mtDNA of Alaskan Eskimos

AJPA DOI: 10.1002/ajpa.22750

Mitochondrial diversity of Iñupiat people from the Alaskan North Slope provides evidence for the origins of the Paleo- and Neo-Eskimo peoples 

Jennifer A. Raff et al.

ABSTRACT

Objectives:

All modern Iñupiaq speakers share a common origin, the result of a recent (∼800 YBP) and rapid trans-Arctic migration by the Neo-Eskimo Thule, who replaced the previous Paleo-Eskimo inhabitants of the region. Reduced mitochondrial haplogroup diversity in the eastern Arctic supports the archaeological hypothesis that the migration occurred in an eastward direction. We tested the hypothesis that the Alaskan North Slope served as the origin of the Neo- and Paleo-Eskimo populations further east.

Materials and Methods:

We sequenced HVR I and HVR II of the mitochondrial D-loop from 151 individuals in eight Alaska North Slope communities, and compared genetic diversity and phylogenetic relationships between the North Slope Inupiat and other Arctic populations from Siberia, the Aleutian Islands, Canada, and Greenland.

Results:

Mitochondrial lineages from the North Slope villages had a low frequency (2%) of non-Arctic maternal admixture, and all haplogroups (A2, A2a, A2b, D2a, and D4b1a–formerly known as D3) found in previously sequenced Neo- and Paleo-Eskimos and living Inuit and Eskimo peoples from across the North American Arctic. Lineages basal for each haplogroup were present in the North Slope. We also found the first occurrence of two haplogroups in contemporary North American Arctic populations: D2a, previously identified only in Aleuts and Paleo-Eskimos, and the pan-American C4.

Discussion:

Our results yield insight into the maternal population history of the Alaskan North Slope and support the hypothesis that this region served as an ancestral pool for eastward movements to Canada and Greenland, for both the Paleo-Eskimo and Neo-Eskimo populations

Link

The prehistory of New World Arctic (Raghavan et al. 2014)

Science 29 August 2014: Vol. 345 no. 6200 DOI: 10.1126/science.1255832

The genetic prehistory of the New World Arctic

Maanasa Raghavan et al.

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.

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.

Link

Reconstructing the origin of Native American populations

A new paper by Reich et al., which echoes the title of a previous one by many of the same authors on India looks at the issue of Native American origins. Nicholas Wade has some good coverage of the new research at the NY Times:

North and South America were first populated by three waves of migrants from Siberia rather than just a single migration, say researchers who have studied the whole genomes of Native Americans in South America and Canada.

I have an informed hunch that this will not be the last paper in the Reconstructing... series.

The supplementary material (pdf) is open access, and lists the data used, some of which has been taken from the literature and some of which is new. There is apparently also a new ADMIXTUREGRAPH software used in a paper which seems to parallel a little the functionality of TreeMix. I don't see a download option for this software yet; perhaps Joe Pickrell who co-authored TreeMix and is now in Harvard may chime in about the differences/applicability of the two pieces of code.

UPDATE: And here is the press release:

Two striking exceptions to this simple dispersal were also discovered. First, Central American Chibchan-speakers have ancestry from both North and South America, reflecting back-migration from South America and mixture of two widely separated strands of Native ancestry. Second, the Naukan and coastal Chukchi from north-eastern Siberia carry 'First American' DNA. Thus, Eskimo-Aleut speakers migrated back to Asia, bringing Native American genes.

Interestingly, I have detected some of this "Native American" component in the Chukchi as part of my world9 calculator.

UPDATE II: Of course, if you look at the map of the sampled populations, you'll notice one big hole: the USA. Petty identity politics contra science? Data on Native groups outside the US have been studied for years, and I doubt that the sky will fall over the heads of the new Canadian and South American groups that participated in this particular study. Hopefully, one day the big hole will be filled, although I'm not holding my breath of that happening anytime soon.

Nature (2012) doi:10.1038/nature11258

Reconstructing Native American population history

David Reich et al.

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1, 2, 3, 4, 5. One contentious issue is whether the settlement occurred by means of a single6, 7, 8 migration or multiple streams of migration from Siberia9, 10, 11, 12, 13, 14, 15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call ‘First American’. However, speakers of Eskimo–Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Link

ADMIXTURE in Siberia, Greenland, and Alaska

I have discovered a great dataset from Rasmussen et al. (2010). The data had been used before in conjunction with an ancient DNA sequence, but for me it is invaluable, as it fills up one of the major holes in Eurasia, namely Siberia, and includes a number of Altaic, Uralic, and other North Eurasian people. I suspect that this will be invaluable in fine-tuning the Northeast Asian ancestry of Dodecad Project members.

To begin with, after I processed the data, I ran ADMIXTURE on it up to K=7. Below you can see the results for K=7:

I'm no expert in linguistics, but it's clear to me that the light blue component corresponds to Altaic speakers. It will be extremely interesting to see what the analysis including other Altaic speakers from my other datasets as well as West Eurasians of Uralic/Altaic language or with "Northeast Asian" admixture will show.

The table below has sample sizes and admixture proportions.

Stay tuned. More to come.

ISBA4 abstracts

Here are some interesting abstracts from the recent 4th International Symposium on Biomolecular Archaeology.

Naglaa Abu-Mandil1 & Terry Brown

Kinship analysis and sex identification of skeletons from two archaeological sites in Greece

Ancient DNA offers unprecedented opportunities for anthropologists and bioarchaeologists to assess the biological relationships of ancient populations. This study is designed to assess the family relationship among skeletons from two different archaeological sites in Greece which can help in shedding light on the ritual practice in Aegean prehistory. Another aim is to identify the sex of these skeletons genetically to confirm the conventional sexing methods. These sites are called Kouphovouno and Bostani. Kouphovouno is an important Neolithic and Bronze Age archaeological site near Sparta in Lakonia, while Bostani is dated back to the Early Helladic period in Ancient Greek history. In both cases the sites are recently excavated and DNA samples from all people who have handled the skeletons are available. Both mtDNA and nuclear DNA markers are being studied in order to identify maternal relationships and to reveal the sex of the skeletons.

Morten Rasmussen et al.
The nuclear genome of an ancient human

We have sequenced the complete genome from an ancient human. It was obtained from 4,000-year-old permafrost-preserved hair; the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20, we recover 79% of the diploid genome, and identify 353,151 highconfidence single-nucleotide polymorphisms (SNPs). Comparisons with SNP data from contemporary populations allow us to explore the migrations and kinship of this extinct culture. Analyses provide evidence of a migration from Siberia into the New World, independent of that giving rise to the modern Native Americans and Inuit. The migration was dated to approximately 5,500 years BP and the closest living relatives are found in North-East Siberia showing no signs of admixture with modern Native Americans or Inuit. We use functional SNP assessment to assign possible phenotypic characteristics of the individual.

This is extremely exciting as it speaks of Y-chromosome results from Central European Neolithic sites, which is a first. It seems to me that migrationism is due for a big comeback. If anyone has attended the symposium and/or has more information on this feel free to leave a comment/send me an e-mail.

Wolfgang Haak et al.
Ancient DNA from Early Neolithic Farmers suggests a major genetic input from the Near East

The Neolithic transition (approx. 8000-4000 BC) is considered one of the most important demographic events in Europe’s past since the initial peopling of anatomically modern humans in the Upper Paleolithic (40,000 BC). Whether this transition has been cultural or driven by large-scale population movements is subject of a long-standing scientific debate in archaeology, anthropology and human population genetics. So far, inferences about the genetic make-up of past populations have been drawn from studies of modern-day Eurasian populations, but ancient DNA studies now provide direct snapshots of specific time frames in the past.

We present new mitochondrial and Y-chromosomal data from Neolithic individualsfrom a Central European early farming site, Derenburg (Germany), which significantly extends the genetic dataset of the Linearbandkeramik (LBK; n=42), and provides the first detailed genetic picture of the earliest Neolithic culture in Central Europe (5500-5000 cal BC). Comprehensive population-genetic analyses utilizing a large database of modern-day Western Eurasian populations (n=23,394) reveal unique genetic features of the LBK population and a clearly distinct mitochondrial haplogroup frequency distribution. Importantly however, the LBK population shows an affinity to populations in the modern-day Near East, suggesting a major genetic input from this region at the time of the advent of farming in Europe.

I wish we knew what the haplogroups of the unambiguously defined samples were...

Silja Dillenberger et al.
Parallel tagged amplicon sequencing of highly degraded Ychromosomal DNA from archaeological skeletons

The intent of the study was to develop a Y-SNP multiplex-PCR suitable for genetic analysis of ancient human remains. Therefore 37 SNPs characterizing Eurasian
haplogroups, with a focus on Europe and Central Asia, were selected in order to get a
high phylogeographic resolution. The 37 SNPs, using amplicon lengths between 64 and 107bp, were co-amplified within 2 multiplex PCRs followed by parallel tagged sequencing on the 454 platform. After testing on 3 recent male and 2 recent female individuals it was applied to 8 male prehistoric samples from Central Asia and Europe. One sample was too poorly preserved for haplogroup identification. Another individual could be narrowed down to Q or R*. The haplogroups of the remaining 6 samples could unambiguously be defined. This shows that this approach is adequate for Y-chromosomal typing of highly degraded ancient human remains.

Five years ago I estimated an 11% contribution of Central Asian Turks to modern Anatolians, which seems quite inline with the following estimate. I will simply note that the number of 1.5 million is probably inflated, as the invaders did not have the same reproductive success as the local population; this means that the "original Turks" were fewer than 11%. Moreover, not all of the Anatolian population of the 11th century became present-day Anatolians; the current Muslims of Anatolia are a part of the 11th century population mixed with the invaders, and hence the number of invaders must've been even smaller.

Inci Togan et al.
An Anatolian Trilogy: Arrival of nomadic Turks with their sheep and shepherd dogs

Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, pastoral nomadic group from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. Central Asian genetic contribution to Anatolia with respect to the Balkans was estimated as 13% by an admixture analysis implemented in LEA. This estimate was obtained by employing nuclear genetic markers. MtDNA and Y-chromosome estimates confirmed this admixture proportion. Based on the population size estimation for Anatolia in 12th century, it can be calculated that at least 1.5 million nomads might have arrived to Anatolia. History tells us that they have arrived to Central and Eastern Anatolia first and only 150 years later they invaded Western Anatolia. Distributions of genetic diversity of domestic sheep and shepherd dogs in Turkey support that as well the language spoken in Anatolia these nomads have changed the genetic landscape of these two domestic species within Turkey. These observations have implications on conservation strategies of domestic sheep in Anatolia which is known to be the cradle of sheep domestication. Results must be confirmed by ancient DNA studies.

Alicia K Wilbur et al.
Ancient tuberculosis before and after the Age of Exploration

The Age of Exploration resulted in contact between human populations that were previously isolated from each other, initiating exchange of ideas, cultigens, and diseases. The modern biogeography of tuberculosis (TB) strains appears to reflect this with, for example, the presence of European type strains in the Americas and elsewhere. Until recently, it was thought that TB originated in the Old World in the last 10,000 years and the presence of TB in the Americas prior to contact was debated. Current estimates of TB’s origins, however, range from 3-6 million years ago. In our research, we attempt to characterize ancient mycobacterial strains from cases of disseminated bone TB in order to understand the phylogenetic relationships between strains of tuberculosis prior to and after the Age of Exploration. DNA was extracted from over 115 samples exhibiting classic tuberculosis lesions obtained from both the New and Old Worlds and ranging in age from 5800 BCE to A.D. 1800. Then, four quantitative PCR assays were used to gauge the preservation of host and pathogen DNA. Human nuclear and mitochondrial, and mycobacterial repetitive (IS6110) and single copy (rpoB) loci were analyzed. These results show that while approximately one third of the samples contain human nuclear and/or mitochondrial DNA, only 10% were positive for mycobacterial DNA. Mycobacterial DNA was usually recovered in the presence of human DNA (75%). In addition, our results suggest that TB strains in the Americas dating prior to European contact did not contain the IS6110 repeat element. From the samples that tested positive for host and mycobacterial DNA, we first selected two from Peru and one from Canada, for subsequent analyses using highthroughput pyrosequencing. Our analyses indicate that both slow-growing (pathogenic) and fast-growing (environmental) species of mycobacteria are present in the samples. However, our analyses also indicate that new methods for targeting specific sequences of interest are necessary to obtain sufficient genome coverage for evolutionary analyses. We will discuss ways of doing this and our current progress in this effort.

The New Scientist reports that the following study discovered a couple of Africans were present in the crew of Columbus.

Vera Tiesler et al.
Age at death, biological ancestry and provenience of Christopher Columbus’ crew at La Isabela, Santo Domingo, (1493-1498). Histological and biomolecular approaches

The site of La Isabela, in the Dominican Republic, was the first colonial town in the Americas. It was settled by Christopher Columbus and his crew at the beginning of AD 1494, and initially housed some 1,500 individuals from a wide array of social, economic and probably ethnic backgrounds. Its graveyard quickly accumulated the mortal remains of those who succumbed to the harsh conditions of the Atlantic crossing and life in the colony. In this study we present the preliminary results of a series of histological and molecular (isotopic and DNA) studies that expand on the macroscopic skeletal information in combination with detailed historical records on the lives of the deceased. Considered jointly, the data sets provide deepened insights into age at death, disease, nutrition, biological ancestry and geographic origins of 49 individuals unearthed between 1983 and 1991 and currently stored at the Museo del Hombre Dominicano in Santo Domingo, Dominican Republic. The analyses were largely funded by the Universidad Autónoma de Yucatan, Merida, Mexico, and National Geographic Society, Washington D.C., US, and received logistical support form the Museo del Hombre Dominicano, Dominican Republic.

Tracey Pierre et al.
American Southwest prehistory through ancient DNA

The American Southwest is one of the best archaeologically known areas of the world. It is also one of the most ethnically and linguistically diverse regions inhabited by contemporary Native American groups in North America. To what extent are the early and late prehistoric Southwest occupants associated with the Mesa Verde, Chaco Canyon, Mimbres and Basketmaker cultures related to today’s Athapaskan, Puebloan and Uto-Aztecan speakers? Is there genetic evidence for an earlier migration into the Southwest by populations ancestral to today’s Southern Athapaskans? Can the spread of farming into the Southwest region by Uto-Aztecan speakers from Mexico be detected in the gene pools of these earlier cultures? How are the former occupants of Chaco Canyon related to other prehistoric and modern inhabitants of this region? Does the current regional diversity reflect the geographical distribution of Southwest cultures prior to European contact? Previous ancient DNA research from the greater Southwest has demonstrated both regional continuity and discontinuity through the study of short-read mtDNA sequences. With the advent of second generation sequencing technology it is now possible to address in finer resolution these microcontinental migrations questions associated with the spread of language families into the American Southwest.

I don't want to comment too much on the following abstract, but I'm always favorably inclined to the prosaic rather than the ornate interpretations of ancient artifacts, unless there is clear evidence to the contrary.

Lucija Šoberl et al.
On the Beaker trail: Investigating the function of British Beakers through organic residue analysis

Beaker pottery is traditionally regarded as a material symbol of social, material and ideological changes that began in the latest Neolithic – these included the appearance of new ceramic technologies, modes of dress and adornment, the introduction of metallurgy and single burial. As far as the pottery goes, meticulous and numerous typological schemes have been produced in the past, but the function of Beakers has never been established on a larger scale from a scientific point of view.

British Beakers are most commonly found with inhumation burials, laid in pits or cists, and often in association with other objects. It has often been supposed that Beakers were produced specifically for grave deposition, since they differ in terms of fabric quality and decoration from those produced for non-funerary use. Due to their elaborate decoration and innovative fine fabric, Beakers have been considered as prestige items. As a consequence of Sherratt’s interpretation of Beakers as drinking cups, used to consume alcoholic beverages or narcotic substances at ritual gatherings, these vessels have gained almost a legendary status as prestige drinking equipment that has not been scientifically contested. The porous fabric of prehistoric pottery has been known to represent a favourable environment for the long term preservation of organic molecules, such as lipids. Beaker potsherds from funerary and non-funerary contexts have been analysed using solvent extraction, followed by gas chromatography, mass spectrometry and isotope ratio mass spectrometry to provide structure identification, biomolecular fingerprints and compound specific δ13C values.

Through analyses of absorbed lipids we can directly address the function and contents of ceramic vessels. Here we present preliminary results of our research project aimed at addressing the function of Beaker pottery through organic residue analyses. Surprisingly, no support is found for the interpretation of Beakers as vessels used in alcohol consumption, and their very status as prestige items might even be questioned.

Melanie Pruvost et al
Nuclear ancient DNA draws picture of wild and early domesticated horses

Domesticated horses played key roles in the history of mankind providing nutrition and offering unprecedented modes of transportation. If the reasons related to the beginning of horse domestication are still unknown, horses were crucial to the life of nomadic pastoralists on the Eurasian steppe and had always have a particular position among domestic animal (warfare capabilities, symbol of social status, human's nutrition). For these reasons, deciphering the spatial and temporal origin of domestic horses is of key importance for understanding the origin of modern human societies. Due to the high variability of mtDNA among modern and ancient horse populations, the genetic analysis failed to reveal either time or place of horse domestication. In this case, the failure has pushed us to look for other genetic markers and to adapt new sequencing methods to ancient DNA. Thus, we were able for the first time to address the question of horse domestication by analyzing nuclear trait markers directly linked to early breeding practice. Coat color is an easily detectable phenotypic trait, which was likely a major goal of animal breeders since the beginning of domestication. Fortunately, single mutations are often responsible for color variants, which make these mutations very valuable for the analysis of SNP via pyrosequencing. We successfully typed for a dozen nuclear markers in more than 90 horse samples from the Pleistocene to medieval times. Through this example, we will present the advantage and limits of our methodological approach. By comparing mtDNA data and the data for coat color selection of horses, we will open the discussion about the perspective of the analysis of nuclear markers in palaeogenetics.

Linus Girdland Flink et al.
The Mediterranean route: analysing early domestic pigs in Southeast Neolithic France by combining Mitochondrial and Nuclear DNA with Geometric Morphometrics

The Neolithisation of Europe followed two main routes of expansion – the northern so called Danubian or Balkanic route and the southern Mediterranean route. Previous research has shown that the earliest domestic pigs in Europe were of Near Eastern descent, and specifically, that the spatiotemporal occurrence of haplotype Y1-6A is well correlated with the Danubian expansion. Whether domestic pigs along the southern route carried the same or divergent haplotypes remains unknown. A current hypothesis argues that early domestic pigs in the northern Mediterranean basin carried a different haplotype but has up to date lacked sufficient data to test it.

Here we report the results of our analysis of an 80bp d-loop fragment, a MC1R SNP that’s causative of dominant black coat colouring, and 2D geometric morphometric (GMM) data from sus remains in early to middle Neolithic layers in southeast France. Our results support the current hypothesis that divergent mitochondrial lineages accompanied the different routes of expansion as we find high prevalence of the Near eastern haplotype Y2-5A, but not a single Y1-6A. By applying GMM shape analysis we can show that individuals that carried a European d-loop signature (Aside haplotype) were significantly differentiated from individuals that carried the Y2-5A haplotype. This could imply a diverse origin that might represent local wild boar and imported domestic pigs. However, at least one individual that belonged to a European mitochondrial lineage also carried a derived allele at the 0301 locus in the MC1R gene – an allele that is assumed to have originated in domestic stock. Combined with previously published data, these results indicate that by 4000 BC, introgression with wild boar was widespread in Europe. For future analyses we aim to apply the integrated use of DNA and GMM to archaeological wild and domestic pig remains from locations across Europe and the Near East. As we demonstrated here, different analytical techniques can be used to answer a variety of questions and their combined use will make small case studies like this one more easily incorporated into a larger framework.

Ben Krause-Kyora et al.
The flying pig, migration or transfer of ideas in prehistory. Molecular genetic and archaeological investigations of Mesolithic and Neolithic pigs (Sus scrofa).

This study shows the reflection of population dynamics, like mobility and migration, in archaeological evidence from pigs. How did the domestication of the pigs take place in Northern Europe? Did domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic or did local European wild boar were also domesticated by this time?

First goal of this study was the development and establishment of extraction methods suited for extraction of DNA from historical samples, the selection of suitable genetic markers, and the establishment of sensitive, reliable and reproducible detection methods. PCRs were established to amplify pig-specific DNA with high sensitivity down to single molecules. Different primer pairs were used to amplify and sequence highly variable regions of the mitochondrial DNA like the dloop, cytb, XXX to determined specific mtDNA haplotypes. Further on specific nuclear DNA were analysed to determine the sex and the paternal haplotypes. The sequences finally aligned and compared to those already deposited in databases. A SNP analyse were established to determine the coat colour.

The results of over 300 individuals from 25 neolithic sites shows that around 4800- 4000 BC domestic pigs are introduced in the archaeological sites in northern Germany. The study points out that the oldest domestic pig in the sample (4600 BC) has a “Near East” haplotype. All other domestic and wild boars show the same “European” haplotype. The conclusion leads to the opinion that the domestic pigs with a maternal “Near East” ancestor were introduced into central Europe with the linear pottery (LBK) culture. After a short period the domestic pigs with “European” haplotypes coexist with the “Near East” haplotypes in the LBK and the Chaseen culture. An explanation could be that the people of the Ertebølle culture adapt the idea of domestication and permuted it on the indigenous wild boar population. With the established methods it is possible to determine the sex and the coat colour of ancient individuals. Further on the study shows the important of the coat colour as a marker for the domestication.

Josef Caruana & Terry Brown
The Maltese through time: A comparison of prehistoric, Roman and modern Maltese mitochondrial DNA haplotypes

The Maltese islands are a small archipelago situated in the middle of the Mediterranean Sea. Throughout history these islands have been dominated by the Mediterranean power of the era due to their strategic importance in controlling the shipping lanes between the eastern and western Mediterranean Sea. This study compares ancient DNA amplifications from a prehistoric site situated on the island of Gozo, two Roman burial sites in Malta, one of which is found in an urban context whilst the other in a rural context, and a sample group from the modern Maltese population. By analysing mitochondrial DNA Hypervariable Region 1, due to its higher copy number and survivability, this project aimed to study if any changes to the population of the islands can be observed through time. Another aim of the study was to see if any unique haplotypes might have survived these colonisations, and might still be present in the modern population. The modern Maltese population was also compared with other modern populations in the region in order to ascertain who it is most closely related to, and thus, which neighbouring influence most closely affected the matrilineal line of the Maltese population.

Paleo-Eskimo whole genome sequenced

From a related NY Times story:

The Greenlander belonged to a Paleo-Eskimo culture called the Saqqaq by archaeologists. On the basis of his genome, the Saqqaq man’s closest living relatives are the Chukchis, people who live at the easternmost tip of Siberia. His ancestors split apart from Chukchis some 5,500 years ago, according to genetic calculations, implying the Saqqaq people’s ancestors must have traveled across the northern edges of North America until they reached Greenland.

...

The Saqqaq man’s genome is so complete that the Danish researchers have been able to reconstruct his probable appearance and susceptibility to disease from the genetic information in his genome. They predict he would have had brown eyes because of variations, at four positions along his DNA, that are associated with brown eye color in East Asians.

He has the East Asian version of a gene known as EDAR, which endows people with hair that is thicker than that of most Europeans and Africans. Another gene suggests he would have had dry earwax, as do Asians and Native Americans, not the wet earwax of other ethnic groups.

Perhaps reflecting the so far somewhat limited reach of personal genomics, the researchers note that the ancient Greenlander was at risk for baldness, a surprising assessment given that all that remains of him is his hair. Dr. Rasmussen said he assumed the man died young.

The importance of this sequence is that it offers us a glimpse into a man who lived before 4,000 years of recent evolution. Obviously we will need to sample more individuals before we can speak about evolutionary change across this time span, and doing so for anyone living in more southernly latitudes where most of humankind have always lived will be tricky.

Nature 463, 757-762 doi:10.1038/nature08835

Ancient human genome sequence of an extinct Palaeo-Eskimo

Morten Rasmussen

Abstract

We report here the genome sequence of an ancient human. Obtained from ~4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Link

mtDNA haplogroup D2a1 in Paleo-Eskimo human

Ancient hair suggests multiple migrations into Americas

An ancient tuft of dark-brown human hair suggests that a tribe of humans trekked from north Asia to settle in what is now Greenland 3500 years ago – and then vanished.

A team of Danish scientists has found that DNA collected from the hair traces back to Asians, not Native Americans or the Eskimos that currently populate the region. This suggests that the first humans to colonise the American Arctic were distinct from the first people who arrived in America more than 14,000 years ago.

The hair – found in northern Greenland – may even be a relic of a steady trickle of human migrations across a harsh Arctic landscape, says evolutionary anthropologist Tom Gilbert of Copenhagen University in Denmark, who led the study. "It's bloody hard work to colonise the Arctic. It is not an easy venture," he adds.

Science DOI: 10.1126/science.1159750

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

M. Thomas et al.

The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World’s northern extremes. However, their origin and genetic relationship to later cultures is unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human, using 3400- to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This suggests that the earliest migrants into the New World’s northern extremes derived from populations in the Bering Sea area, and were neither directly related to Native Americans nor the later Neo-Eskimos that replaced them.

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