Connections between Indus Valley and Mesopotamia

Of interest from the paper:

Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). Most of these individuals have values below the Harappa range. In addition, there are at least three non-local individuals with higher values, including one with an extremely isotope ratio that cannot be from the Harappa region. A more detailed discussion of the Harappa samples will be presented in a future publication on the Harappa cemetery, but it is clear that many of what appear to be local individuals at Harappa are females and they are associated in burial with nearby males who are clearly not local. These preliminary patterns require further testing before major conclusions can be proposed, but it does suggest that they represent a unique population of people from multiple regions of the Indus valley or beyond.

Journal of Archaeological Science
Volume 40, Issue 5, May 2013, Pages 2286–2297

A new approach to tracking connections between the Indus Valley and Mesopotamia: initial results of strontium isotope analyses from Harappa and Ur

J. Mark Kenoyer et al.

Exchange and interaction between early state-level societies in Mesopotamia and the Indus Valley during the 3rd millennium BC has been documented for some time. The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. With the aid of strontium, carbon, and oxygen isotopes, it is now possible to develop more direct means for determining the presence of non-local people in both regions. This preliminary study of tooth enamel from individuals buried at Harappa and at the Royal Cemetery of Ur, indicates that it should be feasible to identify Harappans in Mesopotamia. It is also possible to examine the mobility of individuals from communities within the greater Indus Valley region.

Link

Y chromosomes of Corded Ware at Wroclaw-Jagodno (SW Poland)

From the paper:

Two teeth coming from fossil human skeletons were examined in the Molecular Technology Institute of Forensic Medicine Department, Wroclaw Medical University. It was stated that both teeth came from two men on the basis of the gene of amelogenin variants study. Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*.

Table 2:

It appears that dots represent identity with the reference sequence, so for example M201 has a dot for skeleton 1 which indicates a T at position 15,027,529 (GRCh37) which is the position where this mutation has occurred. So, the attribution of skeleton 1 to haplogroup G seems reasonable, and suggests continuity between the Neolithic population of Europe (where G is over-represented) and this CW individual.

It's not clear to me how skeleton 2 is attributed to J or I or E* on the basis of these SNPs. If anyone can figure it out, post in the comments.

Journal of Archaeological Science doi:10.1016/j.jas.2013.02.002

Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers

Bohdan Gworys et al.

So-called physiological stress markers are extremely valuable in assessing life conditions of old human populations. They constitute effects of adverse environmental conditions, which leave traces on skeleton. Those traces allow for partial assessment of life conditions not only in environmental and social but also cultural aspects for prehistoric populations. The aim of this study is to estimate the influence of general environmental conditions on human organism at the final stage of the Neolithic period – in the Corded Ware culture. Two skeletons discovered in a tumulus on the outskirts of Wroclaw in the Jagodno district have been subjected to assessment. Their age at the moment of death has been determined in both cases on the basis of multi-feature analysis of changes occurring in formation of particular morphologic features of skeleton and teeth. Attention has been paid to the obliteration degree of skull sutures and the surface state of chewing tooth crowns. A comprehensive DNA analysis has been conducted determining sex of the remains. Also bacteriological analysis of the research material has been conducted. Measurements of all available metric features of the skeletons have been performed with the use of the Martin method. Inventory and basic description of the finds accompanying skeleton remains have been carried out as well. Intensity of the following physiological stress markers have been defined and evaluated: Harris lines; cribra orbitalia; cribra cranii. Skull morphology, degree of suture obliteration, surface state of chewing tooth crowns and estimation of degree of bone development of postcranial skeleton indicate that both skeletons detailed age was about 16 – 18 years. Harris lines on the femur were formed in the 2nd and the 3rd year of life and on both tibias – in the 2nd year of life. Obtained results indicate that those people were expose to stress connected with food deficit when they were very young. Poor porotic changes on the skull and isotopic data suggest that their life quality increased at later age.

Link

Stable isotopes and Nubian/Egyptian relationships

Wikipedia on Tombos site:

Tombos in an archaeological site in Northern Sudan. The village of Tombos was located at the third cataract of the Nile, not far from Kerma near the present Karmah. An important granite quarry was located here in the Pharaonic era. Its stone was used mostly to build statues and buildings between the river delta and the southern regions of the kingdom. A statue to the Pharaoh Taharqa, abandoned for over 2700 years, contains inscriptions. About 3000 years ago, there were pyramids dedicated to ten noble Egyptians. 

In 2000, several discoveries were made by the archaeologist, Professor Stuart Tyson Smith of the University of California, Santa Barbara. Smith and his team discovered the remains of a pyramid more than 3,500 years old, and the buried remains of an Egyptian colonial administrator named Siamun and his wife, Wernu. The two mummies were intact, and were buried with Ushabti figurines, a boomerang, and painted Mycenaean terracotta.[1] The burial chamber includes a series of rooms, some plundered by thieves, while others were undisturbed in whole or in part. Also, an epigraphic survey by the British Museum uncovered pharaonic rock-inscriptions.[2]

Might be interesting to look at DNA from remains from the Tombos site, both the ones mentioned in Wikipedia and the likely Egyptian immigrants mentioned in the following article.


Am J Phys Anthropol DOI: 10.1002/ajpa.22235

Strontium isotope (87Sr/86Sr) variability in the Nile Valley: Identifying residential mobility during ancient Egyptian and Nubian sociopolitical changes in the New Kingdom and Napatan periods

Michele R. Buzon, Antonio Simonetti

As a successful technique for identifying residential mobility in other areas, this study investigates the feasibility of using 87Sr/86Sr analysis to track the movements of the ancient peoples of Egypt and Nubia in the Nile Valley, who interacted via trade, warfare, and political occupations over millennia. Dental enamel from faunal remains is used to examine variability in strontium sources in seven regional sites; human enamel samples are analyzed from eight Nile Valley sites in order to trace human movements. The faunal samples show a wide range of 87Sr/86Sr values demonstrating that some animals were raised in a variety of locales. The results of the human samples reveal overlap in 87Sr/86Sr values between Egyptian and Nubian sites; however, Egyptian 87Sr/86Sr values (mean/median [0.70777], sd [0.00027]) are statistically higher than the Nubian 87Sr/86Sr values (mean [0.70762], median [0.70757], sd [0.00036], suggesting that it is possible to identify if immigrant Egyptians were present at Nubian sites. Samples examined from the site of Tombos provide important information regarding the sociopolitical activities during the New Kingdom and Napatan periods. Based on a newly established local 87Sr/86Sr range, human values, and bioarchaeological evidence, this study confirms the preliminary idea that immigrants, likely from Egypt, were present during the Egyptian New Kingdom occupation of Nubia. In the subsequent Napatan period when Nubia ruled Egypt as the 25th Dynasty, 87Sr/86Sr values are statistically different from the New Kingdom component and indicate that only locals were present at Tombos during this developmental time. 

Link

mtDNA of Yumans and Athapaskans

Am J Phys Anthropol DOI: 10.1002/ajpa.22237

Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans

Cara Monroe et al.

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai.

Link

ADMIXTOOLS 1.1 released

A new 1.1 version of ADMIXTOOLS has been released. From the description:

ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. It can be downloaded for LINUX (see documentation). The software package also includes Affymetrix Human Origins Curated Dataset. Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson. The new release fixes a serious bug in qpDstat. 

I've used this software before and posted some D-statistics from it on the blog, so if you find any that look strange, feel free to leave a comment. In any case, I'll be using the new version of qpDstat from now on.

UPDATE (Feb 22): Nick Patterson asked me to post the following for users of ADMIXTOOLS:

Choongwon Jeong of the University of Chicago found a serious bug in qpDstat (computes D-statistics) that sometimes returns D with an incorrect sign.  If you use the program please download ADMIXTOOLS version 1.1 from  the Reich lab web page.  http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

Indo-Europeans galore

A whole bunch of papers in a journal I hadn't heard of before, but written by some of the best known people in this field. I see lots of "Buy pdf" links to accompany them, so if you want to spare me the expense, feel free to e-mail me a copy.

Anyway, here's a list of titles for reference:


Anthony, David Two IE phylogenies, three PIE migrations, and four kinds of steppe - p. 1-21
Balanovsky, Oleg; Utevska, Olga; Balanovska, Elena Genetics of Indo-European populations: the past, the future - p. 23-35
Blazek, Vaclav Indo-European zoonyms in Afroasiatic perspective - p. 37-54
Burlak, Svetlana Languages, DNA, relationship and contacts - p. 55-67
Dybo, Anna Language and archeology: some methodological problems. 1. Indo-European and Altaic landscapes - p. 69-92
Dybo, Vladimir Dialectal variation of Proto-Indo-European in the light of accentological research - p. 93-108
Gamkrelidze, Tamaz; Ivanov, Vyacheslav Indo-European homeland and migrations: half a century of studies and discussions - p. 109-136
Kullanda, Sergey Early Indo-European social organization and the Indo-European homeland - p. 137-144
Mallory, J.P. Twenty-first century clouds over Indo-European homelands - p. 145-154
Kornienko, Tatiana 'Archaeological Research in Northern Mesopotamia and North Caucasus' [Chronicle] - p. 155-162
Korovina, Eugenia 'Problems of the Indo-European Homeland' [Chronicle] - p. 163-166

UPDATE: Someone sent me the Anthony paper. Here is the main figure which suggests a correspondence between the linguistic phylogeny of Ringe et al. and the archaeological reconstruction of out-of-steppe movements of its author:

One of the weakest points of the steppe model is its treatment of Anatolians. Movement marked #1 perhaps takes some populations in an indistinct way into the east Balkans, but does not take them all the way to Anatolia.

The steppe model must propose some kind of early round-the-Black Sea mechanism to bring the Anatolians to their historical seats. This is not trivial; it might seem like a small jump from Thrace (where the endpoint of the first migration, marked with 1 is placed) to Anatolia, but it is in fact in the southern parts of the peninsula that we first find the Anatolian speakers. And, Anatolian place names are also recorded in Greece and its immediate environs, and not at all in the proposed migration route. Thus, the arrow must take the Anatolians further west (to account for the evidence from the Aegean, and then bring them south and east). I don't find this very plausible.

Algerian Y chromosomes and mtDNA

From the paper:

For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean

It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

• The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
• I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
• The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
• The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
• The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Link

Early modern human burials in Eurasia

Early human burials varied widely but most were simple

"We don't know why some of these burials were so ornate, but what's striking is that they postdate the arrival of modern humans in Eurasia by almost 10,000 years," said Julien Riel-Salvatore, Ph.D., assistant professor of anthropology at CU Denver and lead author of the study. "When they appear around 30,000 years ago some are lavish but many aren't and over time the most elaborate ones almost disappear. So, the behavior of humans does not always go from simple to complex; it often waxes and wanes in terms of its complexity depending on the conditions people live under."

The study, which examined 85 burials from the Upper Paleolithic period, found that men were buried more often than women. Infants were buried only sporadically, if at all in later periods, a difference that could be related to changes in subsistence, climate and the ability to keep babies alive, Riel-Salvatore said.

It also showed that a few ornate burials in Russia, Italy and the Czech Republic dating back nearly 30,000 years are anomalies, and not representative of most early Homo sapiens burial practices in Eurasia.

Admixed populations in neighbor-joining trees

Pac Symp Biocomput. 2013:273-84.

The behavior of admixed populations in neighbor-joining inference of population trees.

Kopelman NM, Stone L, Gascuel O, Rosenberg NA.

Abstract

Neighbor-joining is one of the most widely used methods for constructing evolutionary trees. This approach from phylogenetics is often employed in population genetics, where distance matrices obtained from allele frequencies are used to produce a representation of population relationships in the form of a tree. In phylogenetics, the utility of neighbor-joining derives partly from a result that for a class of distance matrices including those that are additive or tree-like-generated by summing weights over the edges connecting pairs of taxa in a tree to obtain pairwise distances-application of neighbor-joining recovers exactly the underlying tree. For populations within a species, however, migration and admixture can produce distance matrices that reflect more complex processes than those obtained from the bifurcating trees typical in the multispecies context. Admixed populations-populations descended from recent mixture of groups that have long been separated-have been observed to be located centrally in inferred neighbor-joining trees, with short external branches incident to the path connecting their source populations. Here, using a simple model, we explore mathematically the behavior of an admixed population under neighbor-joining. We show that with an additive distance matrix, a population admixed among two source populations necessarily lies on the path between the sources. Relaxing the additivity requirement, we examine the smallest nontrivial case-four populations, one of which is admixed between two of the other three-showing that the two source populations never merge with each other before one of them merges with the admixed population. Furthermore, the distance on the constructed tree between the admixed population and either source population is always smaller than the distance between the source populations, and the external branch for the admixed population is always incident to the path connecting the sources. We define three properties that hold for four taxa and that we hypothesize are satisfied under more general conditions: antecedence of clustering, intermediacy of distances, and intermediacy of path lengths. Our findings can inform interpretations of neighbor-joining trees with admixed groups, and they provide an explanation for patterns observed in trees of human populations.

Link

AAPA 2013 abstracts

The program of the 2013 meeting of the American Association of Physical Anthropologists is now online (pdf). As always, there is plenty of interest here, so I'll just highlight a few titles that caught my eye; feel free to add more in the comments.


Neolithic human mitochondrial haplogroup H genomes and the genetic origins of Europeans.

Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less prevalent amongst early Neolithic farmers (~19%) and virtually absent in Mesolithic hunter-gatherers. To investigate this haplogroup’s significance in the maternal population history of Europeans we employed novel techniques such as DNA immortalization and hybridization-enrichment to sequence 39 hg H mt genomes from ancient human remains across a transect through time in Neolithic Central Europe. The results of our population genetic analyses reveal that the current patterns of diversity and distribution of hg H were largely established during the Mid-Neolithic, but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers, which expanded out of Iberia in the Late Neolithic (~2800 BC). Using a strict diachronic approach allowed us to reconcile ‘real-time’ genetic data from the most common European mtDNA hg with cultural changes that took place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. This revealed the Late Neolithic (2800-2200 BC) as a dynamic period that profoundly shaped the genetic landscape of modern-day Europeans. Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.

Preliminary research on hereditary features of Yinxu Population.

... The 37 individuals sampled in this study have been discovered in middle to small size burials, and therefore constitute a representative sample to study Yinxu commoners’ society. Mitochondrial DNA analysis showed that the Yinxu population included the haplogroups D, G, A, C, Z, M10, M*, B, F and N9a. According to the analysis of molecular variance, the distribution frequency and the rare published data, the Yinxu population shows a closest genetic affinity with the populations of Dadianzi and Zhukaigou early Bronze Age sites (Inner Mongolia), but a more distant relation to the historical period populations. The Yinxu population is also very similar to the modern northern Han Chinese. ... 

Investigating lactase persistence in a Medieval German cemetery: A step towards understanding the rise of the European lactase persistence polymorphism (-3910C/T).

Previous ancient DNA-based studies on the Neolithic found that the incidence of LP falls below detection levels in most regions. Our research shows that between the Neolithic and Medieval periods, the frequency of LP rose from near 0% to over 50%. Also, given that the frequency of LP genotypes in modern-day Germany is estimated at 78.5%, our results indicate that rather than being stable by the Medieval period, the lactase persistent genotype has continued to increase in frequency over the last 1000 years. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistent trait and its global cultural implications.

 New Neanderthal remains from Kalamakia cave, Mani peninsula, Southern Greece.

Peeling back the layers: additional evidence for the date of the Petralona skull (Homo heidelbergensis), Greece.

,.. We conclude that there is no white sinter deposited directly on the skull and therefore the initial date of the skull given by Henning et al. and Grun’s revised date of ca. 200 ka are correct.

Analysis of archaic introgression in Ötzi the Tyrolean Iceman, a 5300 year-old prehistoric modern human.

... We carried out a series of comparisons to address these questions. By examining the Neandertal similarity of individuals from the 1000 Genomes Project, we have substantially expanded the sample of Neandertal-human comparisons. We also examined the genome of the Tyrolean Iceman, a European from approximately 5300 years ago. This is the first comparison of Neandertal genomes to the genome of a prehistoric modern human individual.

A quantitative approach for late Pleistocene hominin brain size.

... The results of our study show that Neanderthals have smaller brains than the Pleistocene AMH despite the fact that the latter are smaller in body mass. However, the Holocene AMH (7 populations) have smaller brain sizes than those of Neanderthals. ...

Re-evaluating the functional and adaptive significance of Neandertal nasofacial anatomy.

... Among Middle and Late Pleistocene Homo, there is evidence that nasal morphology varies with climate, albeit within an archaic architectural nasofacial framework. Neandertal internal nasal dimensions are greater in both height and length than archaic humans from sub-Saharan Africa. Furthermore, while other aspects of the nose are relatively broad, superior internal breadth dimensions in Neandertals are narrowed relative to sub-Saharan archaics. These differences parallel those seen in modern humans, indicating that Neandertals had an increased capacity for nasal heat and moisture exchange over their African counterparts and thus exhibit clear evidence for cold-climate adaptation. 

Estimating the date of composition of the Homeric epics

This might be an interesting way of dating literary works for which there are no/conflicting traditions about their date of composition.

Bioessays DOI: 10.1002/bies.201200165

Linguistic evidence supports date for Homeric epics

Eric Lewin Altschuler et al.

The Homeric epics are among the greatest masterpieces of literature, but when they were produced is not known with certainty. Here we apply evolutionary-linguistic phylogenetic statistical methods to differences in Homeric, Modern Greek and ancient Hittite vocabulary items to estimate a date of approximately 710–760 BCE for these great works. Our analysis compared a common set of vocabulary items among the three pairs of languages, recording for each item whether the words in the two languages were cognate – derived from a shared ancestral word – or not. We then used a likelihood-based Markov chain Monte Carlo procedure to estimate the most probable times in years separating these languages given the percentage of words they shared, combined with knowledge of the rates at which different words change. Our date for the epics is in close agreement with historians' and classicists' beliefs derived from historical and archaeological sources.

Link

Ancient mtDNA and gene flow from Siberia to NE Europe

I had mentioned the thesis by the lead author, and now a paper from it has been published. If anyone notices any new material in the new paper, feel free to highlight it in the comments.

PLoS Genet 9(2): e1003296. doi:10.1371/journal.pgen.1003296

Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

Clio Der Sarkissian et al.

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.

Link

Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans (Wall et al. 2013)

The title seems to say it all; such a conclusion was also arrived at by Meyer et al. (high coverage Denisova paper). However, the extent of this ancestry appears to be differently estimated in the new paper:

By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.

Of course, the interesting question is why East Asians have this excess of Neandertal ancestry, given that Neandertals were a west Eurasian-distributed species (for the most part). Similarly, we would not have expected Australo-Melanesians to possess higher Denisovan admixture, and yet they do. Some models of multiregional evolution assumed regional continuity with pre-existing archaic populations in different parts of the world (e.g., Europeans with Neandertals), but clearly much more interesting things were taking place in deep prehistory.

Of particular interest is this conclusion:

In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

The publication of Tianyuan has shown that by ~40kya, differentiation of Asians from Europeans was already on its way, and this is a date close to the disappearance of the Neandertals, the date of which is contested, but one can imagine that already-differentiated Eurasians may have encountered some lingering Neandertal groups.

Genetics doi: 10.1534/genetics.112.148213

Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans

Jeffrey D. Wall et al.

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

Link

Whole genome Y-SNP calling

BMC Genomics 2013, 14:101 doi:10.1186/1471-2164-14-101

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Anneleen Van Geystelen et al.

Abstract (provisional)

Background

Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.

Results

We present an automated approach, 'AMY-tree', which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.

Conclusions

Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.

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Southeast Asian Neolithic dogs

From the paper:

Nevertheless, the close phylogenetic clustering of haplotypes from Thailand, Brunei, Bali, and the Philippines suggests these populations originated from the same source, consistent with a single migration event, whereas the dingoes, NGSDs, and dogs from Taiwan appear sufficiently distinct from these to reflect a distinct migration event (Fig. 2b-c). The clustering of the three Island Southeast Asian populations with Thailand also was more consistent with origination from Mainland Southeast Asia than Taiwan (in agreement with mtDNA findings of Oskarsson et al. 2011).

and:

In light of findings from the present study, it seems clear that both post-Victorian and Neolithic exchanges link eastern and western Eurasian dogs. However, the cause of post-Victorian haplotype sharing between Western breed dogs and Southeast Asian village dogs apparently reflects very recent introduction of Western dogs to the East rather than extraction of Eastern dogs to create Western breeds during the Victorian Era.

and:

Specifically, our aging of this European haplogroup to 5,800 (±SE = 1750) or 8,400 (±SE = 2500) years (depending on the dingo calibration to 3,500 or 5,000 years, respectively) suggests that the connection between pre-Victorian European and Southeast Asian dogs traces only to the Neolithic period and is not of sufficient antiquity to support the hypothesis of a single origin of dogs from Southeast Asia. Thus, although future studies are needed to combine the Y SNPs and STR markers in a geographically broader sampling of dogs than was considered here, our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Paleolithic origin of dogs from this region.

This massive Neolithic expansion of Southeast Asian dogs is testable by looking at early European dogs; these ought not to belong to haplogroup H1. It would also be interesting to speculate about the trade routes and/or population movements that facilitated the spread of dogs from SE Asia to Europe during the Neolithic.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst027

Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals

Benjamin N. Sacks et al.

Dogs originated >14,000 BP, but the location(s) where they first arose is uncertain. The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 SNPs and 5 STRs, from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

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Automated reconstruction of proto-languages

PNAS doi: 10.1073/pnas.1204678110

Automated reconstruction of ancient languages using probabilistic models of sound change

Alexandre Bouchard-Côté et al.

One of the oldest problems in linguistics is reconstructing the words that appeared in the protolanguages from which modern languages evolved. Identifying the forms of these ancient languages makes it possible to evaluate proposals about the nature of language change and to draw inferences about human history. Protolanguages are typically reconstructed using a painstaking manual process known as the comparative method. We present a family of probabilistic models of sound change as well as algorithms for performing inference in these models. The resulting system automatically and accurately reconstructs protolanguages from modern languages. We apply this system to 637 Austronesian languages, providing an accurate, large-scale automatic reconstruction of a set of protolanguages. Over 85% of the system’s reconstructions are within one character of the manual reconstruction provided by a linguist specializing in Austronesian languages. Being able to automatically reconstruct large numbers of languages provides a useful way to quantitatively explore hypotheses about the factors determining which sounds in a language are likely to change over time. We demonstrate this by showing that the reconstructed Austronesian protolanguages provide compelling support for a hypothesis about the relationship between the function of a sound and its probability of changing that was first proposed in 1955.

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