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Saturday, May 23, 2015

SMBE 2015 abstracts


Lots of paleogenomics stuff this year. Good to see. The abstract book is available here. Below are a few highlights:

Genomic signals of migration and continuity in Roman Britain

Martiniano et al.

York (Eboracum) was a provincial city at the edge of the Roman Empire where a number of Roman cemeteries have been excavated. One of these at Driffield Terrace is unusual in a regional and national context, with a large predominance (70.8%) of decapitated young males buried there. They show frequent evidence for trauma consistent with violent life histories and have been alternately speculated as gladiators, soldiers and slaves with potentially foreign origins. Here we report the ~1X genome sequences of seven of these individuals from the Roman period. While six of the Roman burials show affinity with modern British populations, one sample, although indistinguishable in funerary ritual from the other skeletons in the cemetery, shows a clear signal of exogenous origin, with modern affinities pointing towards the Eastern Mediterranean, a clear indication of the cosmopolitan impetus of the Roman empire, even at its western fringe.


Insights into British and European population history from ancient DNA sequencing of Iron Age and Anglo-Saxon samples from East England

Schiffels et al.

British population history is shaped by a series of immigration periods and associated changes in population structure. It is an open question to what extent these changes affect the genetic composition of the current British population. Here we present whole genome sequences generated from 10 individuals, found in archaeological excavations in Hinxton, Oakington and Linton, close to Cambridge, and ranging from 2,300 years before present (Iron Age) until 1,200 years before present (Anglo-Saxon period). We use modern genetic samples from the 1000 Genomes Project and additional external data from Britain, the Netherlands and Denmark to characterize the relationship of these ancient samples with contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that samples from the Anglo-Saxon period are relatively more closely related to central northern Europe, while earlier samples and contemporary British samples are relatively more closely related to Southern European populations. To quantify this series of relationships further, we developed a new method, rarecoal, that fits a demographic model parameterized by split times, population sizes and migration rates to the distribution of shared rare variants across a large number of modern and ancient individuals. We use rarecoal to estimate the history of European population structure within the last 10,000 years and to map our ancient samples onto the European population tree. Our approach provides a unique picture of population history in Europe, and in particular helps characterizing the complex genetic impact of Anglo-Saxon immigrations into Britain.


Ancient DNA reveals patterns of residential continuity and mobility at the onset of the Central European Bronze Age

Mittnik et al.

At the transition from the third to the second millennium BC, the introduction of bronze for the manufacture of tools, weapons and personal ornaments marked a major step in European prehistory. Trade of the metal raw materials and manufactured goods required regular and organized contacts among communities. On the other hand, local population continuity was a prerequisite for the accumulation of wealth, the establishment of enduring social differentiation, and the formation of regional elites.

The archeological record in the Lech Valley in southern Bavaria, Germany, shows a rapid and gapless transition from the Late Neolithic Bell Beaker Phenomenon to the Early Bronze Age. To investigate social and demographic changes associated with the appropriation of the bronze technology, we studied nearly eighty individuals from six burial sites in the region with respect to their maternally inherited mitochondrial DNA (mtDNA).

The results indicate both local genetic continuity spanning the cultural transition, and, following the onset of the Early Bronze Age, a major influx of mtDNA types previously not found in this region. Integrating stable isotope data with the genetic data reveals a picture of a patrilocal society with remarkable mobility in women. While crucial for understanding the change of local demographics, these findings also have implications for the spread of major technological and societal changes across Europe at the beginning of the Bronze Age.


The Genomic connections between early farmers from Iberia and central Europe, and their relationship to populations from modern Spain

Gunther et al.

The neolithization process swept over Europe after the advent of farming lifestyle in the Near East approximately 11,000 years ago. However, the mode of transition and its impact on the demographic patterns of Europe remains an area of open questions. Ancient genomics allow us to analyze individuals involved in these transitions directly and to make comparisons between populations over time. Previous studies have shown close relationships between early Scandinavian farmers and contemporary southern Europeans as well as strong differences between hunter gatherers and early farmers. However, mtDNA composition on the Iberian peninsula and different migration routes suggest a dissimilar history of southwestern Europe. We [obtained?] genomic sequences of eight between 4,000 and 5,600 year old early Iberian farmers from El Portalon, 15 km East of Burgos, Spain. In contrast to a 7,000 year old hunter gatherer from the near-by area La Brana, but similar to the pattern observed for central and northern European farmers, these individuals all show genetic similarities to modern-day southern Europeans, especially to Sardinians and Basques.


450 diverse high coverage whole genome sequences reveal ancient population admixture in modern human populations

Luca Pagani

Complete high-coverage individual genome sequences carry the maximum amount of information for reconstructing the evolutionary past of a species in the interplay between random genetic drift and natural selection. Here we present a novel dataset of 450 human genomes from 156 populations that represent a dense geographic coverage of Eurasia. The genomes, chosen to be representative of each population based on SNP-chip data, were sequenced at 40X on the same platform (Complete Genomics) and processed on a uniform bioinformatics pipeline.

Our dataset has an unprecedented combination of high spatial and genomic coverage. This enabled us to refine current knowledge on continent-wide patterns of heterozygosity, long and short range gene flow, archaic admixture, and changes in effective population size over time. In particular, we have clarified the admixture dynamics of Eurasian populations during the last 3000 years, confirmed and further resolved the genetic relationship between recently sequenced ancient human remains and modern populations, and highlighted significantly higher amounts of Neanderthal gene flows in Island South East Asian and Oceanian populations. We have also assembled an extensive catalogue of genes under positive selection in various human groups.

Finally, ChromoPainter (Lawson et al. 2012) and MSMC (Schiffels and Durbin 2014) have cemented genetic evidence of an early African origin for the people currently inhabiting Papua New Guinea. Our results are compatible with a first migration out of Africa of these Oceanian populations, which subsequently experienced 80% of gene flow from populations coming from the second, main Eurasian out of Africa.


Nuclear and mitochondrial DNA sequences from two Denisovan individuals

Sawyer et al.

Denisovans are a sister-group of Neandertals that were described based on a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave, Altai Mountains. A molar (Denisova 4) found at the same site, has a mitochondrial (mt) DNA sequence similar to Denisova 3. Here we present nuclear DNA sequences from Denisova 4, with the morphological description and the mitochondrial and nuclear DNA sequences from another molar (Denisova 8) from Denisova Cave. Like Denisova 4, this molar is very large and lacks traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals but lower than that among present-day humans. The mtDNA of Denisova 8 is more diverged from and has accumulated fewer substitutions than the mtDNAs of the other two specimens suggesting that Denisovans were present in the cave over an extended period of time.

20 comments:

Matt said...

Just some titles:

Inferring population structure across space and time - Bradburd, Ralph and Coop - We develop a method toestimate the assignments of the ancestry proportions for each individual, as well as the parameters that govern the spatiotemporal decay of relatedness in each population....We demonstrate the utility of this approach using a combination of ancient and modern human individuals sampled throughout Europe.

SpaceMix has entered the fourth dimension? A few other spatial modeling papers listed as well.

Ancient mtDNA analysis of the Eneolithic Tripolye-Cucuteni Culture from Verteba Cave, Ukraine - the Tripolye Culture existed at the intersection of indigenous European hunter-gatherer tribes and socially stratified Neolithic agricultural communities with possible origins in the Near East. Ancient DNA (aDNA) has demonstrated to be an important area of inquiry for investigating ancient groups, especially for peoples who contributed to modern Europe. In this study, we examine aDNA from Verteba Cave (3951 – 2620 calBC) in Ukraine to reconstruct the origins of this Eneolithic culture. Verteba Cave consists of commingled secondary burials. In our preliminary analysis, we sampled a number of left second metacarpal bones as a means of avoiding extracting DNA from the same individual. DNA was extracted from bone based on a modified silica method... Our preliminary results indicate haplogroups that are common among modern Eurasian peoples. Future investigations will examine higher resolution mitogenome sequences and genome-wide SNP variation through target enrichment methods to characterize Tripolye population history Previous mtdna on this same site was just HVRI.

The power of painting: using haplotype patterns to infer history - Hellenthal et al - The widespread availability of densely genotyped individuals representing hundreds of world-wide geographic locations has enabled researchers to reconstruct the ancestral history of numerous populations in unprecedented detail. The currently most powerful approaches to infer history use haplotype information, which exploit correlation patterns among Single-Nucleotide-Polymorphisms (SNPs) to increase precision over the far more commonly-used programs that ignore this information... I illustrate the power of these techniques in applications to world-wide human samples, including a new data collection with hundreds of individuals sampled from 18 groups of the Eastern Highlands of Papua New Guinea. We show the recent and ancient genetic influences of this uniquely isolated region that has been subjected to past outbreaks of the prion-based neurological disorder "kuru", showcasing how the rich information in DNA can help resolve existing controversies among anthropologists, historians and linguists.

Matt said...


Tracing Genetic History of Populations in Myanmar - Peng et al - According to the southern coastal route hypothesis, Myanmar is the entrance from South Asia to Southeast and East Asia. Nowadays, Myanmar is the homeland for various ethnic groups. All make it as a crucial region to study human evolutionary history. Herein, we genotyped ~900,000 genomewide SNPs in 175 unrelated individuals of eight populations representing five ethnic groups: Bamar, Chin, Naga, and Rakhine from Myanmar as well as Jingpo (Kachin) from Yunnan, Southwest China. Incorporating the published data, populations of Myanmar display as basal branches to other Southeast and East Asian populations in the tree of global populations, which is in accordance with the southern route migration hypothesis. Admixture analyses detected gene flows from South Asia in Bamar and Rakhine populations from southern Myanmar rather than Chin, Naga, and Jingpo populations from northern Myanmar.... Interestingly, the genetic evidence are largely in agreement with the model of Sino-Tibetan languages, suggesting certain population expansions from north to south. Thus, our analyses of genome-wide SNPs uncovered a complex history in Myanmar populations. Cool to have more for Southeast Asia, which is really not well covered at all at the moment. Likewise "From social to genetic structures: a genome-wide approach in Southeast Asia".
Ancient genomes improve our understanding of modern human population differentiation - Kay et al - We developed and applied a statistic that jointly analyzes modern and ancient genomes to investigate changes in the frequency of functionally relevant alleles. Using archaic genomes we observed changes in Eurasia that cannot be explained by neutral forces or background selection alone, and that are best explained by the action of recent positive selection. The genomes of several ancient European individuals allowed us to determine the contribution of different European founder populations to these signatures, and their effect in the genetics of present-day European groups. More selection.

Mitochondrial genome diversity in European Upper Paleolithic and Mesolithic huntergatherers - Posth et al - Studies of ancient human mitochondrial DNA (mtDNA) suggest genetic continuity between Upper Paleolithic and Mesolithic hunter-gatherers in Europe, followed by an almost complete replacement with limited genetic admixture by Neolithic farmers. The analyses of European pre-Neolithic mtDNAs revealed a predominance of mitochondrial haplogroups belonging to clade U. By contrast, early Neolithic European farmers were found to belong to a wider range of different mitochondrial clades... In this study high-throughput sequencing technologies are adopted to reconstruct the complete or almost complete mtDNA of Late Pleistocene and Early Holocene modern humans from different archaeological sites in southwestern Germany.

terryt said...

This one is of most interest to me: "450 diverse high coverage whole genome sequences reveal ancient population admixture in modern human populations".

Quote from the abstract:

"highlighted significantly higher amounts of Neanderthal gene flows in Island South East Asian and Oceanian populations".

That should put the cat amongst the pigeons. The Denisova paper will also be of considerable interest.

Matt said...

Re: Pagani, and Denisovan admixture, the estimate is 4-6% of an Oceanian group's ancestry is from the Denisovan clade, so if they are about 20% "First Asian" and all the Denisovan came through "First Asian" then "First Asian" would end up around 25% Denisovan overall.

Qin and Stoneking's preprint here - http://biorxiv.org/content/early/2015/04/03/017475 includes this section -

"Additional Archaic Ancestry in EE/NA Populations - PCA is a descriptive analysis that is useful for indicating potential admixture events, but cannot be used to prove that admixture occurred. We therefore applied formal tests to document potential admixture between archaic hominins and modern humans.

Since EE/NA populations have on average inherited more archaic ancestry than West Eurasian populations (7), we computed f4 statistics (8, 10) of the form f4(Yoruba, Archaic ;French,X), in which X is an EE/NA population. A significantly positive statistic (Z-score> 2) is evidence that EE/NA possesses more Archaic (either Neanderthal or Denisovan) alleles than does the French population. Significantly positive statistics (Z-score> 6) are obtained for all Oceanian populations, which are much higher than those for other EE/NA populations, indicating more archaic ancestry in Oceanians (Fig. 1B and Table S3) ...

In addition to the Oceanian populations, many additional EE/NA populations exhibit significant Z-scores (> 2), indicating they have more archaic alleles than the French population has. However, unlike the Oceanian populations, the inferred amounts of Denisovan and Neanderthal alleles are approximately the same in these EE/NA populations (Fig. 1B). It is thus not clear from this analysis if the additional archaic ancestry in these EE/NA populations reflects Neanderthal ancestry, Denisovan ancestry, or both.

In order to increase the power of these tests, we combined the data from the East Asian, Siberian, and native American populations, and obtained significantly higher signals of archaic ancestry (Z-score =3.12 for Neanderthal and 3.64 for Denisovan, compared to the average single population Z-scores of 2.79± 0.07 for Neanderthal and 3.17±0.08 for Denisovan). To ensure that our results are not influenced by the choice of African (Yoruba) and European (French) reference populations used in this f4 analysis, we repeated the analysis with different reference populations and obtained similar results
.

See if this is stronger with the samples in Pagani (if there are enough).

No island South East Asian populations in their analysis, in the sense of Malays or Indonesians or the Philippines, really (and little mainland South East Asia).

...

More interesting titles -

The genomic analysis of the Andaman islanders gives a new insight on the spread of modern humans in Asia -

Our findings suggest that Andamanese populations don't have a different origin than other Asian populations,contrary to the hypothesis of a first Out-of-Africa that would populate the Andaman Islands, where they would remain, having been substituted in mainland Asia. Their phenotypical differences are mainly due to strong selection on specific type of genes (i.e. height) which might be the result of convergent-evolution producing the Negrito phenotype. Probably an indication with the above that thinking of the Andamanese as in a unified group with very tropical adapted, long resident peoples from South East Asia is not useful.

High-coverage sequencing of the Human Genome Diversity Project (HGDP-CEPH) Panel

The Genetic Architecture of Lightened Skin Pigmentation in the Southern African Khomani San

rozenfag said...

>and highlighted significantly higher amounts of Neanderthal gene flows in Island South East Asian and Oceanian populations.

Could it be that they mistaking Denisovan genes for Neanderthal?

terryt said...

"No island South East Asian populations in their analysis, in the sense of Malays or Indonesians or the Philippines, really (and little mainland South East Asia)".

Thanks for all that information Matt. Regarding the above comment I would guess that SE Asian populations would stand somewhere between Oceanian and East Asian populations as they appear to be the product of a relatively recent movement from East Asia over a more ancient population similar to Australian Aborigines and Melanesians/Papuans. Populations beyond the Solomon Islands should be similar to the island SE Asians.

"Our findings suggest that Andamanese populations don't have a different origin than other Asian populations,contrary to the hypothesis of a first Out-of-Africa that would populate the Andaman Islands"

I think the great southern coastal migration theory has been well and truly debunked. In fact it has never stood up to real scrutiny. For example tha Andaman Islands have probably only been settled within the last 30,000 years or less. And their made Y-DNA, D, is not present in South Asia apart from the in relatively recently arrived Tibeto-Burman speakers.

"Their phenotypical differences are mainly due to strong selection on specific type of genes"

Selection would be considerable because islands support populations of limited size.

"Could it be that they mistaking Denisovan genes for Neanderthal?"

Probably not. I think researchers have a pretty good handle on the differences between the two. Mind you they would share many genes with each other, and with modern humans.

Ramber said...

Out of topic: what is the percentage of ssa in northwest african and east african components in eurogene calculators? what about the north african in gedmatch? is it the same thing as northwest african?

Davidski said...

You can calculate this by cross checking your results with SSA scores from calculators that don't have any north/northeast/northwest African clusters.

Vincent said...

@terryt

"And their made Y-DNA, D, is not present in South Asia apart from the in relatively recently arrived Tibeto-Burman speakers."

False. Cordaux et al. (2004) reported that 2 out of 30 Koragas (a tribal group in South India) have DE (neither D nor E tested). It could very well be D*, D2 - M226.2 or, why not, DE*.

http://hygienecentral.org.uk/pdf/Cordaux%20Forensic.pdf

Davidski said...

Y-chromosome studies from as far back as 2004 are unreliable unless you're just wanting frequencies of the most common haplogroups.

Vincent said...

I've only shown terryt that DE/pre-D is present in South Asia(xTibeto-Burmans). I'm certainly not claiming that its real frequency is 7% as in this study (it could be though, given their population size of ~17.000).

terryt said...

"Cordaux et al. (2004) reported that 2 out of 30 Koragas (a tribal group in South India) have DE (neither D nor E tested). It could very well be D*, D2 - M226.2 or, why not, DE*".

Thanks for the link but all I see is two YAP positives were found. Not necessarily pre-D. Could be the same as Andaman Island D*. To me DE is unlikely. And the haplotype could well have come in with a Tibeto-Burman population from which some males moved south, perhaps by sea if it is in fact Andaman D.

capra internetensis said...

@Vincent

Why not plain old E? In Arunkumar's study of 1680 men from Tamil Nadu, 5 had E, none had D.

terryt said...

"Why not plain old E?"

Quite possible. I didn't think of that.

Arch Hades said...

The British paper looks very interesting. Does this mean the Celtic speakers of Britian were more Mediterranean-like?

Krefter said...

@Arch,

I think it means the Celts of Britain could have some type of genealogical connection to South Europeans(which ones?).

"By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that samples from the Anglo-Saxon period are relatively more closely related to central northern Europe, while earlier samples and contemporary British samples are relatively more closely related to Southern European populations."

The DNA files of 3 of those Celts have been online for many months. They are pretty much identical to Irish, but also very similar to all North Sea people(British, Scandinavian).

This quote from those abstracts is the most interesting to me.

"While six of the Roman burials show affinity with modern British populations, one sample, although indistinguishable in funerary ritual from the other skeletons in the cemetery, shows a clear signal of exogenous origin, with modern affinities pointing towards the Eastern Mediterranean"

The Roman empire was a high-way for the ancient world. I think there's clear East Mediterranean admixture in all of the former Roman empire of Europe.



Grey said...

@Krefter

The Romans described different physical looks among the Celtic tribes so I think it happened before they arrived with Atlantic Megalith and Bell Beaker (or even Pheonicians maybe). The connection with Iberia and beyond due to tin and copper.

http://en.wikipedia.org/wiki/Mining_in_Cornwall_and_Devon#Stone_Age_and_early_Bronze_Age

Krefter said...

@Grey,
"The Romans described different physical looks among the Celtic tribes so I think it happened before they arrived with Atlantic Megalith and Bell Beaker (or even Pheonicians maybe)"

During the Neolithic Iberia and Britain were basically the same. What makes modern Iberians differnt from British is more Neolithic blood, but back then that difference didn't exist. So, Megalithic would be added on top of native British, when Eastern Euro-blood arrived.

Tacitus was just one person. I've seen plenty British-descended people who look Spanish, including my grandpa who's as North Sea-genetically as you can get. Hinxton4 had AA in rs12913832, while just under 5% of modern North Euros do. HGDP Orcadian is mostly brown eyed.



Grey said...

Krefter

"I've seen plenty British-descended people who look Spanish"

That's my point. Romans saw *different* looking people among the native tribes already when they arrived: northern looking in some parts and Mediterranean looking in other parts which makes me think it happened earlier.

(The Romans may have added to it.)

Krefter said...

@Grey,

Whatever, I don't think there's much to discuss here. I guess that's possible, just it must have happened after the Neolithic. It could just be Tacitus is unreliable.