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Post by djoser-xyyman on Sept 6, 2018 8:25:35 GMT -5
Studies to look out for Sept2018
O–DHP–02
Modelling early human lineages in Africa
P. Skoglund1, A. Bergström1
1Francis Crick Institute, London, United Kingdom
Admixture graph models of population history provide a comprehensive framework to reconstruct the
ancestry of ancient and present-day genomes. However, current approaches for admixture graph
inference of population history from larger sets of populations rely on limited searches of the
full possible space of graph models, usually based on a priori historical hypotheses. We introduce
a **new** approach for **automated** searches of admixture graph space through the high-throughput
simulation and evaluation of random graphs, allowing the interrogation of potentially millions of
graphs even for larger sets of populations. We apply this heuristic framework to reconstruct the
diversification of early modern human lineages using ancient genomes from Africa, and find support
for previous evidence of deep structure within west African ancestry that may reflect some of the
earliest diversifications of population lineages contributing to present-day populations. However,
we also find that modelling early African and non-African lineages using ascertained SNP data
captured in ancient samples is complicated by ascertainment schemes biasing comparisons between
populations. Specifically, such ascertainment schemes—including ascertainment in African
populations—overestimate the genetic differentiation of African- and non-African populations and
distort population relationships compared to high-quality genomes. Instead, we show that
outgroup-ascertainment of polymorphisms in Neandertal & Denisovan populations provides a largely
Unbiased set of ancestral variants for studying
populations. This ascertainment scheme and set of variants provides a future
resource for ancient genome-wide capture of ancient DNA inside and outside of Africa.
O–DHP–03
Pleistocene North Africans show dual genetic ancestry from the ancient Near East and sub-Saharan Africa
M. van de Loosdrecht1, A. Bouzouggar2,3, L. Humphrey4, C. Posth1, N. Barton5, A. Aximu-Petri6, B. Nickel6, S. Nagel6, E. H. Talbi7
M. A. El Hajraoui3, S. Amzazi8, J. J. Hublin2, S. Pääbo6, S. Schiffels1, M. Meyer6, W. Haak1, C. Jeong1, J. Krause1
North Africa, connecting sub-Saharan Africa and Eurasia, is important for understanding human history. However, the genetic
history of modern humans in this region is largely unknown before the introduction of agriculture. After the Last Glacial
Maximum modern humans, associated with the Iberomaurusian culture, inhabited a wide area spanning from Morocco to
Libya. The Iberomaurusian is part of the early Later Stone Age and characterized by a distinct microlithic bladelet technology,
complex hunter-gathering and tooth evulsion.
Session • Deep human population prehistory
Here we present genomic data from seven individuals, directly dated to ~15,000-year-ago, from Grotte des Pigeons,Taforalt in
Morocco. Uni-parental marker analyses show mitochondrial haplogroup U6a for six individuals and M1b for one individual,
and Y-chromosome haplogroup E-M78 (E1b1b1a1) for males. We find a strong genetic affinity of the Taforalt individuals with
ancient Near Easterners, best represented by ~12,000 year old Levantine Natufians, that made the transition from complex
hunter-gathering to more sedentary food production. This suggests that genetic connections between Africa and the Near East
**predate** the introduction of agriculture in North Africa by several millennia. Notably, we do not find evidence for gene flow
from Paleolithic Europeans into the ~15,000 year old North Africans as previously suggested based on archaeological
similarities. Finally, the Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by
a mixture of genetic components preserved in present-day West Africans (Yoruba, Mende) and Africans from Tanzania
(Hadza). In contrast, modern North Africans have a much smaller sub-Saharan African component with no apparent link to
Hadza. Our results provide the earliest direct evidence for genetic interactions between modern humans across Africa and
Eurasia.
O–DHP–04
Genomic Analysis of an early Homo sapiens from Europe increases complexity of early European demographic structure
E. A. Bennett1, T. Grange1, E. M. Geigl1
1CNRS-University Paris-Diderot, Institut Jacques Monod, Paris, France
The first modern humans are believed to have entered Europe roughly 45,000 years ago. Recent genomic studies have shown
that two of the oldest sapiens remains in Eurasia, a 37,000-42,000 year old individual from present-day Peştera cu Oase,
Romania (Fu et al., 2015), and a 45,000 year old man from Ust'-Ishim in Western Siberia (Fu et al., 2014), share no direct
lineage with modern Europeans, while a few thousand years later, individuals such as the 37,000 year old remains from
Kostenki, Russia (Fu, et al., 2016), 35,000 year old remains from Goyet in Belgium (Fu et al., 2016), and all subsequent remains
are ancestral to present-day European populations. This early foundation of the current population structure is supported in
East Asia by the 40,000-year-old Tianyuan, who is more closely related to modern East Asians than to ancient or modern
Europeans (Yang, et al., 2017).
These individuals represent at least four distinct populations inhabiting Eurasia 37,000 years ago. However, with so little data,
their true number and the interactions between these early migrant populations during this key period of prehistory is difficult
to discern. In addition, poor DNA preservation and the rarity of skeletal material from this region and time make analyses
challenging. We present genomic data from a 37,000-year-old European, recovered from poorly preserved material (the DNA
having a 40 base pair average fragment length and very low endogenous content) using a combination of several recent
advancements in DNA extraction, purification and library construction techniques. These results enrich our current
understanding of human migrations into Eurasia, early European population structures, and the roots of Upper Paleolithic
industries, and serve to bring into better focus our picture of Europe"s first Homo sapiens inhabitants.
The aboriginal heritage project and the modern human colonization of Australia
J. Teixeira1, R. Tobler1, Y. Souilmi1, P. Kusuma2, P. Bover1, B. Llamas1, A. Rohrlach3, J. Tuke3, N. Bean3, J. Soubrier1
A. Abdullah-Highfold4, S. Agius4, A. O’Donoghue4, I. O’Loughlin4, P. Sutton4, F. Zilio4, K. Walshe4, A. Williams5, C. Turney5
M. Williams1, S. Richards1, R. Mitchell6, E. Kowal7, J. Stephen8, L. Williams9, W. Haak10, F. Racimo11,12, F. Ricaut13, M. Cox14
P. Hallast15,16 , H. Sudoyo2, A. Cooper1
1Australian Centre for Ancient DNA, Adelaide, Australia
The Aboriginal Heritage Project is a collaboration between the Australian Centre for Ancient DNA (ACAD), the South Australian
Museum (SAM), and Aboriginal communities across Australia, which aims to reconstruct the genetic history of Aboriginal
Australia. The project leverages SAM"s unique collection of >5000 hair samples and extensive ethnographic and genealogical
data collected during the University of Adelaide Board for Anthropology Expeditions between 1926-1963. A family and
community based consultation program encouraging participation has received overwhelming support, and allows informed
consent to be gained from hair sample donors, or their descendants. This dataset therefore provides a unique opportunity to
address the population history of Aboriginal Australians, from the Out-of-Africa migration until arrival and settlement in Sahul
~50kya. Our prior analysis of 140 mitochondrial genomes from hair samples collected in Queensland, South Australia and New
South Wales revealed that the initial peopling of Sahul comprised a single, rapid migration along the east and west coasts that
reached southern Australia by >49-45 kya – producing pronounced regional patterns still evident today that suggest the
continuous presence of populations in discrete areas since the original colonisation. Here, we present novel key results to
unveil the detailed population genetic history of Aboriginal Australians. First, Y-chromosome analysis reveals that there are
differences in male- and female-specific migration patterns across Australia, with males moving more often across the
continent. Furthermore, we analyse whole-genome low coverage sequencing data for ~60 unrelated individuals and integrated
this with genetic data from populations in PNG and Indonesia, shedding new light on the migration routes traced by the first
human occupants of Sahul.
O–AMG–02
The impact of reference bias on ancient DNA studies of prehistoric human populations
T. Günther1
1Uppsala University, Uppsala, Sweden
High quality reference genomes are an important resource in genomic research projects. In palaeogenomic studies of human
populations, mapping against the human reference genome is used to identify endogenous human sequences in sequencing
libraries built from ancient human remains. The linear human reference genome represents a single haploid sequence carrying
only one allele at each variant site. A consequence is that DNA fragments carrying the reference allele map over-proportionally
or with higher quality scores. This reference bias can have effects on population genomic downstream analysis when
heterozygous sites are falsely considered homozygous for the reference allele. Due to DNA preservation, ancient DNA studies
usually operate with low sequencing coverages where a variant site is often covered by a single sequencing read only.
Furthermore, fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp
reducing the amount of accepted mismatches between reference and sequenced read. These ancient DNA specific properties
represent limitations for calling the allelic state of the individual potentially exacerbating the impact of reference bias on
downstream analysis.
I investigate reference bias in published ancient DNA sequence data of prehistoric populations. Comparing different strategies
for mapping and data filtering, I illustrate how reference bias can influence the results of downstream analyses such as
population affinities and heterozygosity estimates. The goal is to start a discussion on the potential impact as well as strategies
to mitigate reference bias in ancient DNA studies.
O–AMG–03
Estimation of ancient Nuclear DNA contamination using breakdown of Linkage Disequilbrium
N. Nakatsuka1, E. Harney1, S. Mallick1, N. Patterson2, D. Reich1,2,3
1Harvard Medical School, Genetics, Boston, MA/United States
2Broad Institute, Cambridge, MA/United States
3Howard Hughes Medical Institute, Boston, MA/United States
Ancient DNA (aDNA) has been a revolutionary technology for inferring human history, but inferences can be distorted by
sample contamination during the excavation and handling of samples. Methods for measuring contamination based on
mitochondrial DNA can provide inaccurate assessments of contamination due to high variability across DNA extracts in the
ratio of mitochondrial to nuclear DNA; thus, direct nuclear contamination estimates are important. The best current method
for estimating rates of contamination in aDNA using nuclear genome data focuses on detecting polymorphism on the X
chromosome in males, but this is not effective in females. Methods based on autosomal DNA have been developed for
modern DNA, but these require genotype array data of uncontaminated samples, accurate knowledge of the sample"s
population allele frequencies and/or knowledge of all potential contaminant individuals" SNP genotypes, which are generally
not available for aDNA.
Here we report a novel method for estimating autosomal aDNA contamination using patterns of linkage disequilibrium (LD).
Our algorithm is based on the idea that sequences from a contaminating individual will diminish the LD within the sample
individual, because they are from different haplotypes and therefore should have no LD with the authentic ancient DNA
sample. We use reference panels from 1000 Genomes populations to attain approximate background haplotype and SNP
frequencies and estimate contamination by fitting a maximum likelihood model where contamination and the expected test
sample"s haplotype distribution produce the observed sample"s haplotype distribution.
Our method accurately infers contamination generated in simulations using widely divergent 1000 Genomes populations and
is highly correlated with X chromosome estimates in real ancient samples. The estimates have standard errors less than 2.0%
for contamination of 10% or higher in samples with at least 500,000 reads covering SNPs, and we obtained unbiased estimates
in samples with as low as 16,000 reads. This tool should allow users to detect samples with 5% or more contamination with
high confidence. The software is publicly available online (link to be provided by the time of the meeting).
O–AMG–04
Inferring the selection history of Europe over the last 10000 years using a novel statistical approach
L. Ormond1, J. Bloecher2, K. Kirsanow2, Z. Hofmanova3, K. Wang4, J. Mendoza1, S. Figarska5,6, S. Stefanovic7, T. Terberger8
J. Orschiedt9, J. Burger2, G. Hellenthal1
1University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, London, United Kingdom
2Johannes Gutenberg University Mainz, Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Mainz, Germany
3University of Fribourg, Department of Biology, Fribourg, Switzerland
We describe an efficient new Bayesian statistical model to identify selection in admixed populations using allele counts from
Single Nucleotide Polymorphisms (SNPs) in low and/or high coverage ancient and/or modern genome data. This novel
approach accounts for demography and variation in coverage across loci and samples, and also infers proportions of ancestry
relating populations (e.g. due to admixture) and levels of genetic differentiation among groups. The program can provide both
selection probabilities for individual SNPs and/or jointly test sets of SNPs (e.g.in pathways) for selection effects. We
demonstrate the model's utility through simulations, and showcase its ability to identify previous targets of selection using
DNA from prehistoric and modern humans.
We apply our method to a large dataset of ancient and modern genomes, including 75 previously** unpublished data **from
ancient genomes, that span hunter-gatherer and Neolithic early farmer populations from 12,000 years BC through until the
late Bronze Age. We identify the time periods over which individual SNPs have experienced selection, and we assess the
evidence for selection in sets of SNPs associated with diet, immunity, skin pigmentation and the metabolic syndrome,
illustrating the evolutionary constraints on populations at critical periods throughout the history of Europe.
MitoBench & MitoDB – novel interactive methods for population genetics of human mitochondrial DNA
J. Neukamm1,2,3, A. Peltzer3,4, A. Achilli5,6, O. Balanovsky7,8, C. Barbieri9,10, M. Bodner11, F. Gandini12, E. Macholdt13, A. Olivieri5
M. Pala12, W. Parson11,14, M. B. Richards12, S. Schönherr15, M. Stoneking13, A. Torroni5, M. van Oven16, H. Weissensteiner15
V. Zaporozhchenko7, K. Nieselt3, W. Haak4
Although nuclear human genomes have become more accessible due to modern next-generation sequencing technologies, the
survey of mitochondrial DNA (mtDNA) variation in population genetics, especially in ancient DNA studies, remains extremely
informative. A plethora of methods and tools for mtDNA analysis exist, but typically rely on different file formats and often
require manual interaction with the data for downstream analysis steps that can be rather cumbersome and result in an
increased risk of errors in analytical processing. Furthermore, it is typically difficult to obtain suitable comparative data.
Although many public and in-house databases are available, they generally encompass only partially overlapping subsets of all
available samples, sometimes with different extents of missing information. Moreover, the number of complete mitogenomes
is growing exponentially, from both modern and ancient populations, making it difficult for scholars in the field to keep up
with the available information. To tackle these issues, we present MitoBench and MitoDB.
MitoBench is a workbench to interactively analyze and visualize complete mitochondrial genomes with a focus on population
genetic applications. The graphical user interface is kept simple to make it suitable also for users** without **prior knowledge of
computational methods. Additional information such as metadata and summary statistics are provided. Currently, MitoBench
offers automatic file conversion tools to connect the workbench with existing analysis software such as BEAST, Arlequin, and
others as well as some basic analysis methods such as Fst calculation and principal component analysis.
Moreover, MitoBench is linked to MitoDB, a database of mitochondrial DNA reference data. The current prototype
encompasses 2,504 complete mitogenomes from the 1000 Genome Project and will be extended continuously. MitoDB also
offers users to register and upload their own datasets to collaborate and share their data with other researchers.
Our ultimate aim is to provide a central reference database of population genetics studies on mtDNA that can be easily
accessed via the workbench, enabling users to perform typical analysis procedures much faster, more reliably and more
conveniently than before.
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Post by djoser-xyyman on Sept 6, 2018 9:13:42 GMT -5
P–001
Migration and social organisation studies through ancient genomic analysis of multi-faith populations from Medieval Sicily
(ERC Project Sicily in Transition, SICTRANSIT)
A. Monnereau1, P. Orecchioni2, A. Molinari2, M. Carver1, C. Speller1
1University of York, Archaeology, BioArCh, York, United Kingdom
2University of Rome 2 (Tor Vergata), Rome, Italy
Introduction: The Middle Ages (6th to 13th century) in the Mediterranean area witnessed successive conquests bringing with
them new social rules, and ideological regimes, whether Christian or Islamic. The SICTRANSIT project examines the impact of
these ideological transitions in Sicily, combining archaeological, molecular, anthropological, ceramics and Isotopic studies.
Sicily is an ideal location to study these questions: at the confluence of the East, West and Arab world, Sicily has witnessed
four major changes from Byzantine to Aghlabid to Fatimid to Norman to Swabian. Each of these transitions potentially brought
new networks of exchange, new social rules as well as new groups of migrants with their own genetic patrimony.
Objectives: In this project, we apply ancient DNA analysis to over 50 samples from human remains spanning the 6th to 13th
century from different sites in Sicily, in order to: 1) examine evidence for genetic continuity / discontinuity or for large scale
population shifts over this key period; 2) identify the relationship between Medieval populations and contemporary Sicilians;
3) to determine to what extent population affinity is linked to faith-based identity (Christians/Muslims cemeteries).
Methods: We extract DNA from petrous bones, long bones or teeth, build double-stranded libraries and sequence them using
a whole-genome approach. We characterise the proportion of endogenous DNA, and assess patterns of authenticity based on
sequence length and misincorporation patterns. We apply the programs LASER (PCAs) and ADMIXTURE to examine similarity
to modern populations (HDGP dataset).
Results: Preliminary analyses of both teeth, long and petrous bones, indicate a range of sample preservation, ranging from 0%
to at least 15% endogenous DNA. Average fragment length and damage estimates are consistent with authentic ancient
template. For samples with low endogenous DNA preservation, only sex identification could be accomplished. For high quality
samples, nuclear data produced estimates of ancestry, including at least one individual of West African descent.
Conclusion: This ongoing project brings new information for reconstructing human migration in the Mediterranean during the
Middle Ages and its consequences on spatial allele variation in the modern population, as well as new insight into faith-based
identity.
P–002
Kinship relationships and genomic origins of the peoples buried in an early Medieval cemetery in central Europe
D. Díez del Molino1,2, M. Krzewinska2, A. Juras3, M. Chyleński4, L. Pospieszny5, A. Götherström2
Historical cemeteries represent valuable sites to study the economic, political and social structures of the populations living on
an specific epoch in time and in a particular geographical location. The richness of archaeological finds and wealthy artifacts
that have been found in this early Medieval cemetery in central Europe, including high-quality jewelry, ornaments, coins and
amulets, suggest that those buried there probably had a high social status. At the same time, many of the burials seemed to be
composed of couples, suggesting that the cemetery was used for an elite of dwellers and their families in the context of
important trading routes. In this study we used ancient DNA techniques to sequence the complete nuclear genomes of more
than 20 individuals buried in a cemetery that was used for a period comprising about a hundred years (950-1050 AD). We
analyze the social structure and funerary practices of the population they represent by disentangling close kinship
relationships between the individuals. We also use this data together with an extensive panel of European reference samples,
evidence from archaeological material, and patterns of strontium isotopes, to explore the origins and genetic affinities of the
peoples buried in the cemetery, and to place them in the broader genetic context of the peoples of the Middle Ages in Europe.
Ancient genomes from Iceland reveal the making of a human population
S. S. Ebenesersdottir1
1deCODE genetics, Reykjavik, Iceland
Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using
genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and
admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in
Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive
genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic
gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily
useful for the discovery of genotype-phenotype associations.
P–004
Ancient genome-wide analysis of the early Neolithic mass grave individuals from Talheim, Germany
L. Granehäll1, C. Wurst1, J. Wahl2,3, A. Zink1, F. Maixner1
The Talheim mass grave is one of the earliest evidence of violent massacres of Early Neolithic Farmers in Europe. An
excavation in 1983 unearthed 34 individuals dated to the Linearbandkeramik Culture (LBK, approx. 5000 BC). Two-thirds of the
individuals displayed severe head trauma, in positions to the back and right of the skull indicating that they were attacked
from behind. Individuals of all age groups and both sexes were discovered suggesting that the mass grave contained an entire
population, killed and buried at the same time. Anthropological analyses suggested a possible kinship between the individuals,
and a strontium isotope analysis showed that at least three of the adult individuals had been born in another geographical
location. Altogether, the current data point to the massacre of a complete community from a late LBK village.
In this study, we perform a molecular analysis of the Talheim individuals aiming to determine their genetic sex and to infer a
possible kinship structure. First shotgun data of petrous bone samples from 29 of the individuals indicate the presence of
ancient human DNA (up to 61% endogenous content) with relatively low overall mitochondrial contamination rates.
Preliminary analyses of the uniparental markers indicate possible paternal as well as maternal relationships among some of
the individuals. In order to extend the kinship analysis, we will combine high throughput sequencing with an enrichment
capture to analyse both autosomal genetic variants and the complete mitochondrial genomes. The planned in-depth genetic
characterisation of the Talheim individuals will provide a unique snapshot of the family structure of an LBK population which
may further help to understand this violent massacre.
P–006
Why were 17 people buried in a well in 12th century Norwich? – genome-wide analysis of Medieval human remains from
Chapelfield, Norwich, UK
T. Booth1, S. Brace1, Y. Diekmann2, Z. Faltyskova2, M. Thomas2, I. Barnes1
1Natural History Museum, Earth Sciences, London, United Kingdom
2University College London, Department of Genetics, Evolution and Environment, London, United Kingdom
In 2004 human remains were recovered from a spoil heap of construction work on the Chapelfield shopping centre in Norwich,
UK. Archaeological investigations discovered that the bones had come from a circular shaft that had probably constituted the
bottom of a well. Excavation of the well shaft produced a disarticulated comingled assemblage of human remains representing
at least 17 individuals (six adults and 11 children). The stratigraphic relationships between the skeletons combined with
radiocarbon dating and pottery typology indicated that the bodies had been buried over a short period of time in 12th-13th
Centuries AD, and possibly deposited in a single event. The well was located close to the Jewish quarter of the Medieval city,
which may be significant given that late-12th Century Britain is notorious for documented incidents of violence towards Jewish
communities. However, there were no detectable signs of trauma on the Chapelfield bones. Possible alternative explanations
for this unusual burial event include a local epidemic, famine or a divergent form of funerary treatment afforded to certain
individuals because of their economic, social or religious circumstances. Here we present genome-wide shotgun and capture data from the Chapelfield human remains. All individuals analysed show
greatest affinities with modern Ashkenazi Jewish and **Southern European?** populations.Chronological modelling of radiocarbon
dates using Bayesian inferences produce a range centred on 1190 AD, the date of a historical massacre of Jews in Norwich. We
infer that the individuals recovered from the Chapelfield site do indeed represent victims of a documented anti-Semitic
pogrom. Most recent palaeogenomic studies have been concerned with demographic processes that took place over hundreds
or thousands of years, but this result demonstrates their power in producing dramatic material evidence of single historical
events. In providing information on a European Jewish people who lived before the Medieval population bottleneck, these
data will also facilitate novel insight into their ancient population history, including admixture with other European groups.
P–007
Ancient DNA from Misión Salesiana, Tierra del Fuego
A. Stone1, S. Winingear1, J. Motti2, M. Nieves-Colon1,3, K. Harkins4, P. Garcia Laborde2, R. Guichon2
Beginning in 1492 and lasting even today, the encounters between Europeans and Native American populations have had
major demographic, social, biological and ecological impacts. While first discovered by Europeans in 1520, European
settlement of Tierra del Fuego did not begin until the second half of the 19th century. Analysis of biological data from a
cemetery population at Misión Salesiana ("Nuestra Señora de la Candelaria") in Tierra del Fuego provides insight into the local
population history in this region of South America after contact. Misión Salesiana was established in 1893 to assimilate and
Christianize the remaining local indigenous population, the Selk"nam. The mission cemetery includes burials from the
community as well as the mission, averaging ~100 years old. Samples of tooth and bone from 32 individuals were used for DNA
extraction. In-solution hybridization capture was successfully used to recover the mitochondrial genomes from 25 individuals.
Mitochondrial lineages C and D are predominately represented in the sample (appearing in 50% and 41% of the individuals,
respectively). Two individuals have haplotypes which are found in European populations, which is reflective of either
admixture or interment of European individuals in the mission cemetery. The whole mitochondrial genome data were
analyzed for measures of diversity and the cemetery population was compared to other South American populations, both
ancient and modern. These studies of diversity yield insight into both inter and intra group variation in Native South American
populations. Genome-wide SNP analyses are currently in progress
P–009
Reconstructing the demographic history of dingoes using ancient genomic data
S. Y. Kwong1, Y. Souilmi1, K. J. Mitchell1, E. H. Reed2, A. Cooper1
1University of Adelaide, Australian Centre for Ancient DNA, Adelaide, Australia
2University of Adelaide, Earth Sciences, Adelaide, Australia
The dingo is a dog-like quadrupedal mammal native to Australia. Due to its morphological similarity to modern domestic dogs,
it is generally considered to be either a member of Canis familiaris (the domestic dog) or a separate but closely related species
within the Canis genus. However, the precise taxonomy and evolutionary history of the dingo remain a subject of controversy.
It has been challenging to reconstruct the demographic history of dingoes using modern genomic data due to recent
admixture with European dogs. Here we present whole-genome data (17X) from a dingo fossil dated between 993-1146 CE
(95% CI) excavated from a cave beneath the Nullarbor Plain. Population genomic analyses of our ancient data place the dingo
within the diversity of various modern village dog breeds from Island South-East Asia (ISEA), and in particular suggest that the
dingo is closely related to village dogs from Vietnam and Borneo in addition to the New Guinea Singing Dog (a wild dog
population). Our results confirm the dingo"s status as a member of Canis familiaris, settling a decades long debate about the
dingo"s taxonomy. Further, we suggest that the****** ancestor of the dingo originated in central Africa***** and migrated across Asia into
South Asia, finally arriving in northern Australia via islands including Borneo. From that point, the species began to proliferate
across the Australian continent. To determine the dingo"s population split time from ISEA dogs we computed the FAB statistic
using our ancient dingo data along with genomic data from modern New Guinea Singing Dogs and Basenji (a domestic dog
breed). Simulated data were generated via msprime and Approximate Bayesian Computation was used to compute a 95%
credible interval of the population split time. From this we constructed an informed demographic model depicting the dingo"s
evolutionary history from the common ancestor of dogs.
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Post by djoser-xyyman on Sept 6, 2018 13:52:54 GMT -5
To edit...in the future
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Maternal genetic origin of the Avar period (7th century) nomadic elite in the Carpathian Basin
V. Csáky1, D. Gerber1,2, A. Szécsényi-Nagy1, B. G. Mende1, G. Csiky3, I. Koncz4, T. Vida4
1Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Laboratory of Archaeogenetics, Budapest, Hungary
2Eötvös Loránd University, Department of Genetics, Budapest, Hungary
3Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
4Eötvös Loránd University, Institute of Archaeological Sciences, Budapest, Hungary
A nomadic group known as Avars migrated from the Inner-Asian steppes and arrived at the Carpathian Basin in 568 AD, where
they have founded the empire called as Avar Khaganate. The Avar population were heterogeneous in anthropological and
archaeological characters, while the debate about their Asian connection is long present in the archaeological research and
their genetic origin is still unknown. The previous studies of the control region of mitochondrial DNA of a small Avar groups
showed mixed Eurasian genetic composition with predominant European elements.
In our study we investigated 27 Avar period individuals from Danube–Tisza Interfluve with a primary focus on the elite,
distinguished by richly furnished burials and certain prestige artefacts. The skulls of these individuals showed Mongoloid
craniometric traits in different extent. The aim of our research was to describe the maternal genetic composition–based on
whole mitochondrial genomes–of the leading stratum of the 7th century Avar population.
The isolation and DNA-library preparation, as well as the capture methods and sequencing on Illumina MiSeq platform were
performed in the Laboratory of Archaeogenetics of IA RCH of Hungarian Academy of Sciences in Budapest. The results were
evaluated with descriptive population genetic and statistical methods, as well as with phylogenetic analyses.
The mitochondrial genome sequences of the investigated samples from 11 different cemeteries encompass the entire range of
the Eurasian haplogroups with a dominance of Asian lineages, which represent 64 % of the variance. The haplogroup based
analyses (PCA and Ward-type clustering) shows Asian, especially Central-Asian character of the Avar period elite. The sequence
based analyses (MDS) and also phylogenetic results reflect the East-Asian and Central-Asian genetic connections as well.
Our results correspond to the anthropological and archaeological, historical assumptions about the Central-Asian connection
of the Avar elite, that has been attested by certain artefact types known from the Eurasian steppe and appearing in the
Carpathian Basin only after the Avar conquest. Moreover, it provides even more detailed information, how a nomadic elite
even after settling, remained part of the connection network of the Eurasian steppe and valued its tradition by preserving its
maternal genetic ancestry through generations
P–013
Indian genetic heritage in Southeast Asian populations
P. Changmai1, E. Altınışık1, E. Yüncü1, O. Flegontova1, J. Kampuansai2, W. Kutanan3, H. Pamjav4, S. Schiffels5, D. Reich6
P. Flegontov1
1Faculty of Science, University of Ostrava, Department of Biology and Ecology, Ostrava, Czech Republic
2Faculty of Science, Chiang Mai University, Department of Biology, Chiang Mai, Thailand
3Faculty of Science, Khon Kaen University, Department of Biology, Khon Kaen, Thailand
4 Institute of Forensic Genetics, Budapest, Hungary
5Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
6Harvard Medical School, Department of Genetics, Boston, MA/United States
Mainland Southeast Asia (MSEA) is a region which has a high linguistic diversity and complex population history. Over a
hundred of languages from 5 language families are spoken in MSEA. Anthropological and archaeological evidence suggested
multiple waves of migration into this region. Early states in MSEA were established with a substantial cultural influence from
India. Indian influence persisted and became fundamental for the regional cultures. Here we analyzed new genome-wide
genotype data for 12 populations from Thailand, along with published data for other MSEA populations. Results of allele
frequency-based and haplotype-based methods reveal Indian admixture in Thai, Cambodians, Mon, Khmer, and some other
Austroasiatic speakers which are historically linked to the early Indianised states, while Indian admixture is absent in
Austroasiatic speakers which are hill tribes (Htin) and hunter-gatherer populations (Mlabri and Maniq). The results support the
hypothesis that the Indian gene flow actually came with Indian culture. We further constructed admixture graphs to
investigate the spread of Tai-Kadai languages in MSEA. A best-fitting model among more than 10,000 models tested showed
that the present-day Central Thai originated via admixture of a local population closely related to present-day Austroasiatic
speakers (already having Indian admixture) and a population closely related to Tai-Kadai speakers from South China, with the
later population contributing slightly more than 50%. After this admixture event, the descendant population received a further
pulse of Indian gene flow. Thus, the Central Thai population has an elevated Indian admixture proportion, as compared to local
Austroasiatic-speaking groups. We were not able to model the Central Thai population without a local Austroasiatic-speaking
population as an ancestry source. This result clearly contradicts previous studies based on uniparental markers (mitochondrial
DNA and Y chromosome) which suggested demic diffusion of Tai-Kadai-speaking populations from China with a minimal level
of admixture with local MSEA populations.
P–014
Genetic identity and relatedness of pre-Dogon and early Dogon populations (Mali)
N. Dlamini-Stoll1, J. Krause1, A. Mayor1
1University of Geneva, Genetics and Evolution, Geneva, Switzerland
For over two millennia, the Dogon Country in central Mali has experienced constant interactions of groups of people from
different cultural domains. The subject of identity of these early inhabitants of the region, before the arrival of the Dogon
people around the 15th century AD, remains unclear. Our current bio-archaeological research focuses on questions concerning
the identities, genetic relationships and relatedness of pre-Dogon and modern Dogon populations, as well as their mobility,
ways of life, diet and health.
Within this research, we also evaluate the genetic contribution of the ancient pre-Dogon populations on current Dogon
people. To address this question, 48 ancient DNA samples belonging pre-Dogon and early Dogon individuals dating between
the 13th and 16th c. AD are currently being analysed. All samples come from Cave C, the largest of the sepulchral burial caves
found in the Bandiagara Escarpment, containing more than 3 000 buried individuals. This paper will present the results of the
aDNA analyses in order to shed light on people"s origins and relatedness.
P–034
Search for Plasmodium spp. in ancient Sardinian Populations
M. Michel1
1MHAAM, Harvard University , Department of Human Evolutionary Biology, Cambridge, United States
Robust evidence indicates that malaria has exerted a strong selective pressure on the human genome, leading to the
emergence of multiple resistance alleles across human populations. The historical record attests to the presence of malaria
throughout large parts of the Mediterranean until the modern era; in Italy, for example, malaria remained endemic until the
20th century, when government-sponsored interventions eradicated P. falciparum from its last reservoirs in Palermo province
in Sicily.1 Despite the evolutionary and historical importance of this pathogen, genomic evidence regarding the distribution of
Plasmodium spp. in the ancient world remains limited. Previous studies have identified P. falciparum DNA in skeletal remains
from two Roman sites in southern Italy (Vagnari, 1st-4th century CE, and Velia, 1st-2nd century CE),2 and a PCR-based
investigation reported a P. falciparum amplicon from a 5th century site in Umbria.3 Given these successes and the long history
of malarial endemicity in Italy, this study investigates the presence of Plasmodium DNA in individuals from ancient Sardinia.
This study includes samples from two sites, Villamar and Monte Sirai, located in south-central and southern Sardinia,
respectively. Both sites date to the Punic period, with radiocarbon dating of samples ranging from 805-540 calBCE for Monte
Sirai and from ~800-400 calBCE for Villamar. At Monte Sirai, 14C dates for multiple burials appear to fall within the same
temporal interval, raising the possibility of a pathogenic cause of death. To investigate the presence of malaria at these sites,
DNA from dental pulp was extracted, prepared into libraries, and sequenced via next generation shotgun sequencing.
Metagenomic data was processed using MALT to identify reads matching to known pathogen species. If present, identification
of Plasmodium species will add knowledge regarding the geographic and temporal distribution of malaria in the ancient world.
References
1. Majori, G. Short history of malaria and its eradication in Italy with short notes on the fight against infection in the
Mediterranean Basin. Mediterr J Hematol Infect Dis (2012).
2. Marciniak, S. et al. Plasmodium falciparum malaria in 1st- 2nd century CE southern Italy. Current Biology (2016).
3. Sallares, R., and S. Gomzi. Biomolecular archaeology of malaria. Anc Biomol (2001).
P–035
Clinical metagenomics applied to the Iceman and other mummified human remains
F. Maixner1, F. Boulund2, K. Thorell2, K. Reinhard3, C. Wurst1, L. Engstrand2, T. Rattei4, N. Segata5, A. Zink1
1Eurac research, Institute for Mummy Studies, Bolzano, Italy
2Karolinska Institute, Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
3University of Nebraska-Lincoln, School of Natural Resources, Lincoln, NE/United States
4University of Vienna, CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Vienna, Austria
5University of Trento, Centre for Integrative Biology, Trento, Italy
Clinical metagenomics (CM) combines high throughput sequencing methods with bioinformatics approaches to analyze
modern patient samples. It is considered to be one major component of future clinical analyses that contribute to the
diagnosis and management of several diseases. Beside its potential in the identification of pathogens, CM can identify
community shifts in the human microbiota indicating disease developments such as obesity or cancer.
In a recent study, we screened gastrointestinal (GI) tract biopsies of the Iceman, a 5300-year-old European Copper Age
mummy, for the presence of Helicobacter pylori. By using CM diagnostics and targeted genome capture, we determined the
presence of H. pylori and reconstructed its complete genome. Our study provided, beside the indication for a possible disease
manifestation in the mummy, interesting new details on the origin of the stomach pathogen in Europe. The application of
technological and conceptual advances in the Iceman study has paved the way for future studies on H. pylori in other ancient
human remains. Currently, we are analyzing coprolite material and GI content of precious historical mummies from the
American, African and Asian continents. Furthermore, the Iceman GI tract data indicates the presence of other intestinal
microbiome members, possibly allowing for future reconstruction of a majority of the original GI tract microbiome of the
Iceman.
The application of CM on dated ancient specimens opens a window into the past that enables scientists to address unique
evolutionary research questions. Both reconstructed ancient pathogen genomes, and the composition of ancient microbiomes
will provide new insights into the evolutionary history of bacterial-mediated diseases.
P–047
Ancient DNA and isotopic analysis of archaeological remains from Guam
M. G. B. Foody1, P. W. Ditchfield2, S. H. Ambrose3, J. E. Eakin4, M. Almeida5, D. Vieira5, A. Brandão6, T. Rito7,8, J. O. S. Hackland9
L. B. Aguon10, R. F. Y. Blas10, M. Pala1, R. L. Hunter-Anderson11, M. B. Richards1, S. J. Oppenheimer12, P. Soares5, C. J. Edwards12
1Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, United Kingdom
2School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, United Kingdom
3Department of Anthropology, University of Illinois, 607 S Mathews Avenue, Urbana, IL/United States
41005 Headingly NW, Albuquerque, NM/United States
5Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
6Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
7Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
8ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
9Department of Biomedical Sciences, University of California Riverside, Riverside, CA/United States
10Department of Parks and Recreation, Guam Historic Resources Division, 490 Chalan Palasyo, Agana Heights, Guam 96910, Guam
111513 Wellesley Drive NE, Albuquerque, NM/United States
12School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, United Kingdom
Guam, located in the tropical north-western Pacific, is the largest island in Micronesia and the most southerly of the Mariana
Islands. While linguistic and modern DNA studies have inferred that the ancestors of the indigenous Chamorros were southeast
Asian migrants who arrived as early as 2,000 BC, geology and archaeology indicate that the first human groups arrived
500 years later.
Marianas prehistory is divided by archaeologists into two main periods: Pre-Latte (c. 1,500 BC to AD 1000) and Latte (AD 1000–
1521). For the first thousand years of the Pre-Latte Period, human interment was not practiced. The Naton Beach Site, on
Guam's leeward west coast, represents the earliest dated burial and permanent settlement.
Stable isotopic analyses on bone collagen carbon and nitrogen, and tooth enamel oxygen, carbon and strontium, have been
completed on seven ancient individuals from the Naton Beach Site. One of these individuals has been radiocarbon dated to the
late Pre-Latte period, 774–509 cal. BC; a time associated with a distinctive pottery style that disappeared from the
archaeological record around 900 years later. After a "transitional" era of several centuries, the Latte Period began,
characterised by different ceramics, uniquely shaped stone pillar house foundations, and the cultivation of rice – all cultural
traits that were not found elsewhere in Oceania at that time.
Genome-wide analysis is currently underway for two individuals from the Naton Beach cemetery. The resulting data will be the
first ancient DNA from Guam's oldest burial site. Both uni-parental and autosomal genetic information will be used to assess
possible migration routes of the first settlers of Guam. The resulting data will be compared to the modern Chamorro
population (n = 14) and other Micronesian populations (10 Nauru and 10 Kiribati) to determine potential genetic continuity, as
well as the possible source of the people bringing the Latte culture to Guam. Mitochondrial haplotypes will be compared to 80
full mitogenomes from modern Micronesian populations, including previously published data from the western Pacific.
P–056
Phenotypic inference based on ancient DNA of Iron Age individuals from Luistari in Southern Finland
A. D'Aurelio1,2, K. Majander2,3,4, H. Etu-Sihvola5, L. Arppe5, T. C. Lamnidis3, M. J. Oinonen5, J. Krause3,4, P. Onkamo2,6
E. Salmela2,3
1University of Rome Tor Vergata, Department of Biology, Rome, Italy
2University of Helsinki, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Helsinki, Finland
3Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
4University of Tübingen, Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, Tübingen, Germany
5University of Helsinki, Laboratory of Chronology, Finnish Museum of Natural History, Helsinki, Finland
6University of Turku, Department of Biology, Turku, Finland
Introduction: Among the potential uses of ancient DNA (aDNA) data is the prediction of ancient individuals' phenotypes. Such
knowledge can complement the insights gained from archaeological, osteological and stable isotope analyses, thus
illuminating for example the morphology, health and disease of past populations and individuals.
Objectives: The aims of our study are threefold: first, expanding the set of phenotypes typically inferred from aDNA data;
secondly, estimating the effect of various factors - such as sequencing coverage and the genetic architecture of the
phenotypes - on the confidence of the phenotype prediction; and third, applying these insights in the phenotype inference of
ancient individuals from Finland.
Methods: We studied six individuals (5 males, 1 female) from the archaeological site of Luistari, Eura in Southern Finland.
Based on radiocarbon dating, these individuals originate from the 8th to 13th centuries AD. After DNA extraction, indexed
libraries were prepared, enriched for a genome-wide set of 1.2 million single-nucleotide polymorphisms (SNPs) using insolution
capture, and sequenced on an Illumina HighSeq 4000 instrument. A set of 118 SNPs were chosen from this dataset,
including loci for frequently inferred phenotypes such as hair or eye color and lactose tolerance as well as loci contributing to
other potentially interesting phenotypes. The genotypes of these SNPs were obtained by samtools command mpileup, and the
phenotype inference was done by manual inspection of the genotypes of each individual. Genotype probabilities were
calculated based on the read depth of the observed variant(s) and the variant frequencies from the modern Finnish
population.
Results: The number of successfully genotyped SNPs was 10-43 per individual. Despite the low sequencing coverage (average
read depth 1.7 for the genotyped SNPs), 50% of these genotypes could be inferred with reasonably high certainty (> 85%). The
corresponding phenotypes range from physical appearance (hair and eye color) to diseases and metabolic features.
Conclusion: Phenotype estimation based on ancient DNA can produce information that is potentially highly relevant both
individually and in the context of population history. However, the availability of such insights is limited by a combination of
data quality (low sequencing coverage) and the true complexity of phenotypes.
P–058
The genetic makeup of enslaved Africans from early Colonial Mexico City
R. Barquera1,2, D. I. Hernández-Zaragoza2,3, N. B. Felipe4, T. C. Lamnidis1, V. Acuña-Alonzo6, L. Márquez-Morfín5, J. Krause1
1Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
2Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
3Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
4Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
5Osteology Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
The multiple ethnic roots of the modern day Mexican populations are largely a result of genetic admixture among Africans,
Europeans, Native Americans and Asians during the New Spain period. Although the presence of people of African origin and
their descendants in diverse historical periods in Mexico is documented through exhaustive historical studies, little has been
done to look into the African roots that came into the Americas from a genetic perspective, especially outside of the
populations bearing the most African ancestry according to modern DNA data. Here we used an archaeogenetic approach, by
analyzing ancient human genomes, including uniparental markers, together with strontium isotopes and ethnohistorical
information to track down the origins of three enslaved Africans from Mexico City buried at the San José de los Naturales
Royal Hospital (Hospital Real de San José de los Naturales). Uniparental markers, HLA haplotypes and admixture estimates
point to a common West African origin for the three individuals, whereas D-statistics show that despite their genetic
relationship to human groups speaking Niger-Congo languages, they all have different genetic origins. When taken together,
the molecular evidence allowed us to provide insights into the origin of these three individuals who were probably among the
first enslaved Africans to reach the central plateau of New Spain in the 16th century.
The early history of Neanderthals and Denisovans
A. Rogers1
1University of Utah, Anthropology, Salt Lake City, UT/United States
We use Legofit to study the past several hundred thousand years of human evolutionary history. Our results show that (1)
Neanderthals and Denisovans separated early in the Middle Pleistocene; (2) their ancestors survived a bottleneck of
population size; (3) 3-8% of Denisovan DNA derives from a "hyperarchaic" population that separated from other hominins
about 2 mya; (4) about 1% of Neanderthal DNA derives from the ancestors of modern humans. Our results also (5) support
previous estimates of gene flow from Neanderthals into modern Eurasians.
This work was supported by grant BCS-638840 from the National Science Foundation and by the Center for High-Performance
Computing, University of Utah.
P–064
Patterns of ancient DNA preservation in a Palaeolithic human tooth from Les Cottés Cave, France
M. Hajdinjak1, M. Soressi2,3, J. J. Hublin3, M. Meyer1
1Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
2Faculty of Archaeology, Leiden University, Leiden, Netherlands
3Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Leipzig, Germany
Introduction: The scarcity of human remains from the beginning of the Upper Palaeolithic in Europe, and the small number of
individuals from which genome-wide data has been obtained, make it difficult to reconstruct the genetic history of early
modern humans and late Neandertals. A particular challenge stems from the small amounts of endogenous DNA and high
proportions of microbial and present-day human contamination.
Objectives: The human molar investigated here comes from the backdirt of previous excavations at the Les Cottés cave and
cannot be associated with a particular archaeological context. As the site contains a well-dated stratigraphy of Mousterian,
Châtelperronian, Protoaurignacian and Early Aurignacian, we aimed to determine to which hominin group the tooth belongs
and to reconstruct relationship of this individual to archaic hominins, as well as ancient and present-day humans.
Methods: Initially we removed removed 17.6 mg of dentine for DNA extraction. Three additional samples of 18, 20 and 25 mg
of dentine were removed from three different spots in order to investigate whether sampling other parts of the specimen may
improve the yield of ancient human DNA.
Results: The mitochondrial genome of the tooth reconstructed from putatively deaminated DNA fragments falls basal to the
haplogroup R, and using 10 securely dated ancient modern humans as calibration, we estimated it to be 46,060 years old (95%
HPD: 31,098 to 62,221 years BP). Attempts to analyze the nuclear genome of the specimen by direct sequencing of the first
sample were hampered given that not more than 0.2 human genomes could be recovered and that 89% of the nuclear
sequences derived from modern human contamination. The subsequent DNA extracts varied by several orders of magnitude in
their content of nuclear genomes (0.06, 0.17 and 4.3-fold genomes) and the levels of present-day human contamination (13%,
0.2% and 0%). We are currently reconstructing large parts of the nuclear genome from the extract that yielded most ancient
DNA, and that illuminate the relationship of this individual to ancient and present-day populations.
Conclusions: Our results illustrate that DNA preservation can vary greatly within one specimen and that the removal of
multiple small sub-samples instead of one larger sample, coupled with decontamination procedures can drastically improve
the likelihood of isolating sufficiently pure and large enough amounts of DNA for comprehensive genetic analyses.
P–083
Mitogenomic data indicate Central Asian origin of the Hungarian conquerors admixed with Srubnaya descendants
T. Török1, E. Neparáczki1, Z. Maróti2, T. Kalmár2, K. Maár1, P. Bihari3, I. Nagy3, E. Fóthi4, I. Pap4, î Kustár4, G. Pálfi5, I. Raskó6
A. Zink7
1University of Szeged, Department of Genetics, Szeged, Hungary
2University of Szeged, Department of Pediatrics and Pediatric Health Center, Szeged, Hungary
3SeqOmics Biotechnology Ltd., Mórahalom, Hungary
4Hungarian Natural History Museum, Department of Anthropology, Budapest, Hungary
5University of Szeged, Department of Biological Anthropology , Szeged, Hungary
6Biological Research Centre, Institute of Genetics, Szeged, Hungary
7EURAC, Institute for Mummies and the Iceman , Bolzano, Italy
Introduction It has been widely accepted that the Finno-Ugric Hungarian language was brought into the Carpathian Basin in
the late 9th century by the conquering Hungarians. Based on linguistic arguments it was expected that the Conquerors may
show more genetic affinity to other Uralic speaking groups than modern Hungarians.
Objectives Ancient DNA research makes it possible to trace the origin and genetic relation of prehistoric individuals and
populations. In order to shed light on the genetic origin of the Conquerors we sequenced more than 100 mitogenomes from
the earliest Conqueror cemeteries and compared them to sequences of all publicly available modern and ancient databases.
Methods We used the Next Generation Sequencing method combined with hybridization enrichment. Phylogenetic method
was applied to find the closest matching mitogenome sequences to that of individual Conquerors. We have created ancient
and modern Eurasian mitogenome population databases to identify populations with most similar mitogenome composition to
the Conquerors. Besides conventional population genetic methods we also used novel algorithms called Shared Haplogroup
Distance and MITOMIX, which are especially suitable to uncover past population admixtures.
Results Phylogenetic analysis revealed that about one third the Conqueror maternal lineages derived from Central-Inner Asia,
from a territory corresponding to the ancient Xiongnu empire. The most similar population to the Conquerors are modern
Volga Tatars, which according to historical and anthropological sources most probably derives from Onogur ancestors of both
groups. Population genetic analysis indicated that their East Eurasian component can be traced back to ancestors of modern
Tuvans, Buryats and Central Asians, while their West Eurasian component most likely originated from the Bronze Age
Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe.
Conclusion Our data indicate that all potential ancestors of the Conquerors were steppe nomadic people derived from
multiple sources. Their ultimate East Eurasian source may be linked to the Xiongnus, which was brought to the Pontic steppe
most probably by Onogur groups, which then admixed there with other nomads. Available data imply that the Conquerors did
not have a major contribution to the gene pool of the Carpathian Basin, raising doubts about the Conqueror origin of
Hungarian language
P–091
Population dynamics at Late Chalcolithic and Early Bronze Age Arslantepe, Anatolia
E. Skourtanioti1, J. Choongwon1, Y. S. Erdal2, M. Frangipane3, P. W. Stockhammer1,4, M. Burri1, J. Krause1, W. Haak1,5
1Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
2Hacettepe University, Department of Anthropology, Ankara, Turkey
3Sapienza University of Rome, Dipartimento di Scienze dell’Antichità, Rome, Italy
4Ludwig-Maximilians-University of Munich, Institut für Vor- und Frühgeschichtliche und Provinzialrömische Archäologie, Munich, Germany
5The University of Adelaide, Australian Centre for Ancient DNA, Adelaide, Australia
While Anatolia was highlighted as the genetic origin of early Neolithic European farmers, the genetic substructure in Anatolia
itself as well as the demographic and cultural changes remain unclear. In eastern Anatolia, the archaeological record reflects
influences from North-Central Anatolia, the northeastern sectors of Fertile Crescent and the Caucasus, and suggests that some
of these were brought along with the movement of people. Central to this question is the archaeological site of Arslantepe
(6th-1st millennium BC), strategically located at the Upper Euphrates, the nexus of all three regions. Arslantepe also developed
one of the first state societies of Anatolia along with advanced metal-technologies. Archaeological research suggests that
conflicts with surrounding groups of pastoralists affiliated to the Caucasus might have contributed to the collapse of its palatial
system at the end of the Chalcolithic period (4th millennium BC). To test if these developments were accompanied by genetic
changes, we generated genome-wide data from 18 ancient individuals spanning from the Late Chalcolithic period to the Early
Bronze Age of Arslantepe. Our results show no evidence for a major genetic shift between the two time periods. However, we
observe that individuals from Arslantepe are very heterogeneous and differentiated from other ancient western and central
Anatolians in that they have more Iran/Caucasus related ancestry. Our data also show evidence for an ongoing but also recent
confluence of Anatolian/Levantine and Caucasus/Iranian ancestries, highlighting the complexity of the Chalcolithic and Bronze
Age periods in this region.
P–093
Tiwanaku – exploration of the population's characteristics, provenance and changes for the pre-Columbian culture upon the
Lake Titicaca using genetic methods
D. Popovic1, M. Baca1, G. Agresti1, D. Ulloa1, M. Ziolkowski2, M. Molak-Tomsia3
1University of Warsaw, Centre of New Technologies, Warsaw, Poland
2University of Warsaw, Centre for Precolumbian studies, Warsaw, Poland
3Polish Academy of Sciences, Museum and Institute of Zoology, Warsaw, Poland
Tiwanaku was a culture that flourished in the Lake Titicaca Basin between 4th and 11th century AD and made one of the most
significant cultures of the Pre-Columbian times. We intend to generate low coverage genomic data and mtDNA genome
sequences from human remains excavated from archaeological sites to explore some of the unresolved aspects of Tiwanaku
culture such as: (i) Where did the victims of ritual human sacrifices made during religious rituals in the Akapana ceremonial
center come from. Archaeological research suggests that the victims were non-locals and most probably warriors captured
during military raids. (ii) How and why did the settlement pattern change happen after the demise of Tiwanaku culture. The
obtained genetic data will allow to determine the relationships and affinities between the individuals and populations, the
provenance of the particular individuals as well as the direction and source of gene flow between the studied populations. To
this point we obtained sequences of mitochondrial genomes from 33 individuals representing Tiwanaku and post-Tiwanaku
periods. We used this data to test whether there are signs of demographic change after the demise of Tiwanaku culture.
P–094
Paleogenomics of populations in France, from the Neolithic to the Bronze Age
S. Brunel1, L. Cardin2, D. Garraud2, E. M. Geigl1, T. Grange1, M. Pruvost3
1Institut Jacques Monod, Paris, France
2Institut de recherche criminelle de la gendarmerie nationale (IRCGN), Pontoise, France
3PACEA UMR5199, Bordeaux, France
Expanding from Anatolia into Europe about 7,500 years ago, the Neolithic culture based on agriculture followed two different
routes, through the Balkans along the Danube northwards to the Hungarian plain and from there westwards to arrive in the
Parisian Basin, and along the coastline of the Mediterranean basin to arrive in Southern France and Spain. Both migration
waves eventually reached the territory of present-day France, where the Neolithic culture further evolved and was later
replaced by the Bronze Age culture, over the course of the third and second millennia BC. While France is a geographic
crossroads that provided multiple opportunities for interaction between populations of different origins, as is well
documented by the archaeological record, the underlying demographic processes were not yet explored at a territory-wide
scale .
Here we present the complete mitochondrial genomes, Y chromosome markers and genotypes on a number of nuclear loci of
interest obtained through a DNA enrichment approach of 163 Mesolithic, Neolithic and Bronze Age individuals sampled from
three regions of present-day France, the North, the East, and the South. This study provides, for the first time, a highresolution
4000-year transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes
associated with known phenotypes. This transect that comprises two major cultural transitions (Mesolithic-Neolithic and
Neolithic-Bronze Age), reveals contrasting population dynamics between northern and southern France. The study of 120
nuclear SNPs, covering both physical and physiological traits, allowed us to follow the evolution of the allelic frequency over
time of several phenotypes that characterize modern Europeans. This study fills a large gap in the understanding of the
peopling of western Europe from the Mesolithic to the Bronze Age, completing the knowledge of the global process of the
Neolithization of Europe.
P–096
Genomic diversity of ancient individuals from the Iceman´s territory in the Eastern Italian Alps
V. Coia1, C. Wurst1, A. Paladin1, G. Cipollini1, F. Maixner1, A. Zink1
1EURAC Research, Institute for mummy studies, Bolzano, Italy
Since the prehistory, the Eastern Italian Alps have been a meeting point for people with different origin. Various cultural
material as well as funerary rituals documented in this region during the Copper Age (~3700-2200 a.C), suggests several
contacts with non-local cultures from east and west Europe during that time. The Tyrolean Iceman (3360-3100 cal. BC) is the
best representative of the Copper Age in the Eastern Alps. So far, besides the Tyrolean Iceman, only one Mesolithic sample
(Veneto Dolomites) has been genetically analysed from this area. Therefore, there is a lack of regional ancient genomic data to
better understand the genomic diversity of prehistoric alpine groups. Comparison with ancient and modern samples, have
shown that the Iceman clusters with Early Neolithic farmers from different parts of Europe and with Neolithic individuals from
Anatolia. In addition, European individuals contemporary of the Iceman cluster together. These Copper Age individuals also
differ from the Iceman in their ancestry and admixture patterns, showing different proportions of Neolithic, hunter gatherers
and Eastern (Yamnaya) ancestry components. Since the Iceman alone cannot be considered as representative of the genomic
diversity of this alpine area, we are analyzing in this study seven additional prehistoric individuals from the Iceman´s territory.
Two samples have approximately the same dating of the Iceman while the other are dating to the Middle Neolithic and to the
Copper-Early Bronze Age. The new data will give us the opportunity to better understand the genomic diversity of Eastern
Italian Alps and the Iceman´s genetic history. Furthermore, with additional genomic data from this crucial South-eastern
European area, we will contribute to know more about the main demographic events that occurred in prehistoric Europe. First
shotgun analyses of four pars petrosa samples indicate high percentage of endogenous content (from ~9% to 52%) and low
mitochondrial contamination rates. All individual will be now further subjected to deeper sequencing aiming to perform
genome-wide comparative analyses with the Iceman and a dataset of European and Near Eastern ancient individuals.
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