Cosmic impact event ~12.8kya caused the Younger Dryas

PNAS doi: 10.1073/pnas.1301760110

Evidence for deposition of 10 million tonnes of impact spherules across four continents 12,800 y ago

James H. Wittke et al.

Airbursts/impacts by a fragmented comet or asteroid have been proposed at the Younger Dryas onset (12.80 ± 0.15 ka) based on identification of an assemblage of impact-related proxies, including microspherules, nanodiamonds, and iridium. Distributed across four continents at the Younger Dryas boundary (YDB), spherule peaks have been independently confirmed in eight studies, but unconfirmed in two others, resulting in continued dispute about their occurrence, distribution, and origin. To further address this dispute and better identify YDB spherules, we present results from one of the largest spherule investigations ever undertaken regarding spherule geochemistry, morphologies, origins, and processes of formation. We investigated 18 sites across North America, Europe, and the Middle East, performing nearly 700 analyses on spherules using energy dispersive X-ray spectroscopy for geochemical analyses and scanning electron microscopy for surface microstructural characterization. Twelve locations rank among the world’s premier end-Pleistocene archaeological sites, where the YDB marks a hiatus in human occupation or major changes in site use. Our results are consistent with melting of sediments to temperatures >2,200 °C by the thermal radiation and air shocks produced by passage of an extraterrestrial object through the atmosphere; they are inconsistent with volcanic, cosmic, anthropogenic, lightning, or authigenic sources. We also produced spherules from wood in the laboratory at >1,730 °C, indicating that impact-related incineration of biomass may have contributed to spherule production. At 12.8 ka, an estimated 10 million tonnes of spherules were distributed across ∼50 million square kilometers, similar to well-known impact strewnfields and consistent with a major cosmic impact event.

Link

More population structure in the Netherlands (Lao et al. 2013)

There was a recent article on the topic by Abdellaoui et al., and here is another one.

Investigative Genetics 2013, 4:9 doi:10.1186/2041-2223-4-9

Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history

Oscar Lao et al.

Abstract (provisional)

Background

The presence of a southeast to northwest gradient across Europe in human genetic diversity is a well-established observation and has recently been confirmed by genome-wide single nucleotide polymorphism (SNP) data. This pattern is traditionally explained by major prehistoric human migration events in Palaeolithic and Neolithic times. Here, we investigate whether (similar) spatial patterns in human genomic diversity also occur on a micro-geographic scale within Europe, such as in the Netherlands, and if so, whether these patterns could also be explained by more recent demographic events, such as those that occurred in Dutch population history.

Methods

We newly collected data on a total of 999 Dutch individuals sampled at 54 sites across the country at 443,816 autosomal SNPs using the Genome-Wide Human SNP Array 5.0 (Affymetrix). We studied the individual genetic relationships by means of classical multidimensional scaling (MDS) using different genetic distance matrices, spatial ancestry analysis (SPA), and ADMIXTURE software. We further performed dedicated analyses to search for spatial patterns in the genomic variation and conducted simulations (SPLATCHE2) to provide a historical interpretation of the observed spatial patterns.

Results

We detected a subtle but clearly noticeable genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern and a southern group. Furthermore, we observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands, similar to earlier findings from across Europe. Simulation analyses indicate that this genomic gradient could similarly be caused by ancient as well as by the more recent events in Dutch history.

Conclusions

Considering the strong archaeological evidence for genetic discontinuity in the Netherlands, we interpret the observed clinal pattern of genomic diversity as being caused by recent rather than ancient events in Dutch population history. We therefore suggest that future human population genetic studies pay more attention to recent demographic history in interpreting genetic clines. Furthermore, our study demonstrates that genetic population substructure is detectable on a small geographic scale in Europe despite recent demographic events, a finding we consider potentially relevant for future epidemiological and forensic studies.

Link

Review on germline mutation rate in humans (Campbell and Eichler 2013)

This is a nice little review of the state of the art in germline mutation rate estimation in humans. This was previously estimated using paleontological calibrations (especially the human/chimp split), but a slower mutation rate emerged on the basis of whole genome data from humans. There may be problems with the latter (because of false positive/negative mutations using whole genome sequencing), but the problem is an important one due to the use of the mutation rate to estimate time depth of common ancestry. In any case, the table on the left summarizes the results of several studies on the topic.


Trends in Genetics, 17 May 2013 doi:10.1016/j.tig.2013.04.005

Properties and rates of germline mutations in humans

Catarina D. Campbell, Evan E. EichlerSee Affiliations

Summary

All genetic variation arises via new mutations; therefore, determining the rate and biases for different classes of mutation is essential for understanding the genetics of human disease and evolution. Decades of mutation rate analyses have focused on a relatively small number of loci because of technical limitations. However, advances in sequencing technology have allowed for empirical assessments of genome-wide rates of mutation. Recent studies have shown that 76% of new mutations originate in the paternal lineage and provide unequivocal evidence for an increase in mutation with paternal age. Although most analyses have focused on single nucleotide variants (SNVs), studies have begun to provide insight into the mutation rate for other classes of variation, including copy number variants (CNVs), microsatellites, and mobile element insertions (MEIs). Here, we review the genome-wide analyses for the mutation rate of several types of variants and suggest areas for future research.

Link

An avalanche of Tibetan genetic data (Qi et al. 2013)

A very impressive data dump on Tibetan genetic variation gives us an excellent picture on both the Y-chromosome and mtDNA side. There are two interesting things about Tibetans -at least to me. First, their mtDNA is dominated by haplogroup M9, which is ~39 thousand years old, suggesting an early settlement after the dispersal of modern humans across Eurasia.

Second, their Y-chromosomes are dominated by Y-haplogroup D, the sister clade of African haplogroup E, which links in some (unspecified, but I'm guessing old) time depth with such diverse peoples as the Andaman Islanders and the Ainu. Mongolians also share haplogroup D, but this is perhaps not surprising given the well-known links between Mongolia and Tibet. One might attribute the high Tibetan D frequency to drift, but drift acts randomly, and I don't think it's a coincidence that it acted in the same way in three quite different and fairly isolated corners of Eurasia to produce the Tibetan/Andaman/Ainu local peaks in an otherwise rather barren haplogroup D landscape.

There are other interesting details, such as the presence of R1a*(xM17) in Tibet, a haplogroup that has a patchy distribution in Asia. In a sample size of ~2,354 it's possible to get one of these less successful relatives of mega-groups like R-M17, and their systematic study may help root in space the earliest history of these lineages.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst093

Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau

Xuebin Qi et al.

Tibetans live on the highest plateau in the world, their current population size is nearly 5 million, and most of them live at an altitude exceeding 3,500 meters. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population history. However, the chronological profile of the Tibetan Plateau's colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal (n = 2,354) and maternal (n = 6,109) lineages as well as genome-wide SNP markers (n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to around 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the Last Glacial Maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic.

Link

Evolutionary history of Uralic languages (Honkola et al. 2013)

Journal of Evolutionary Biology DOI: 10.1111/jeb.12107

Cultural and climatic changes shape the evolutionary history of the Uralic languages

T Honkola et al.

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both ‘biotic’ interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both ‘biotic’ and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution.

Link

Toba eruption did not cause volcanic winter in Africa ~75ka

PNAS May 14, 2013 vol. 110 no. 20 8025-8029 doi: 10.1073/pnas.1301474110

Ash from the Toba supereruption in Lake Malawi shows no volcanic winter in East Africa at 75 ka

Christine S. Lane et al.

The most explosive volcanic event of the Quaternary was the eruption of Mt. Toba, Sumatra, 75,000 y ago, which produced voluminous ash deposits found across much of the Indian Ocean, Indian Peninsula, and South China Sea. A major climatic downturn observed within the Greenland ice cores has been attributed to the cooling effects of the ash and aerosols ejected during the eruption of the Youngest Toba Tuff (YTT). These events coincided roughly with a hypothesized human genetic bottleneck, when the number of our species in Africa may have been reduced to near extinction. Some have speculated that the demise of early modern humans at that time was due in part to a dramatic climate shift triggered by the supereruption. Others have argued that environmental conditions would not have been so severe to have such an impact on our ancestors, and furthermore, that modern humans may have already expanded beyond Africa by this time. We report an observation of the YTT in Africa, recovered as a cryptotephra layer in Lake Malawi sediments, >7,000 km west of the source volcano. The YTT isochron provides an accurate and precise age estimate for the Lake Malawi paleoclimate record, which revises the chronology of past climatic events in East Africa. The YTT in Lake Malawi is not accompanied by a major change in sediment composition or evidence for substantial temperature change, implying that the eruption did not significantly impact the climate of East Africa and was not the cause of a human genetic bottleneck at that time.

Link

mtDNA from Minoan Crete (Hughey et al. 2013)

A very exciting (and open access) new paper on Minoan mtDNA adds new ancient DNA data from the southeastern corner of Europe and from a critical period at the beginning of European history.

The authors are able to reject Arthur Evans's idea that Minoan civilization had a North African origin, since North Africans bear the least similarity to the Minoans among the considered populations. Of course it's possible that Bronze Age North Africa had not yet experienced Sub-Saharan African gene flow -which probably accounts for its distinctiveness today (no African L mtDNA was found in the Minoan sample).

On the other hand, the similarities between the Minoans and other ancient European mtDNA samples probably testifies to Minoans being indeed related to the Neolithic population of Europe. This is particularly interesting in the case of Minoan Crete, which may have been visited in pre-Neolithic times, but  was permanently settled only during the Neolithic, thus minimizing the possibility of an inclusion of a Paleolithic substratum as may be the case in parts of continental Europe.

Supplementary Table S2 shows haplogroup designations of the Minoan individuals which seems to encompass a wide variety:

One thing to note is the absence of mtDNA haplogroup N1a that so typifies central European Neolithic, and also the presence of some haplogroup U5a/U which seems typical of Paleolithic Europeans. I'd be interested in hearing any additional observations people might have on this data.

From the paper:

The PCA analysis also highlights the high affinity of the Minoans to the current inhabitants of the Lassithi plateau as well as Greece. Among the top 10 nearest neighbours to our Minoan population sample, four are Greek populations and two of these from Lassithi prefecture (Fig. 5). The close relationship of the Minoans to modern Cretans is also apparent, when analysis is restricted to populations originating from Greece (Fig. 6b). Particularly in respect to the first PCA (capturing 92% of the variance of this particular subset of the data), the Minoans are extremely close to the modern Lassithi population, the populations from the islands of Chios and Euboea, as well as the populations of Argolis and Lakonia (Southern Greece ) (Fig. 6b). Thus, the modern inhabitants of the Lassithi plateau still carry the maternal genetic signatures of their ancient predecessors of the Minoan population.

It seems that there is (at least in terms of mtDNA) continuity in Crete since the Bronze Age, just as there is in Sardinia. And, indeed there appears to be some similarity between Bronze Age Sardinia and Minoan Crete (see Tables S5 and S6 of the supplement).

This is very exciting stuff which was probably made possible -in part- by the preservation of the material in a sealed cave ossuary, but hopefully more ancient DNA is to be had from Greece and surrounding regions.

UPDATE (From Nature News):

It is likely, says Stamatoyannopoulos, that the Minoans descended from Neolithic populations that migrated to Europe from the Middle East and Turkey. Archaeological excavations suggest that early farmers were living in Crete by around 9,000 years ago, so these could be the ancestors of the Minoans. Similarities between Minoan and Egyptian artefacts were probably the result of cultural exchanges across the navigable Mediterranean Sea, rather than wholesale migrations, he adds. 

Wolfgang Haak, a molecular archaeologist at the University of Adelaide in Australia, thinks that Crete’s early history is probably more complicated, with multiple Neolithic populations arriving at different times. “It's nevertheless good to see some data — if authentic — from this region of Europe contributing to the big and complex puzzle,” he says. 

Stamatoyannopoulos notes that his team’s findings are limited, because mitochondrial DNA represents only a single maternal lineage for each individual — a mother’s mother, and so on. With Johannes Krause, a palaeogeneticist at the University of Tubingen in Germany, the team now plans to sequence the nuclear genomes of Minoans and other ancients to learn more about their history. 

“For the last 30, 40 years there’s been a growing sense that Minoan Crete was created by people indigenous to the island,” says Cyprian Broodbank, a Mediterranean archaeologist at University College London. He welcomes the latest line of support for this hypothesis. “It’s good to have some of the old assumptions that Minoans migrated from some other high culture scotched,” he says.

Nature Communications 4, Article number: 1861 doi:10.1038/ncomms2871

A European population in Minoan Bronze Age Crete

Jeffery R. Hughey et al.

The first advanced Bronze Age civilization of Europe was established by the Minoans about 5,000 years before present. Since Sir Arthur Evans exposed the Minoan civic centre of Knossos, archaeologists have speculated on the origin of the founders of the civilization. Evans proposed a North African origin; Cycladic, Balkan, Anatolian and Middle Eastern origins have also been proposed. Here we address the question of the origin of the Minoans by analysing mitochondrial DNA from Minoan osseous remains from a cave ossuary in the Lassithi plateau of Crete dated 4,400–3,700 years before present. Shared haplotypes, principal component and pairwise distance analyses refute the Evans North African hypothesis. Minoans show the strongest relationships with Neolithic and modern European populations and with the modern inhabitants of the Lassithi plateau. Our data are compatible with the hypothesis of an autochthonous development of the Minoan civilization by the descendants of the Neolithic settlers of the island.

Link

Facial reconstruction of 5,600-year old Maltese woman

Source: Revealed...the face of a Maltese woman 5,600 years ago

Heritage Malta also launched a 3D virtual reconstruction of facial features based on one of the prehistoric skulls (over 5,000 years old) found at the Xaghra Stone Circle in Gozo. It revealed, for the very first time, what one of the earliest Maltese actually looked like.
It was a face which was much closer to what one would expect from a woman of our day and age rather than that of a person who lived on the islands over 5,000 years ago.

Links between Mycenaeans and Scandinavia

Three papers on a similar theme. An excerpt from a source mentioned in the second paper:

Det visar sig att alla undersökta svenska föremål utom ett enda - en slaggbit - kommer från gruvor och malmfyndigheter från platser på Cypern, Sardinien, Iberiska halvön, Massif Central i nuvarande Frankrike, Tyrolen samt Brittiska öarna. Kopparn har transporterats hit och i utbyte har man skeppat tillbaka stora mängder bärnsten. Fram träder en bild av en tid då internationella kontakter över stora vatten var självklarheter, och det redan cirka 2000 år innan vikingarna gav sig iväg på sina färder. [Google Translate]: It turns out that all examined Swedish subject except one - a slaggbit - comes from mines and ore deposits from sites in Cyprus, Sardinia, the Iberian Peninsula, the Massif Central in the current France, Tyrol and the British Isles. Copper has been transported, and in return it has been shipped back large amounts of amber. What emerges is a picture of a time when international contacts over large water was obvious, and there are already some 2000 years before the Vikings set off on their journeys.

From the third paper:

Both the lead isotope and chemical analyses have undoubtedly showed that the copper from the 33 Scandinavian Bronze Age artefacts diverges significantly from Scandinavian copper ores and that the copper must have been imported from elsewhere. The results furthermore indicate that there are variations in metal supply that are related to chronology, in resemblance with artefacts from Scandinavia as well as from other parts of Europe indicating analogous trade routes for copper, during the respective periods. Maritime networks and changing sources of metal seem to have been a key feature for Scandinavia in the Bronze Age.

Archaeology, Ethnology and Anthropology of Eurasia

Volume 40, Issue 2, June 2012, Pages 99–103

Grave Circle B at Mycenae in the Context of Links Between the Eastern Mediterranean and Scandinavia in the Bronze Age

I.B. Gubanov

Artifacts from royal burial graves Gamma and Omicron of grave circle B at Mycenae attest to cultural ties between the Eastern Mediterranean elite and that of the Scandinavian Early Bronze Age (mid- and late 2nd millennium BC). The appearance of the running spiral motif and representations of ships with rams in Scandinavia coincide with the beginning of the Mycenaean civilization. These facts, along with the finds of Baltic amber only in the royal burials at Mycenae but not in Crete, suggest that a principal role in the introduction of these cultural elements in Scandinavia during the Scandinavian Bronze Age (periods I–III according to Montelius) was played by the Mycenaean elite.

Link

Journal of Geography and Geology Vol 5, No 1 (2013)

The Bronze Age in SE Sweden Evidence of Long-Distance Travel and Advanced Sun Cult 

Nils-Axel Mörner, Bob G. Lind

The Bronze Age of Scandinavia (1750-500 BC) is characterized by the sudden appearance of bronze objects in Scandinavia, the sudden mass appearance of amber in Mycenaean graves, and the beginning of bedrock carvings of huge ships. We take this to indicate that people from the east Mediterranean arrived to Sweden on big ships over the Atlantic, carrying bronze objects from the south, which they traded for amber occurring in SE Sweden in the Ravlunda-Vitemölla–Kivik area. Those visitors left strong cultural imprints as recorded by pictures and objects found in SE Sweden. This seems to indicate that the visits had grown to the establishment of a trading centre. The Bronze Age of Österlen (the SE part of Sweden) is also characterized by a strong Sun cult recorded by stone monuments built to record the annual motions of the Sun, and rock carvings that exhibit strict alignments to the annual motions of the Sun. Ales Stones, dated at about 800 BC, is a remarkable monument in the form of a 67 m long stone-ship. It records the four main solar turning points of the year, the 12 months of the year, each month covering 30 days, except for month 7 which had 35 days (making a full year of 365 days), and the time of the day at 16 points representing 1.5 hour. Ales Stones are built after the same basic geometry as Stonehenge in England.

Link

Journal of Archaeological Science
Volume 40, Issue 1, January 2013, Pages 291–304

Moving metals or indigenous mining? Provenancing Scandinavian Bronze Age artefacts by lead isotopes and trace elements

Johan Ling et al.

The aim of this study is to further the discussion as to whether copper was extracted locally or imported to Sweden during the Bronze Age or if both of these practices could have coexisted. For this purpose, we have carried out lead isotope and chemical analyses of 33 bronze items, dated between 1600BC and 700BC. Among these are the famous Fröslunda shields and the large scrap hoard from Bräckan and other items from three regions in southern Sweden which are also renowned for their richness in copper ores. It is obvious from a comparison that the element and lead isotope compositions of the studied bronze items diverge greatly from those of spatially associated copper ores. Nor is there any good resemblance with other ores from Scandinavia, and it is concluded that the copper in these items must have been imported from elsewhere. The results furthermore indicate that there are variations in metal supply that are related to chronology, in agreement with other artefacts from Scandinavia as well as from other parts of Europe. Altogether these circumstances open up for a discussion regarding Scandinavia’s role in the maritime networks during the Bronze Age.

Link

Lakes in SE Arabia ~60 thousand years ago

From the paper:

From the current archaeological evidence, it seems that after MIS 5, the different lithic traditions within Arabia develop along separate trajectories, with no indication of additional input from Africa. Recent genetic evidence (Fernandes et al., 2012) also indicates that the relict distribution of minor haplogroups N1, N2 and X, reflects an ancient ancestry of these groups within the Arabian Peninsula which, the authors conclude, then spread from the Gulf region toward the Near East and Europe between 55 and 24 ka. The potential occurrence of increased humidity within the Arabian interior during MIS 3 would, therefore, have been instrumental in determining the success and trajectory of the autochthonous development of early human communities within the region at this time. Although Rosenberg et al. (2012) may be correct in their description of Arabia between ca. 75 and 10.5 ka as a natural barrier for human dispersal, it is possible that indigenous inhabitants may have persisted in environmental refugia around Arabia, such as the Gulf Oasis (e.g. Rose, 2010). The occurrence of a pluvial phase during the early stages of MIS 3, therefore, may have facilitated a range expansion of early humans previously contained within such refugia. To address these important issues, we present a multiproxy record of an early MIS 3 wet phase from a palaeolake sequence within the continental interior of SE Arabia.

Quaternary International Available online 22 February 2013

An early MIS 3 pluvial phase in Southeast Arabia: Climatic and archaeological implications

Ash Parton et al.

Climatic changes in Arabia are of critical importance to our understanding of both monsoon variability and the dispersal of anatomically modern humans (AMH) out of Africa. The timing of dispersal is associated with the occurrence of pluvial periods during Marine Isotope Stage (MIS) 5 (ca. 130–74 ka), after which arid conditions between ca. 74 and 10.5 ka are thought to have restricted further migration and range expansion within the Arabian interior. Whilst a number of records indicate that this phase of aridity was punctuated by an increase in monsoon strength during MIS 3, uncertainties regarding the precision of terrestrial records and suitability of marine archives as records of precipitation, mean that the occurrence of this pluvial remains debated. Here we present evidence from a series of relict lake deposits within southeastern Arabia, which formed at the onset of MIS 3 (ca. 61–58 ka). At this time, the incursion of monsoon rainfall into the Arabian interior activated a network of channels associated with an alluvial fan system along the western flanks of the Hajar Mountains, leading to lake formation. Multiproxy evidence indicates that precipitation increases intermittently recharged fluvial systems within the region, leading to lake expansion in distal fan zones. Conversely, decreased precipitation led to reduced channel flow, lake contraction and a shift to saline conditions. These findings are in contrast to the many other palaeoclimatic records from Arabia, which suggest that during MIS 3, the latitudinal position of the monsoon was substantially further south and did not penetrate the peninsula. Additionally, the occurrence of increased rainfall at this time challenges the notion that the climate of Arabia following MIS 5 was too harsh to permit the further range expansion of indigenous communities.

Link

Deleterious mutational load and recent population history (Simons et al. 2013)

arXiv:1305.2061 [q-bio.PE]

The deleterious mutation load is insensitive to recent population history

Yuval B. Simons, Michael C. Turchin, Jonathan K. Pritchard, Guy Sella (Submitted on 9 May 2013)

Human populations have undergone dramatic changes in population size in the past 100,000 years, including a severe bottleneck of non-African populations and recent explosive population growth. There is currently great interest in how these demographic events may have affected the burden of deleterious mutations in individuals and the allele frequency spectrum of disease mutations in populations. Here we use population genetic models to show that--contrary to previous conjectures--recent human demography has likely had very little impact on the average burden of deleterious mutations carried by individuals. This prediction is supported by exome sequence data showing that African American and European American individuals carry very similar burdens of damaging mutations. We next consider whether recent population growth has increased the importance of very rare mutations in complex traits. Our analysis predicts that for most classes of disease variants, rare alleles are unlikely to contribute a large fraction of the total genetic variance, and that the impact of recent growth is likely to be modest. However, for diseases that have a direct impact on fitness, strongly deleterious rare mutations likely do play important roles, and the impact of very rare mutations will be far greater as a result of recent growth. In summary, demographic history has dramatically impacted patterns of variation in different human populations, but these changes have likely had little impact on either genetic load or on the importance of rare variants for most complex traits.

Link

Phylogeography of Bantu languages (Currie et al. 2013)

Proc. R. Soc. B 7 July 2013 vol. 280 no. 1762 20130695

Cultural phylogeography of the Bantu Languages of sub-Saharan Africa

Thomas E. Currie et al.

There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees of Bantu languages and map them onto geographical space in order to assess the likely pathway of expansion and test between dispersal scenarios. The results clearly support a scenario in which groups first moved south through the rainforest from a homeland somewhere near the Nigeria–Cameroon border. Emerging on the south side of the rainforest, one branch moved south and west. Another branch moved towards the Great Lakes, eventually giving rise to the monophyletic clade of East Bantu languages that inhabit East and Southeastern Africa. These phylogenies also reveal information about more general processes involved in the diversification of human populations into distinct ethnolinguistic groups. Our study reveals that Bantu languages show a latitudinal gradient in covering greater areas with increasing distance from the equator. Analyses suggest that this pattern reflects a true ecological relationship rather than merely being an artefact of shared history. The study shows how a phylogeographic approach can address questions relating to the specific histories of certain groups, as well as general cultural evolutionary processes.

Link

The Geography of Recent Genetic Ancestry across Europe (Ralph and Coop 2013)

This paper first came out last July on the arXiv and went through four versions there before its final form which has now appeared in PLoS Biology. It's great that its early release allowed other people to read it without having to wait for the completion of the peer review process.

I think that this is a good model: journals have the right and obligation to subject papers to close scrutiny according to their own procedures, but this process ought not interfere with the early availability of research results or the ability of anyone other than the chosen reviewers to comment on new results.

PLoS Biol 11(5): e1001555. doi:10.1371/journal.pbio.1001555

The Geography of Recent Genetic Ancestry across Europe

Peter Ralph, Graham Coop

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

Link

Deep common ancestry of Eurasiatic languages (Pagel et al. 2013)

From the paper:

Posterior support at internal nodes of the tree is low, as we might expect of a linguistic tree of this age, but all exceed chance expectations (SI Text) and the internal topology does not affect our estimates of the age of the superfamily. All inferred ages must be treated with caution but our estimates are consistent with proposals linking the near concomitant spread of the language families that comprise this group to the retreat of glaciers in Eurasia at the end of the last ice age ~15 kya (4, 17). The 95% CIs around the root-age are consistent with the initial separation of these families occurring before the development of agriculture beginning ~11 kya (26).

A few comments:

• The common ancestry of Inuit-Yupik with Chukchee-Kamchatkan lends some support to the idea of Old/New World contacts postdating the initial colonization of the Americas
• (Note that the superimposition of the tree on the map does not indicate migratory paths)
• The deep divergence of Proto-Dravidian from the rest of the tree raises the issue of the genetic identity of the Proto-Dravidians. Today, Dravidian speakers are concentrated on the southern parts of India -with the notable Brahui exception in Pakistan- so one is tempted to associate them with the long diverged "Ancestral South Indian" genetic component whose closest living relatives live in the Indian Ocean. On the other hand, hypothesized relationships between Dravidian and extra-Indian languages, such as those postulated here might suggest that Proto-Dravidian was spoken by people more closely related to other Eurasians.
• More generally, the hypothesis of post-glacial contacts between diverse parts of Eurasia might suggest that differentiation between Eurasian peoples did not proceed in isolation after the initial Out-of-Africa settlement. And, if there were indeed post-glacial movements, of people spreading "Proto-Eurasiatic" languages, these may be detectable by archaeogenetic means.

With the two earliest offshoots being Proto-Dravidian and Proto-Kartvelian, it would be tempting to seek some Central Asian proto-homeland for these languages; the remaining languages seem to occupy (mostly) areas that were substantially glaciated. There was of course large-scale language replacement during the Neolithic and even later time periods, so one can hypothesize that other extinct languages may also have belonged to this greater family, and it would be interesting to see if membership could be supported for any of them.

ScienceNOW has a fairly good high-level discussion. The paper is open access.

PNAS May 6, 2013, doi: 10.1073/pnas.1218726110

Ultraconserved words point to deep language ancestry across Eurasia

Mark Pagel et al.

The search for ever deeper relationships among the World’s languages is bedeviled by the fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 to 9,000 y. On the other hand, quantitative modeling indicates that some “ultraconserved” words exist that might be used to find evidence for deep linguistic relationships beyond that time barrier. Here we use a statistical model, which takes into account the frequency with which words are used in common everyday speech, to predict the existence of a set of such highly conserved words among seven language families of Eurasia postulated to form a linguistic superfamily that evolved from a common ancestor around 15,000 y ago. We derive a dated phylogenetic tree of this proposed superfamily with a time-depth of ∼14,450 y, implying that some frequently used words have been retained in related forms since the end of the last ice age. Words used more than once per 1,000 in everyday speech were 7- to 10-times more likely to show deep ancestry on this tree. Our results suggest a remarkable fidelity in the transmission of some words and give theoretical justification to the search for features of language that might be preserved across wide spans of time and geography.

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Small-bodied humans from the Terminal Pleistocene in Tanzania

East Africa is known for the tall and lean physiques of many of its current inhabitants, but there has been speculation -on linguistic or other grounds- that it was once home to people similar to the present-day Bushmen of southern Africa. A new publication on small-bodied humans from Tanzania may be related to this hypothesis.

From the paper:

New discoveries, such as B-1 from Mlambalasi, may renew discussion on the presence of small-bodied people in East Africa. Based on the few comparable skeletal samples, this individual does not conform to the typical tall, robust, and linear body proportions of previously reported East African LSA populations. Instead, itssmall body size has more in common with southern African peoples. This does not necessarily imply a biological link between these LSA populations. Hypotheses for why small size develops include the need for thermoregulation, limited food supply, enhanced mobility, and high mortality influencing early reproduction (Perry and Dominy, 2009; Pfeiffer and Harrington, 2011). In southern Africa, small body size may be linked to energetics and accident avoidance. The rate of injury among the South African LSA populations is lower than other mobile hunter-gatherer groups, which Pfeiffer (2007) interprets as possibly related to reduced body mass. Ethnographic studies of modern Khoesan emphasize the centrality of the bow and arrow and persistence hunting, in which small, energetically efficient bodies prove advantageous (Tobias, 1978). Small body size may have emerged multiple times, perhaps amidst the low population densities and climatic instability of the LSA. Given that early modern humans may have endured a population crisis (Harpending et al., 1993; Ambrose, 1998a; Lahr and Foley, 1998; Reich and Goldstein, 1998), and that there is some evidence for increased diversity among earlier populations (Crevecoeur et al., 2009), one characteristic of some terminal Pleistocene and early Holocene groups may have been a small body size. Exploring the incidence of scope of this pattern in East African and other early modern humans may shed light on the importance of body size in human evolution.

International Journal of Osteoarchaeology DOI: 10.1002/oa.2323

Terminal Pleistocene Later Stone Age Human Remains from the Mlambalasi Rock Shelter, Iringa Region, Southern Tanzania†

E. A. Sawchuk1, P. R. Willoughby

This paper introduces research at the Mlambalasi rock shelter in the Iringa Region of southern Tanzania. The deposits are composed of a historic and Iron Age occupation, a microlithic Holocene Later Stone Age (LSA), and then a macrolithic Late Pleistocene LSA. Middle Stone Age deposits are also present on the slope in front of the rock shelter. Excavations in A.D. 2002, 2006, and 2010 yielded fragmentary human remains as well as pottery, iron, stone tools, faunal bone, and glass and ostrich eggshell beads. Among the human remains, four individuals are present: two adults and a juvenile were found in the same LSA context, and another adult associated with the Iron Age/historic period. The most complete skeleton is an adult of indeterminate sex that was found in situ in an LSA deposit. Charcoal in proximity to the bone was AMS radiocarbon dated to 12,925 cal BC (OxA-24620), which is consistent with radiocarbon dates on giant land snail shells from above and below the remains. The skeleton exhibits a series of pathological changes such as extensive dental wear and carious lesions, as well as damage most likely caused by termites, post-mortem. The most striking aspect of this individual is its small size; stature and body mass estimations place it in the range of historic Khoesan from southern Africa. Consequently, this research adds to the discourse regarding the existence of small-bodied people in the East African LSA. Findings from this new skeletal sample will contribute to studies of human biology and variation in Africa during the terminal Pleistocene and Holocene. This article is protected by copyright. All rights reserved.

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