocations in the Pacific revealed by ancient mitogenomes

remote-oceania-vanuatu-lapita

Open access Complex history of dog (Canis familiaris) origins and translocations in the Pacific revealed by ancient mitogenomes, by Creig et al., Scientific Reports (2018).

Abstract:

Archaeological evidence suggests that dogs were introduced to the islands of Oceania via Island Southeast Asia around 3,300 years ago, and reached the eastern islands of Polynesia by the fourteenth century AD. This dispersal is intimately tied to human expansion, but the involvement of dogs in Pacific migrations is not well understood. Our analyses of seven new complete ancient mitogenomes and five partial mtDNA sequences from archaeological dog specimens from Mainland and Island Southeast Asia and the Pacific suggests at least three dog dispersal events into the region, in addition to the introduction of dingoes to Australia. We see an early introduction of dogs to Island Southeast Asia, which does not appear to extend into the islands of Oceania. A shared haplogroup identified between Iron Age Taiwanese dogs, terminal-Lapita and post-Lapita dogs suggests that at least one dog lineage was introduced to Near Oceania by or as the result of interactions with Austronesian language speakers associated with the Lapita Cultural Complex. We did not find any evidence that these dogs were successfully transported beyond New Guinea. Finally, we identify a widespread dog clade found across the Pacific, including the islands of Polynesia, which likely suggests a post-Lapita dog introduction from southern Island Southeast Asia.

canis-familiaris
A map of Southeast Asia and the Pacific showing the source location of the specimens and associated haplogroups (assignment to haplogroup follows Duleba and colleagues) and the median-joining network. The boundary between Near and Remote Oceania is also shown. Symbols identify the type of sequence: filled circle, ancient mitogenome; half circle, partial ancient sequence; hollow circle, modern mitogenome. Node colours represent the haplogroup, grey, A; red, A2b2, green, A2b3; yellow, A4’5; blue, B.

Conclusion:

The dispersal of dogs across the Pacific is inseparably linked to the relationships between dogs and people. Unlike movement across continental landmasses, Pacific dogs must have been transported by people across the waters that separate islands. The ancient mitogenomes sequenced from archaeological dog specimens presented here offer a novel series of individual insights into the history of dog translocation from Southeast Asia as it occurred prior to the influence of modern European dog breeds. We generated seven mitogenomes and five partial sequences from ancient MSEA, ISEA and Pacific dogs, and four modern dingoes. Despite the small sample size, our results reveal levels of complexity and discontinuity in the introduction and movement of dogs, which are mirrored in the archaeological and linguistic evidence, suggesting at least three introductions of dogs to the wider Pacific region, in addition to the earlier appearance of the dingo in Australia. Further mtDNA studies of ancient dogs and modern village populations throughout the region may contribute additional data that can be used to evaluate these hypothesised dispersals. Autosomal and Y-chromosome analyses also have the potential to generate additional information about dog dispersal, which could reveal different dispersal signatures based on sex, or phenotypic characteristics, though the environmental conditions in the region are not particularly conducive to aDNA preservation.

Our molecular genetic analyses reveal one of the earliest dogs present in ISEA around 3,000 years ago from Timor-Leste possesses a mtDNA lineage not found elsewhere in the region. We also found similarities between mtDNA of modern dingoes and NGSDs and an ancient Taiwanese sequence, which supports previous observations about possible links between Y-chromosome markers of modern dingoes and a modern Taiwanese sample. More work is required to address whether these connections reflect the genetic diversity of a shared ancestral population in mainland China, or attest to a currently unknown dispersal event linking the two populations. Archaeological evidence for the introduction of dogs to Oceania as part of the LCC is extremely limited. Nonetheless, we demonstrate that mitogenomes from dogs in terminal Lapita and post-Lapita levels of archaeological sites along the south coast of mainland New Guinea also show affinities with an Iron Age dog specimen from Taiwan, raising the possibility of at least one introduction of dogs during Austronesian expansions ultimately from the north. Finally, we have identified a major late introduction of dogs across the islands of Oceania beginning around 2,000 years ago, which appears to have originated in MSEA, not Taiwan, and culminated in the establishment of dog populations in initial colonisation-era sites throughout East Polynesia.

phylogenetic-dingo
Molecular phylogenetic analysis by maximum likelihood method, implemented in MEGA71. The evolutionary history shown inferred by using the maximum likelihood method based on the Hasegawa-Kishino-Yano model. The tree with the highest log likelihood (-25257.5243) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.0500)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 0.0010% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 45 nucleotide sequences. There were a total of 16774 positions in the final dataset.

Also related, open access Elucidating biogeographical patterns in Australian native canids using genome wide SNPs, by Cairns et al., PLOS One (2018).

Abstract:

Dingoes play a strong role in Australia’s ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.

dingo-australia-pca
Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’). Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW dingoes, dark green for NGSD, light green for Borneo village dogs, orange for Vietnam village dogs, yellow for Portugal village dogs and grey for Australian cattle dogs. (A) PC 1 versus PC 2. (B) PC 1 versus PC 3.

As I said in a previous post, the study of dogs may be useful to trace population migrations and to assess strong cultural contacts. Especially, as in this case, when crossbreeding among cultures is not easy…

Related:

Paleoenvironment in mid- to late Holocene in the Cis-Ural steppes, and Epigravettian in Eastern Europe

Dynamics of paleoenvironments in the Cis-Ural steppes during the mid- to late Holocene, by Khokhlova, Morgunova, Khokhlov, and Golyeva, Quaternary Research (2018), 1–15.

Interesting excerpts:

About the studied site

The Turganik settlement in the Orenburg Region constitutes part of the so-called Ivanovo microregion of cultural heritage monuments, along with the Mesolithic Starotokskaya site; an Ivanovskoye multi-layered settlement (Neolithic, Eneolithic [or Chalcolithic], Late Bronze Age); Toksky I and Toksky II settlements attributed to the Late Bronze Age (the Timber-Grave archaeological culture); an Ivanovsky ground burial dated to the Eneolithic; and the Ivanovsky kurgan cemetery of the Early Iron Age (Fig. 1).

The ancient settlements are located at the Turganik River mouth, where the river joins the Tok River (the Samara River drainage basin). The Turganik River enters an old channel of the Tok which continues to flow due to that fact. Both valleys are wide and dissected by multiple river channels. The floodplain landscapes are mostly wet meadows with rich herb and grass vegetation, pastures, and hay fields. On both sides of the Turganik River, and farther along the right side of the Tok valley there are flat-topped elevations, with occasional forests (Chibilev, 1996). The Turganik settlement was positioned on a slightly elevated surface at the confluence of the Turganik and Tok rivers, on the right side of the valley. The settlement was inhabited in the Eneolithic and the Late Bronze Age, the fifth to fourth millennia BC.

turganik-cis-ural-steppe
(a and b) Location of the studied region and (c) the objects of the cultural heritage in the microregion: 1, Turganik settlement; 2, Toksky II settlement; 3, Ivanovsky dune with Ivanovsky ground cemetery; 4, Ivanovskoye II multi-layered settlement; 5, Staro-Tokskaya site; 6, Toksky I settlement; 7, Ivanovsky I kurgan cemetery.

Results and discussion

Pollen assemblages of the Atlantic optimum ~ 5500 yr BP indicate some increase in moisture supply and related afforestation of the floodplain (Lavrushin and Spiridonova, 1995). As follows from our data, the site was abandoned at that time and the no-longer-functioning cultural layer VI was gradually buried under deposits of frequent floods. According to the 14C ages obtained on archeological materials, the age of layer VI (or the second stage of the Eneolithic epoch on the Turganik settlement) may be dated to 4237–3790 cal yr BC, that is, somewhat earlier than the Holocene optimum suggested by palynologists.

Layer V shows another interval marked by increasing climate aridity and the dominance of grass steppes. As stated by the above-cited authors, the climate at the time that layer V was functioning was even dryer than during the formation of layer VI. That is confirmed by our data on the layer V composition, was formed during early Pit-Grave culture (the Early Bronze Age), in the range from 3800–3360 BC, according to the dates obtained on archeological materials (Morgunova et al., 2016b). As follows from the above, the maximum of aridity coincided with the Atlantic optimum.

It follows from the above that the Atlantic period of the Holocene was mostly characterized by arid environments; the peak of aridity fell on the early Bronze Age, the time of the early (Repino) stage of the Yamnaya culture in the Cis-Ural steppes. The Subboreal and Subatlantic periods were relatively colder and more humid, though short episodes of aridity could occur and some of them happened to be recorded in the sequence under study.

The reconstructed history of the climate changes in the Cis-Ural steppes during three intervals of the Holocene is in a good agreement with the results obtained in other regions. According to Alexandrovskiy (1996, 2000; Alexandrovskiy et al., 1999, 2004), the Atlantic period was the most arid one in the south of Russia, the subsequent intervals being comparatively wetter and colder. The extreme aridity was recorded on the Ukraine territory at the final Atlantic period, a few less arid chrono-intervals having been identified over the entire period (Kotova, 2009).

There are, however, other schemes of climate fluctuations in the central part of the Russian steppe zone; a few of them consider the Atlantic period to be humid, or even the most humid, as compared with the second half of the Holocene (Ivanov, 1992; Demkin, 1997). Also acceptable is a scenario of climatic fluctuations occurring at different times in different regions (Chendev et al., 2010). Further investigations and accumulation of empirical data would help to gain a better insight into the problem.

Conclusions

The ancient people inhabited the place from 5000 to 4000 BC (actually throughout the Atlantic period), when the place was not subjected to flooding. At the time of human habitation, the climate was mostly arid. Paleosols of that time are attributable to the Kastanozems (Endosalic Protosodic). They developed under grass (or herb and grass) steppes. The peak of aridity falls on the final Atlantic period. At the end of Eneolithic epoch (the fifth millennium BC) and in the Early Bronze Age (the fourth millennium BC) there were short-term but violent floods, which forced people to leave the habitable place.

During the Subboreal and Subatlantic periods of the Holocene, the climate became more humid, the floods became regular, the vegetation was dominated by meadow forbs and herbs growing on meadow-chernozem soils (Luvic Chernozem [Stagnic]), and the settlement was completely abandoned. In general, the studied sedimentary record at the Turganik archeological site reveals traceable climate change towards lower temperatures and increasing humidity in the second part of the Holocene, with occasional episodes of aridity that did not affect the general trend.


Interesting also the paper Collagen stable isotopes provide insights into the end of the mammoth steppe in the central East European plains during the Epigravettian, by Drucker et al., Quaternary Research (2018), 1-13

east-europe-mammoth
Location of the sites considered in this study.

About the studied site

The central East European plains are famous for their Epigravettian sites that date to around 15–12 14C ka BP (ca. 18.2–13.8 cal ka BP) and display impressive large structures made from the bones of woolly mammoth (Mammuthus primigenius; e.g., Gladkih et al., 1984; Soffer, 1985; Hoffecker, 2002). The origin of the large accumulations of mammoth remains is still a matter of debate, with the main hypotheses being the collection of natural occurrences versus active hunting (e.g., Soffer, 1985; Haynes 1989; Svoboda et al., 2005). In favor of this second scenario, studies of the mammoth remains of Yudinovo (Germonpré et al., 2008) concluded that the mammoths were hunted and, at Mezhyrich, mammoths were obtained by combined procurement via collection of carcasses and active hunting (Péan, 2015). Hunting practices were observed in older sites of the Gravettian culture in the Dnieper and Desna valleys (Demay et al., 2016).

Between ca. 22 and 12 14C ka BP (ca. 26.2–13.8 ka cal BP), the Dnieper and Desna basins correspond to the southern part of the geographical distribution of the woolly mammoth (Markova et al., 2013; Kahlke, 2014). Over time their distribution shifted northwards, while the density of the mammoth population decreased (Markova et al., 2013). According to Markova et al. (2013), the combined effect of gradual warming and growing human pressure is most likely to have had a negative impact on the mammoths, resulting in their local extinction in the Russian and Ukrainian plains around 14–12 14C kaBP (ca. 17.0–13.8 ka cal BP; Stuart et al., 2005).

Discussion and conclusion

mammoth-horse-canid
Measured δ34S and δ15N values on bone collagen of mammoth, large canid, and fox from Mezhyrich (M), Buzhanka 2 (B), Yudinovo (Y), and Eliseevichi (E).

Humans could have taken advantage of the mammoth vulnerability, as reflected by lower δ15N values, to access animals that died naturally, collect bones, and hunt the most fragile individuals. This, with the possible assistance of domesticated dogs as hunting partners, could have countered a possible return to more suitable conditions for mammoth (Sablin and Khlopachev, 2002; Shipman, 2015). Our results confirm at least that mammoth specimens from Mezhyrich, Buzhanka 2, and, to a lesser extent, Eliseevichi were part of late mammoth populations surviving in sub-optimal conditions. They were thus most likely vulnerable to any pressure from environmental and/or human origin. Detecting further such cases among the late surviving mammoth populations using stable isotopic tracking may be a way to test if mammoth populations still had an optimal ecology or were metastable and, therefore, vulnerable to extinction. For instance, the insular Holocene population of mammoth on Saint Paul Island exhibited low and variable δ15N values, indicating suboptimal ecological conditions preceding their final disappearance (Graham et al., 2016).

The results of δ34S analyses showed no differences among mammoth according to the site but possibly a forage range partitioning between mammoth and coexisting large ungulates. Thus, variability in the mobility pattern for the mammoth between the high and low δ15N groups, such as migratory versus sedentary individuals, is not supported so far. We consider that rapid environmental modifications over time, probably not detectable through radiocarbon dating, can be a valid alternative explanation. Combined with direct competition with other large herbivores, such as the horse, and hunting of the most vulnerable individuals, the loss of their optimal habitat was likely to be the driving factor behind the local extinction of the mammoth in the central East European plains.

Related:

Native American genetic continuity and oldest mtDNA hg A2ah in the Andean region

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies by Criollo-Rayo et al., Forensic Sci Int Genet (2018), in press, corrected proof.

Abstract (emphasis mine):

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia.

andean-y-dna-mtdna
Ancestral uniparental haplogroups and diversity in Tolima. Geography of sampling locations. The
top and middle sections show the frequency of Native American mtDNA haplogroups and NRY lineages for all
populations. Gene diversity is shown below their respective pie chart. The lower part depicts the geography of the
region where the sampling sites of Ortega and Pijao are closely located in Tolima’s Magdalena river valley and
Ibague, Planadas and Nasa located in the Andes cordilleras (additional geographic details are shown in SF1).

Highlights from the paper:

  • MtDNA suggest a pre/post Columbian genetic continuity in the Colombian Andes.
  • Y-chromosome diversity follows a clinal gradient in the studied region.
  • Sex-biased/male-driven admixture process, involving Pijao women with European men.
  • Admixed closer to Indigenous resguardos have a higher Native American ancestry.

Also interesting is the recent paper Mitochondrial lineage A2ah found in a pre‐Hispanic individual from the Andean region, by Russo et al., in American Journal of Human Biology (2018), with an interesting sample from the Regional Developments II period (540 ± 60 BP).

phylogeny-a2ah-mtdna
Phylogeny of the A2ah mitochondrial lineage based on HVR I sequences. Both MaximumParsimony andMaximumLikelihood reconstructions led to the same typology. The tree was rooted with the RSRS. Sample ID: Cueva: Pukara de La Cueva, STACRUZ: Santa Cruz, BNI: Beni, BR: South-eastern Brazil, TobaChA: TobaGranChaco

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