July 26, 2015

Paleoamericans galore

Two new papers in Nature and Science add to the debate on Native American origins. The first study (in Nature) detects that some Amazonians have a few percent ancestry from a group related to Australasians, which suggests that early native Americans were not homogeneous but came in two flavors: the main one found all over the Americans and the Australasian-related one. The second study (in Science) looks at ancient "Paleoamerican"-postulated populations and finds that they don't have any particular relationship to Australasians. Thus, whatever population brought the "Paleoamerican" admixture into the Amazon, it remains to be found.

Nature (2015) doi:10.1038/nature14895

Genetic evidence for two founding populations of the Americas 

Pontus Skoglund et al.

Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1, 2, 3, 4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5, 6, 7, 8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.

Link

Science DOI: 10.1126/science.aab3884

Genomic evidence for the Pleistocene and recent population history of Native Americans

Maanasa Raghavan1,*, Matthias Steinrücken2,3,4,*, Kelley Harris5,*, Stephan Schiffels6,*, Simon Rasmussen7,*, Michael DeGiorgio8,*, Anders Albrechtsen9,*, Cristina Valdiosera1,10,*, María C. Ávila-Arcos1,11,*, Anna-Sapfo Malaspinas1* et al.

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Link

July 21, 2015

British origins (with ancient data)

Related:


bioRxiv http://dx.doi.org/10.1101/022723

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo-Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo-Saxon period). We use present-day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today’s British are more similar to the Iron Age individuals than to most of the Anglo-Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo-Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo-Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Link

July 12, 2015

Phylogeographic refinement of haplogroup E

Genome Biol Evol (2015) 7 (7): 1940-1950.

Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent

Beniamino Trombetta et al.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.

Link

Y-chromosomes of Sicilian and Calabrian Arbereshe

European Journal of Human Genetics advance online publication 1 July 2015; doi: 10.1038/ejhg.2015.138

Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe

Stefania Sarno et al.

The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.

Link

mtDNA from Xiaohe cemetery

BMC Genetics 2015, 16:78 doi:10.1186/s12863-015-0237-5

Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China

Chunxiang Li et al.

Abstract

Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

Link

Complex demographic history of Western Central African Pygmies

bioRxiv doi: http://dx.doi.org/10.1101/022194

Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh et al.

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Link

July 05, 2015

Γιατί πρέπει να ψηφίσουμε ΝΑΙ στις 5 Ιουλίου

Απευθύνω το παρόν σε όσους ειλικρινά πιστεύουν πως βοηθούν την Ελλάδα ψηφίζοντας Όχι στο δημοψήφισμα της 5 Ιουλίου.

Υπάρχουν φυσικά και οι άλλοι, οι οποίοι υστερόβουλα θέλουν να επικρατήσει το Όχι: είτε γιατί έχουν διαφυλάξει τα χρήματα τους σε θυρίδες ή το εξωτερικό και προσδοκούν να κερδίσουν από τη δραχμή, είτε γιατί προσβλέπουν σε μια καταστροφική προεπαναστατική κατάσταση που θα τους βοηθήσει να αδράξουν την εξουσία.

Υπάρχουν όμως και ορισμένοι που ειλικρινά πιστεύουν πως το Όχι θα βοηθήσει την πατρίδα. Σ'αυτούς λοιπόν απευθύνομαι. Είτε πιστεύετε πως με το Όχι θα επιτευχθεί μια καλύτερη συμφωνία για την Ελλάδα, είτε θεωρείτε πως το Όχι είναι ζήτημα εθνικής ανεξαρτησίας και περηφάνιας και νομίζετε πως μετά από τόσο χρόνια κηδεμονίας από την Τρόικα ήρθε ο καιρός να ανακτήσουμε τις τύχες της χώρας μας.

Αν πιστεύετε πως το Όχι θα οδηγήσει σε μια καλύτερη συμφωνία, αναρωτηθείτε πώς θα το εκλάβουν στο εξωτερικό, αφού με τους ξένους πιστωτές θα πρέπει τελικά να συνενοηθούμε.

Οι μεν, που θέλουν την Ελλάδα εκτός Ευρωζώνης, θα εκλάβουν φυσικά το Όχι ως εκδήλωση της βούλησης του Ελληνικού λαού να απορρίψει τα προγράμματα βοήθειας που επιτρέπουν την συνεχιζόμενη παραμονή της χώρας στη νομισματική ένωση.

Οι δε, που επιθυμούν ακόμα την παραμονή της Ελλάδας στην Ευρωζώνη, δεν μπορούν να προσφέρουν κάτι καλύτερο, γιατί από τη μια θα κατηγορηθούν πως ενέδωσαν στον εκβιασμό της Ελλάδας και θα γίνουν ευάλωτοι σε ανάλογους εκβιασμούς από άλλες χώρες με δημοσιονομικό πρόβλημα.

Επιπλέον, η δημοσιονομική επιδείνωση εξαιτίας του κλεισίματος των τραπεζών οδηγεί σε μεγαλύτερη ύφεση την οικονομία και αυξάνει την ανάγκη προσαρμογής. Απορρίπτοντας την συμφωνία, ο Ελληνικός λαός δεν θα πάρει μια καλύτερη συμφωνία -αν πάρει καν μια συμφωνία- αλλά μια χειρότερη, αφού, προφανώς, η υπάρχουσα πρόταση -πέρα από το ότι δεν υπάρχει επισήμως πλέον στο τραπέζι- θα έχει απορριφθεί συνάμα και από τον Ελληνικό λαό.

Αλλά κι ακόμα κι αν οι έξω θελήσουν να επιτύχουν συμφωνία μετά το Όχι, τί σας κάνει να πιστεύετε πως οι έσω θα την επιτύχουν; Επί πέντε μήνες προσπαθούσαν τάχα να κάνουν συμφωνία, οδηγώντας την πραγματική οικονομία σε ολοένα και χειρότερη κατάσταση. Όταν κάποιος που δεν κατόρθωσε να φέρει συμφωνία σε πέντε μήνες υποστηρίζει πως θα την επιτύχει σε μια ώρα (Βαρουφάκης) ή 48 ώρες (Τσίπρας), λογικό είναι να δυσπιστούμε στην έπαρση τους.

Αλλά κι αν νομίζετε πως πράγματι δεν θα υπάρχει καλύτερη συμφωνία και η Ελλάδα θα οδηγηθεί στη Δραχμή, αναλογιστείτε τις συνέπειες σε ανθρώπινη δυστυχία που θα σημάνει μια τέτοια προοπτική σε μια χώρα εξαρτημένη από τις εισαγωγές για βασικά αγαθά όπως τα τρόφιμα, φάρμακα, και καύσιμα. Κι ακόμα -αν υποτεθεί- πως η περίοδος προσαρμογής είναι βραχύβια και η οικονομία αρχίσει πάλι να αναπτύσσεται, νομίζετε πραγματικά πως αυτό θα ωφελήσει την πατρίδα; Άλλωστε ο υπερδανεισμός, η αποσάρθρωση της παραγωγής, το πελατειακό κράτος και όλα όσα οδήγησαν την Ελλάδα στην καταστροφή γεννήθηκαν και άνθισαν και επί δραχμής. Δεν είναι το νόμισμα που οδηγεί μια κοινωνία στην ευμάρεια αλλά η συνετή ή μη χρήση της νομισματικής πολιτικής.

Αν πάλι νομίζετε πως το Όχι είναι ζήτημα αξιοπρέπειας και εθνικής περηφάνιας, σκεφτείτε πως η πραγματική περηφάνια δεν προέρχεται από το να έχεις τη δυνατότητα να κάνεις αυτό που θες εσύ, αλλά από το να κάνεις σε κάθε περίσταση αυτό που είναι χρήσιμο και σωστό, είτε το έχεις σκεφτεί μόνος του (όπως θα έπρεπε) είτε κατ' ανάγκη επειδή αυτό επιβάλλεται από κάποιον άλλο.

Τόσα χρόνια, οι ψηφισμένες Ελληνικές κυβερνήσεις έκαναν αυτό που ήθελαν, χωρίς να ρωτάνε κανένα ξένο πιστωτή, εφόσον μπορούσαν ακόμα να δανείζονται από τις αγορές. Ήταν πραγματικά περήφανες και αξιοπρεπείς ή έσκαβαν, με τη διόγκωση του χρέους, το λάκο στον οποίο στη συνέχεια έπεσε ολόκληρη η χώρα;

Ή ήταν αναξιοπρεπές πως χάρη στους ξένους πιστωτές και τις προσταγές τους άνοιξε η συζήτηση για κάποιες προφανείς αδυναμίες του Ελληνικού Δημοσίου όπως το πελατειακό κράτος με τους υπεράριθμους δημόσιους υπαλλήλους, τα μαϊμού επιδόματα, η συνταξιοδότηση ανθρώπων στο άνθος της παραγωγικής τους ηλικίας, τα ρετιρέ του Δημοσίου, και μια σειρά από άλλες ατέλειες της οργάνωσης της Ελληνικής πολιτείας που -εξαιτίας της χρηματοδοτικής ασφυξίας- αναγκαζόμαστε να αντιμετωπίσουμε.

Όλα αυτά φυσικά δεν ήταν άγνωστα στην Ελληνική κοινωνία στην προ-Μνημονιακή εποχή. Λίγο πολύ όλοι τα γνωρίζαμε αλλά οι περισσότεροι τα θεωρούσαν ήσσονος σημασίας και αδιαφορούσαν να περικόψουν τα μικροπρονόμια της τάδε ή δείνα οικονομικής ομάδας αφού φαινόντουσαν πως λίγο επηρέαζαν την δική τους ζωή. Η εποχή του Δε Βαριέσαι έληξε όταν συνειδητοποιήσαμε πως όλα αυτά τα οποία δηκτικά σχολιάζαμε αλλά στην πράξη επιτρέπαμε έχουν συνέπειες οι οποίες τελικά μας αφορούν και τους ίδιους.

Η πτώση του βιοτικού επιπέδου δεν είναι αποτέλεσμα των Μνημονίων, αλλά της χρεωκοπίας του Δημοσίου, το οποίο δεν μπορούσε πλέον να δανείζεται και να μοιράζει λεφτά. Αντιθέτως, χάρη στα Μνημόνια, το Ελληνικό κράτος (το οποίο μόλις το 2014 κατόρθωσε να αποκτήσει ένα μικρό πρωτογενές πλεόνασμα) μπόρεσε να μαλακώσει την ανάγκη προσαρμογής: χωρίς τα προγράμματα, η εξίσωση πρωτογενών δαπανών-εξόδων θα έπρεπε να είχε γίνει κατευθείαν και απότομα από το 2010.

Την Κυριακή, λοιπόν, σκεφτόμαστε το συμφέρον μας και επιλέγουμε τον δύσκολο δρόμο των μεταρρυθμίσεων μέσα στην Ευρώπη και όχι τις ψευδαισθήσεις όσων νομίζουν πως υπάρχει εναλλακτική οδός. Τα αγαθά, άλλωστε, κόποις κτώνται.

June 24, 2015

Oase1 had a Neandertal ancestor no earlier than ~200 years before his time

Several important conclusions of the discovery that Oase1 had a Neandertal ancestor 4-6 generations before his time (37-42 thousand years ago):
  • This is a smoking gun that modern humans interbred with Neandertals, following up on the publication of the Ust'Ishim and Kostenki-14 genomes; these two had longer Neandertal chunks than modern humans, from which it was estimated that their Neandertal admixture happened more than 50,000 years ago, roughly what one gets when looking at Neandertal chunks in modern humans alone. The Oase1 has even longer Neandertal chunks, and Neandertal admixture happened in its very recent past. 
  • So, it seems that Neandertal admixture was not a one-off event but is bracketed at least by the period 50-40 thousand years ago and happened in at least two places: Europe and the Near East.
  • The fact that the earliest European sample (N=1) has a recent Neandertal ancestor indicates that Neandertal admixture in the earliest Europeans cannot have been extremely rare or non-existent; if it were, the chances of finding one with the first try would be extremely low.
  • It is unlikely that Neandertals were killed off by modern humans immediately after the arrival of the latter in Europe, as the Oase1 is dated well after the arrival of modern humans to Europe.
  • Modern Europeans don't seem to be particularly related to the population of Oase1. After one substracts contamination and Neandertal admixture, what is left over is actually closer to East Asians than modern Europeans. But, it's equally close to East Asians and European hunter-gatherers. This can be explained if modern Europeans have ancestry from the mysterious "Basal Eurasians" via the Neolithic farmers.
Why did the Neandertals (and the significantly-Neandertal admixed AMH like Oase1) disappear? My bet is on the Campanian Ignibrite eruption.

Nature (2015) doi:10.1038/nature14558

An early modern human from Romania with a recent Neanderthal ancestor

Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel, Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich & Svante Pääbo

Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Link

June 20, 2015

DNA from hot climates technically feasible

From the paper:
Ten petrous bones were selected from archaeological specimens, representing a wide range of geographical locations and climatic contexts (Table 1, for repository information see S1 File). The specimens were selected from Central Europe, Central Asia, Southeast Asia, the Levant, Anatolia, and North Africa. The specimens are from Holocene archaeological contexts dated to between 10,000–1,800 calibrated years before present (cal. BP). The samples from Nubia, Jordan and Turkmenistan are from hot and arid regions. The sample from Turkey is from the Eastern Mediterranean (northwestern Turkey); the samples from Hungary and Serbia are from the Carpathian Basin/Southeast Europe, while the two samples from Cambodia and Vietnam are from tropical/subtropical Southeast Asia. We also included a metatarsal bone for one Neolithic individual from Hungary (Polgár Ferenci hát, PF280-443) as a control to confirm the differences between petrous and non-petrous reported in the previous study [8].
and:
It has recently been demonstrated [8] that petrous bone samples yield exceptionally high percentages of endogenous ancient DNA. Here we have shown that both the total amount of endogenous DNA that can be recovered as well as the percentage of all reads that represents endogenous DNA vary substantially for different parts of the petrous bone. Our results have several implications for aDNA studies. The results support the hypothesis that dense bone parts are especially suitable for ancient DNA research, with the densest part of the petrous bone, that which composes the otic capsule, providing the best results. For our samples the yields obtained for this part (part C) exceed those obtained for part B (i.e. dense bone part of the petrous outside the otic capsule) by up to 65-fold and those from part A by up to 177-fold. It is therefore apparent that while high endogenous yields can be obtained from part B, and hence from any dense part in the petrous, optimal yields should be obtained from bone sample taken directly from the otic capsule.
and:
Finally, our results show that endogenous yields from the five samples which originated from hot (either arid or humid) regions were always lower than 1% including extractions from part C of the petrous bone. However, deamination patterns suggest for two (Ain Ghazal and Vat Komnou) of the three samples for which we obtained sufficient numbers of reads that the obtained sequences are likely endogenous to the bones (S3 Fig). In contrast, the deamination pattern for the third sample, Man Bac, suggests that the human reads obtained are more likely to represent contamination than endogenous ancient DNA. These results suggest that it may be possible to obtain endogenous DNA from part C also for samples with relatively low amounts of endogenous DNA from hot environments, although extreme caution will be necessary in the interpretation of the results obtained from such samples.


PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

Ron Pinhasi et al.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.

Link

June 18, 2015

Kennewick Man was a Native American

Nature (2015) doi:10.1038/nature14625

The ancestry and affiliations of Kennewick Man

Morten Rasmussen, Martin Sikora, Anders Albrechtsen, Thorfinn Sand Korneliussen, J. Víctor Moreno-Mayar, G. David Poznik, Christoph P. E. Zollikofer, Marcia S. Ponce de León, Morten E. Allentoft, Ida Moltke, Hákon Jónsson, Cristina Valdiosera, Ripan S. Malhi, Ludovic Orlando, Carlos D. Bustamante, Thomas W. Stafford Jr, David J. Meltzer, Rasmus Nielsen & Eske Willerslev

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (BP)1. His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted2. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans2. In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

Link

June 13, 2015

Into, out of, and across the Eurasian steppe

A new paper in Nature adds to the earlier study in the same journal by presenting data from 101 ancient Eurasians. The year is not yet halfway over, but it seems that the ancient DNA field is moving towards a new norm of studying dozens of individuals at a time and comprehensively tackling the "big problems" that have vexed archaeologists, linguists, and historians for decades if not centuries.




The first conclusion of the new study is the detection of the migration from the steppe to Europe that was the title piece of the earlier study. The authors do not present quantitative estimates of the amount of demographic replacement effected by the Yamnaya-to-Corded Ware migration, so it will be interesting to see if there are any minor significant differences in these. But, the two papers have different Yamnaya and Corded Ware samples, and yet arrive at qualitatively similar conclusions, so at least this part of the story should be considered firmly "settled".

The second conclusion is the migration from the European steppe to the Afanasievo culture of the Altai. This has been long-hypothesized based on the physical type of the Afanasievo people and their possession of a similar pastoralist/wheeled vehicle toolkit that would have allowed them to cover the huge difference between Europe and the Altai. This confirms movement #2 of the Anthony/Ringe model, although I doubt that this migration had anything to do with Tocharians as detailed below. But, it did happen.

The third conclusion is that the later steppe cultures of the Sintashta and Andronovo (putative Indo-Iranians according to some), were not a continuation of the Yamnaya-Afanasievo people, but had extra Neolithic farmer ancestry. So, it seems that Neolithic farmers entered the steppe, and the development of steppe cultures did not happen in isolation. Whether this involved migration of Corded Ware people (as the authors prefer), who were already a mixture of Yamnaya and Neolithic farmers, or some other mixture of Neolithic farmers with steppe populations (e.g., Tripolye plus Yamnaya) remains to be seen.

The fourth conclusion of the paper is that these steppe cultures were also later replaced by people of at least partial East Asian or "Native American"-like ancestry.  So, it seems that movements into the steppe happened both on the western end (as the incursion of Neolithic farmer ancestry into the Sintashta proves), but also on the eastern end, with the Europeoid populations of western origin receiving admixture from the eastern periphery of the Eurasian steppe.

As for the Yamnaya, the authors do not find a very strong signal of admixture (as did the earlier study), which they attribute quite plausibly to the lack of eastern hunter-gatherers in their dataset. On the other hand, they claim that the "Caucasus" genetic component in the steppe populations was of steppe ancestry rather than Near Eastern/Caucasian origin as was claimed in the earlier paper. This is based on the statistic D(Yoruba, Armenia BA; Yamnaya, Corded Ware) that is not significantly different from zero. However, Corded Ware is a mixture of Yamnaya and European Neolithic, so the sign of this statistic is determined by the sign of the statistic D(Yoruba, Armenia BA; Yamnaya, European Neolithic). If Yamnaya was simply a steppe population, descendants of local people without ancestry from the Middle East/Caucasus, then this statistic would be positive because of the shared Middle Eastern ancestry of Armenia BA and European Neolithic. Whereas, if Yamnaya is a mixture of a steppe population and a Middle Eastern/Caucasian one, then the statistic would be positive/negative for the respective parts, which would be consistent with an average not different from zero. I am sure that when the new data is re-analyzed together with the eastern hunter-gatherers it will be clear that the Yamnaya are not a pure steppe population.

Nonetheless, I am quite glad to read a sentence such as this:
Populations in northern and central Europe were composed of a mixture of the earlier hunter-gatherer and Neolithic farmer10 groups, but received ‘Caucasian’ genetic input at the onset of the Bronze Age (Fig. 2).
It seems that my prediction the the West_Asian component would appear in post-5ka Europeans and was related to Indo-Europeans has been adequately confirmed by the last two papers.

Speaking of the Caucasus/Middle East, it seems clear as a first approximation that the Bronze Age Armenians are quite similar to modern Armenians. Whether the genetic continuity of Armenians extends beyond the Bronze Age, or Armenians were formed by mixture in the Bronze Age remains to be seen. The question of Armenian linguistic origins is of course separate as it is commonly understood that the Armenian language is unrelated to Anatolian languages and may have arrived in Armenia from the Balkans at around the Bronze Age-Iron Age transition.

The authors also study some phenotypic traits such as lactase peristence (Yamnaya had some, but overall prevalence was much lower than modern Europeans, hence lots of selection to the present), and skin eye pigmentation. Like Wilde et al., and Mathieson et al., the steppe populations seem to have had brown eyes. Given that so did Neolithic Europeans, and (presumably) ancient Middle Easterners/Caucasians, I think it's a good bet that Proto-Indo-Europeans (whatever solution to the PIE urheimat one accepts) were a brown-eyed people, or in the very least far from the blue-eyed "Aryans" of racial mythology. Even the Bronze Age and Iron Age Asians seem to have been a predominantly brown-eyed people, although the derived HERC2 allele seems to be at a higher frequency in them than in the steppe Europeans.

The story of the Y-chromosomes seems very interesting, although these are not resolved to fine detail. The most interesting aspect of this part of the work is the appearance of haplogroup J in Iron Age samples from Russia, Armenia, and the Altai. This may tie in to the question of the Tocharian origins, which I have claimed were associated with R1b, rather than R1a (as the Indo-Iranians were). The modern Uygurs (who are partially of Tocharian origin) have both J2 and R1b, so were the recipients of West Eurasian elements other than the R1a that so seem to have dominated the eastern steppe, including the Afanasievo. I continue to think there's no evidence that the Afanasievo is Proto-Tocharian, as it's in the wrong place and 3,000 years before the attestation of Tocharian. 

Overall this is an amazing study which adds a lot to what we know about Bronze Age Eurasia. Hopefully there is more to come in the second half of 2015, but for the time being there is plenty to chew on.

Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Population genomics of Bronze Age Eurasia

Morten E. Allentoft, Martin Sikora, Karl-Göran Sjögren, Simon Rasmussen, Morten Rasmussen, Jesper Stenderup, Peter B. Damgaard, Hannes Schroeder, Torbjörn Ahlström, Lasse Vinner, Anna-Sapfo Malaspinas, Ashot Margaryan, Tom Higham, David Chivall, Niels Lynnerup, Lise Harvig, Justyna Baron, Philippe Della Casa, Paweł Dąbrowski, Paul R. Duffy, Alexander V. Ebel, Andrey Epimakhov, Karin Frei, Mirosław Furmanek, Tomasz Gralak, Andrey Gromov, Stanisław Gronkiewicz, Gisela Grupe, Tamás Hajdu, Radosław Jarysz, Valeri Khartanovich, Alexandr Khokhlov, Viktória Kiss, Jan Kolář, Aivar Kriiska, Irena Lasak, Cristina Longhi, George McGlynn, Algimantas Merkevicius, Inga Merkyte, Mait Metspalu, Ruzan Mkrtchyan, Vyacheslav Moiseyev, László Paja, György Pálfi, Dalia Pokutta, Łukasz Pospieszny, T. Douglas Price, Lehti Saag, Mikhail Sablin, Natalia Shishlina, Václav Smrčka, Vasilii I. Soenov, Vajk Szeverényi, Gusztáv Tóth, Synaru V. Trifanova, Liivi Varul, Magdolna Vicze, Levon Yepiskoposyan, Vladislav Zhitenev, Ludovic Orlando, Thomas Sicheritz-Pontén, Søren Brunak, Rasmus Nielsen, Kristian Kristiansen & Eske Willerslev

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Link

June 10, 2015

101 ancient genomes from Bronze Age Eurasia

New data has been posted online. This seems related to this earlier post. Hopefully the study linked to this data will appear soon, but genome bloggers can get to it thanks to the early data release.

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. 

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

Link

June 09, 2015

Nilo-Saharan component

Scientific Reports 5, Article number: 9996 doi:10.1038/srep09996

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Begoña Dobon et al.

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

Link

May 30, 2015

Out of Egypt or Out of Ethiopia?

I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.

For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.

For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.


AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Luca Pagani et al.

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

Link

May 21, 2015

More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:
The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.


Related:
Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

May 13, 2015

Neandertal in the (immediate) family tree

Early European may have had Neanderthal great-great-grandparent
One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.

The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone's genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).