Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Abstract:

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Link to study


Expect a blog post soon enough at the main blog on this exciting paper's interesting new finds...

Bene Israel = South Asians + Jews?

Abstract:

The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of these ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 438 individuals from 32 other Jewish and Indian populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, PCA, ADMIXTURE, identity-by-descent sharing, admixture LD decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They share genetic ancestry with other Jewish populations to an extent not observed for any other Indian population. Putting the results together point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19-33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which has led to increased prevalence of recessive diseases in this population. This study also provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.

Link to study

Eight thousand years of natural selection in Europe

Mathieson et al.

Abstract:

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Link to study

All Africans have some Eurasian admixture?

Llorente et al.

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Link to study

Maykop culture's people: The source of the Caucasian-like ancestry in the Yamnaya?

As David mentioned over at Eurogenes, we'll be seeing what some peoples of the Maykop culture   looked like genomically as Oxford University recently donated Maykop samples to the Reich lab.

As has been stated in the past on the Anthromadness blog; Haak et al. 2015 found what looked to be a West Asian ancestry carrying element in the Yamnaya Pontic-Caspian Steppe pastoralists and characterized it as Armenian/Cacuasian-like.

From what I understand, some in the genome blogging world have connected this element to the illusive "Teal component" which looks be a mixture between Ancient North Eurasian-related ancestry and West Asian / Near Eastern ancestry.

I'm no expert on the archaeological nature of these cultures (the Yamnaya and Maykop) but there seems to have definitely been some rather deep interactions between them whilst the Maykop culture geographically sat between the Yamnaya and West Asia to the south which has led some to believe that the Maykop are the source of the West Asian-esque input in the Yamnaya.

Only time will tell...

Link

New Human species discovered

National Geographic & Science Magazine

"Delezene’s own fossil pile contained 190 teeth—a critical part of any analysis, since teeth alone are

often enough to identify a species. But these teeth weren’t like anything the scientists in the “tooth booth” had ever seen. Some features were astonishingly humanlike—the molar crowns were small, for instance, with five cusps like ours. But the premolar roots were weirdly primitive. “We’re not sure what to make of these,” Delezene said. “It’s crazy.”he same schizoid pattern was popping up at the other tables. A fully modern hand sported wackily curved fingers, fit for a creature climbing trees. The shoulders were apish too, and the widely flaring blades of the pelvis were as primitive as Lucy’s—but the bottom of the same pelvis looked like a modern human’s. The leg bones started out shaped like an australopithecine’s but gathered modernity as they descended toward the ground. The feet were virtually indistinguishable from our own.

“You could almost draw a line through the hips—primitive above, modern below,” said Steve Churchill, a paleontologist from Duke University. “If you’d found the foot by itself, you’d think some Bushman had died.”

But then there was the head. Four partial skulls had been found—two were likely male, two female. In their general morphology they clearly looked advanced enough to be called Homo. But the

braincases were tiny—a mere 560 cubic centimeters for the males and 465 for the females, far less than H. erectus’s average of 900 cubic centimeters, and well under half the size of our own. A large brain is the sine qua non of humanness, the hallmark of a species that has evolved to live by its wits. These were not human beings. These were pinheads, with some humanlike body parts.

Berger himself thinks the right metaphor for human evolution, instead of a tree branching from a single root, is a braided stream: a river that divides into channels, only to merge again downstream. Similarly, the various hominin types that inhabited the landscapes of Africa must at some point have diverged from a common ancestor. But then farther down the river of time they may have coalesced again, so that we, at the river’s mouth, carry in us today a bit of East Africa, a bit of South Africa, and a whole lot of history we have no notion of whatsoever. Because one thing is for sure: If we learned about a completely new form of hominin only because a couple of cavers were skinny enough to fit through a crack in a well-explored South African cave, we really don’t have a clue what else might be out there."


Link 1 & Link 2

Notes:

1. The above text isn't a pristine excerpt and a good amount of text here and there was skipped. I of course emphasize reading the articles I've linked to. 

DNA from Neandertal relative may shake up human family tree

Ann Gibbons, Science Magazine News

"The close affinity with Neandertals, but not with Denisovans or modern humans, suggests that the lineage leading to Neandertals was separate from other archaic humans earlier than most researchers have thought. That means that the ancestors of modern humans also had to split earlier than expected from the population that gave rise to Neandertals and Denisovans, who were more closely related to each other than they were to modern humans. (Although all three groups interbred at low levels after their evolutionary paths diverged—and such interbreeding may have been the source of the Denisovan mtDNA in the first Sima fossil whose DNA was sequenced.) Indeed, Meyer suggested in his talk that the ancestors of H. sapiens may have diverged from the branch leading to Neandertals and Denisovans as early as 550,000 to 765,000 years ago, although those results depend on different mutation rates in humans and are still unpublished.

That would mean that the ancestors of humans were already wandering down a solitary path apart from the other kinds of archaic humans on the planet 100,000 to 400,000 years earlier than expected. “It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong."

Link

There are populations in West Asia seemingly more Basal Eurasian than Early European Farmers

Upon encountering that tweet by Iosif Lazaridis of Harvard Med I figured I'd drop him the following email:

Where he promptly replied with:

It ultimately seems as though there are groups in West Asia like Negev Bedouin Bs (who will show more of "Near Eastern" ancestry like what shows up in David over at Eurogenes' K=8 ADMIXTURE analysis than Early European Farmers) seemingly richer in Basal Eurasian ancestry than Early European Farmers.

The issue though is quite simply that many or most of these groups tend to have African ancestry (tends to be East African-related) and that ultimately makes whether or not they are more Basal Eurasian an iffy matter complicated by their African admixture even if it is accounted for as best as possible.

My personal opinion is that populations richer in "Near Eastern/ENF" will prove to be more Basal Eurasian than Early European Farmers but something's surely needed in order to be sure here; more ancient DNA data from West Asia. 

Notes:

1. The West Asian / Near Eastern populations less rich in Basal Eurasian that Lazaridis noticed are probably ones like Anatolians, Caucasians and Iranians whom are all rich in MA-1 ("Ancient North Eurasian") related ancestry and will even show some notable Western European Hunter-Gatherer-related ancestry like the case is with various Anatolian Turks. These groups will actually show less of "Near Eastern/ENF" than Early European Farmers so it would make sense. I can't be sure about them being the particular groups that seem to be less Basal Eurasian than Early European Farmers but it's just an educated guess...

West Asians have less Basal Eurasian than Early European Farmers

Iosif Lazaridis of Lazaridis et al. 2013-2014

"EEF=WHG+Near East. To account for BE in EEF, Near East must have even more. But (Non-African admixed) modern Near East has less"

Interesting words from Iosif Lazaridis where he said via a recent tweet that Early European Farmers whom as I've often said in some manner or other are "Western European Hunter-Gatherer-related ancestry + West Asian/Near Eastern", according to him have more Basal Eurasian (BE) ancestry than non-African admixed West Asians. It's an interesting revelation on his part to say the least.

As a friend of mine states:

"He also points out that the divergent element in EEF and modern Europeans is absent not only in WHG, ANE and ENA, but also the ancient Ust'-Ishim, Oase and EHG genomes."

Rethinking the dispersal of Homo sapiens out of Africa

Groucutt et al.

Abstract:

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the

late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.


Link to study 1 & link 2

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

Flegontov et al.

Abstract:

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic
hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language
family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralicspeaking
Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, determined mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that the Kets belong to the cluster of Siberian populations related to Paleo-Eskimos. Unlike other members of this cluster (Nganasans, Ulchi, Yukaghirs, and Evens), Kets and closely related Selkups have a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed. 


Link to study

Testing modern human out-of-Africa dispersal models and implications for modern human origins

Reyes-Centeno et al.


Abstract:

The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor–descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity.


Link to study


Notes:

There are arguments against this model and the current genetic evidence doesn't really support this but as David says things over at Eurogenes; if this is confirmed via ancient DNA results then the old idea of "Eastern Non-Africans/East Eurasians" may just collapse  and things will look a whole lot more complex. But this seems to be more based on skull morphology? So its reliability is honestly pretty damn low in my humble opinion. 

Strata on loanwords from Arabic and other Semitic languages in Northern Somali

By Giorgio Banti

Excerpt:

An Ancient South Arabian (ASA) loanword in NS was identified by Cerulli (1959: 119), i.e., NS addôon m. ‘slave’. But a systematic study of the contacts between ASA, Himyaritic, and NS has not been done yet. Nevertheless, a few possible ASA (or Himyaritic) loanwords can be identified in NS.

 NS addôon m. and addóon f. ‘slave’ (pl. addoomó m.) has -n < -m in syllable coda, a regular development in NS (cf. § 1.) Cerulli (1959: 119) connected it with Sabaic ’dm ‘servants, vassals, religious servants’. This particular semantic development of the well-known Semitic root ’DM still survives in Modern Yemeni Ar. ’awādim ‘domestics’ (Ricks 1989: 5). Notice that -oo- is here probably from *-a- or *-ā-, a development that took place in the donor language, not in NS. Modern South Arabian (MSA) languages have several instances of accented *-āɹ- > -ōɹ- (> -ūɹ-).

NS gêel m. ‘camel’ has -ee- < -aa-, that is still preserved, e.g., in NS compounds like haruub-gâal m. ‘vessel for milking camels’ or daba-ggáalle m. ‘ground squirrel’ (lit. ‘having a camel tail’), etc. East Cushitic *gaala ‘camel’ is from Semitic *gamal- ‘id.’ and the most likely intermediary has been a language spoken in Southern Arabia when camels were introduced to the eastern Horn ca. 2000 years ago, as argued in Banti (2000: 49 f.). Gml ‘camel’ is well attested in Sabaic. However, the loss of -m- is not regular in ASA, nor in NS or any known East Cushitic language, and points to a different language: loss of -m- between vowels occurs several times in Southern Ethiosemitic and in MSA.

Link to paper

When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin

Rivollat et al.

Abstract:

An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.


Link to study

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

Raghavan et al.

Abstract:

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 to study

Genetic evidence for two founding populations of the Americas

Skoglund et al.

Abstract:

Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. 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). 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 to study

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

Pinhasi et al.

Abstract:

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 to study

Important notes:

Dienekes touches upon some of the relevance of what this study talks about here. One thing I would note is that many of the samples apparently gathered in this paper will eventually be touched upon in studies similar to the likes of Allentoft et al. 2015 or Lazaridis et al. 2013 from what I've heard.

This study has an incredible mass of ancient genomes and while some seem to be quite low coverage; we're in for quite the wallop when all of these samples are made available and/or touched upon in a genomic study someday.

And finally; some decent discussions about this paper went on here.

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

Schiffels et al.

Abstract:

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 to study

High-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe

Sarno et al.

Abstract:

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 to study

An early modern human from Romania with a recent Neanderthal ancestor

Fu et al.

Abstract:

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 Eurasia. Here we analyse DNA from a 37,000–42,000-year-old 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 to study

New Paper about the Phylogeny of Haplogroup E

Trombetta et al.


Abstract:

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 to 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 5 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 SNP-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 kya. Time frames, phylogenetic structuring and socio-geographic distribution of E-V1515 and its subclades are consistent with a multi-step demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to sub-equatorial 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 to study

Reconstructing Austronesian population history in Island Southeast Asia

Lipson et al.

Abstract:

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.


Link to study