Provisional program

TALKS AND POSTERS -- PLENARY SESSIONS

December 8 and December 10, 2016

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TALK PLENARY SESSIONS

Genetic History of the Dutch population

ALTENA Eveline1, Risha Smeding1, Thirsa Kraaijenbrink1, Kristiaan van der Gaag1,2, Eileen Vaske1, Paul Reusink1, Anna Friedler1, Yoan Diekmann3, Mark G. Thomas3, Peter de Knijff1.

1 Forensic Laboratory for DNA Research, Dept. of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.

2 Current address: Dept. biologische sporen, Netherlands Forensic Insitute, Den Haag, the Netherlands.

3 Dept. of Genetics, Evolution and Environment, University College London, London, UK.

Although the Netherlands is a small country, previous studies indicated complex geographic patterns of genetic variation in the modern Dutch population. Based on archaeological and historical evidence, and the dynamic Dutch landscape, it is most likely that patterns of genetic variation in the modern population were primarily shaped since medieval time. A clear understanding of when and how the modern patterns emerged, however, requires genetic data from historic Dutch populations.

We analyzed several Dutch archaeological population samples from different locations and from a time range between the early medieval period and the post-medieval period. This collection of nearly 800 skeletons was examined for autosomal, Y-chromosomal and mitochondrial variation. The resulting dataset, together with comparable data from more than 2000 modern Dutch individuals, allows us to review our historical genetic past in detail, both in time and space. Finally, we test for population continuity by statistical modelling of frequency changes in mitochondrial and Y-chromosomal haplogroups.

 

TALK PLENARY SESSIONS

RECONSTRUCTING HUMAN DIFFUSION AND COLLAPSE IN THE AMERICAS

BARBIERI Chiara1, Ghirotto Silvia2, Arias Leonardo3, Sandoval Jose4, Sevini Federica5, De Fanti Sara6, Franceschi Zelda7, Franceschi Claudio5, Luiselli Donata6, Stoneking Mark3, Fujita Ricardo4, Heggarty Paul1, Powell Adam1

1 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany

2 Department of Life Sciences and Biotechnologies, University of Ferrara,

Ferrara, Italy

3 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

4 Centro de Genetica y Biologia Molecular, Universidad San Martin de Porres (USMP), Lima, Peru

5 C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy

6 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy

7 Dipartimento di Storia Culture Civiltà, University of Bologna, Bologna, Italy

The Americas, with their relatively recent history of population diffusion and collapse after European contact, represent an ideal case-study for testing the genetic footprints left by demographic changes. Native American mtDNA genomes have been successfully employed to reconstruct the timing and magnitude of the initial population expansion into the continent. However, previous studies were based on collections of individual lineages and were missing actual population samples. This limited perspective lacked the resolution to explore regional population spread and diversification. Furthermore, the recent collapse was not adequately tested in populations with different prehistories and in different regions.

In this study we focus on Meso- and South-America to explore 1 the diversification of populations who crossed the Isthmus of Panama into South America and 2 the traces of a recent demographic collapse in various sets of population mitogenomes. Our dataset comprises 320 full mtDNA genomes from 13 populations from Mesoamerica and from different ecogeographic regions of South America: the Andes, Amazonia and the Gran Chaco. A Bayesian approach is employed to reconstruct population demographies and to test different scenarios of expansion and collapse.

Our results suggest different prehistories for the populations studied, irrespective of their geographic location. Similarities between Mesoamerican and Andean populations indicate a possible connection on the Pacific coast, which is tested with spatially-informed simulations. Coalescent simulations support the recent collapse in most of our populations, helping us to understand the impact of recent events on population mitogenomes.

In conclusion, populations in the Americas experienced different demographic trajectories and strong diversification, which possibly drove the high cultural and linguistic diversity reported today. Including mtDNA genomes from modern populations along with ancient samples promises to shed light into the past of the Americas and into the demographic dynamics behind population divergence.

 

TALK PLENARY SESSIONS

A Bronze Age lineage dominates the Y-chromosome landscape in the Iberian Peninsula

F. CALAFELL1, P. Villaescusa2, N. Solé-Morata1, A. Carracedo3, K. Rouault4, C. Férec4, O. Hardiman5, A. Santurtun6, S. Jiménez7, M. F. Pinheiro8, B. M. Jarreta9, M. M. De Pancorbo2

1 Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain

2 BIOMICs Research Group, Lascaray Research Center, University of Basque Country UPV/EHU, Vitoria-Gasteiz, Spain

3 Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain; Galician Foundation of Genomic Medicine (SERGAS), CIBERER (University of Santiago de Compostela), Santiago de Compostela, Spain.

4 Inserm UMR1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest 15 Cedex 2, France.

5 National Neuroscience Centre, Beaumont Hospital, Dublin, Ireland.

6 Unit of Legal Medicine, Department of Physiology and Pharmacology, University of Cantabria, Santander, Spain

7 Institute of Legal Medicine of Alicante, Spain.

8 National Institute of Legal Medicine and Forensic Sciences, Portugal.

9 Laboratory of Genetics and Genetic Identification, University of Zaragoza, Spain.

The genetic landscape of the Iberian Peninsula is dominated (as in the rest of Western Europe) by haplogroup R1b, which comprises two thirds of the Y chromosomes; the rest is divided roughly equally between E-M35, G, I, and J. Within R1b, R1b-S116 (also known as P312 dominates, with ~60% in Spain;it further trifurcates into three major branches having distinct geographical distributions: M529 (L21 radiating from the British Isles, U152 in France, Switzerland and N. Italy, and DF27 in the Iberian Peninsula. DF27 is poorly known, and we have sought to characterize its distribution and diversity, with the aim of reconstructing its history. We have typed DF27 and six of its derived SNPs, as well as 16 Y-STRs in 2,993 males from 32 populations located in Spain, Portugal, France and Ireland; SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project. We confirmed that DF27 is the most frequent haplogroup in Iberia, with an average frequency ~45%, while it dropped to <15% right across the Pyrenees. Within Iberia, it ranged from 40% in most populations to ~75% in Basques. Elsewhere, it showed high frequencies in Colombia and Puerto Rico, which implies it can be used to trace Iberian male migrations into the Americas.

       However, our most striking result is how young DF27 is. We estimated from STR variation that DF27 originated 4,000±150 years ago (ya); it took it just 120 generations to grow to ~12 million carriers in Iberia and ~75 million in Central and South America (assuming just 1/3 paternal Iberian ancestry). This places the origin of DF27 in the early Bronze Age, and at least 2,000 years after the arrival of the Neolithic, which was supposed to be the last major event that shaped the European genetic landscape. The DF27 expansion may be part of a global trend, in which bursts of male lineages have been observed at different periods, and in different geographical regions (Poznik et al. 2016.

Poznik et al. 2016. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 486:593-9

 

TALK PLENARY SESSIONS

Genomic insights into the settlement of Australia by modern humans

Laurent Excoffier and the Australian Genome consortium
Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland
Swiss Institute of Bioinformaics, 1015 Lausanne, Switzerland

The exact settlement history of Sahul (Australia, New Guinea and Tasmania) remains largely unknown. Indeed, there is still an intense discussion on whether the ancestors of Australo-Papuans left Africa earlier than Eurasians, and the exact divergence time and levels of gene flow between Australian Aborigines and Papuans are uncharacterized. A detailed analysis of high-coverage genomes of 83 Aboriginal Australians and 25 Papuans from the New Guinea Highlands reveals that Sahul was colonized by the ancestors of Australo-Papuan more than 50 kya and that these two groups diverged 25-40 thousand years ago (kya), with very little subsequent gene flow. The fact that this divergence occurred long before the separation of Australia and Papua (only some 10Kya), suggests the existence of an ancient population structure in Sahul. Moreover, all studied Pama-Nyungan speaking Aboriginal Australians seem to descend from a single founding population that differentiated as early as ~10-32 kya. At odds with a previous genomic study, we have no evidence for two exits out of Africa, but we infer an early divergence of Australian and Papuan ancestors from Eurasians, about 57 kya. Interestingly, the evidence for a single exit out of Africa is only found if we explicitly take into account archaic admixture in Australo-Papuans.

 

TALK PLENARY SESSIONS

DISSECTING THE ROLE OF DEMOGRAPHY AND NATURAL SELECTION IN SHAPING THE GENOMIC BACKGROUND OF LOW- AND HIGH-ALTITUDE NEPALI POPULATIONS FROM THE GAURISHANKAR REGION

GNECCHI RUSCONE Guido Alberto 1, JEONG Choongwon 2, DE FANTI Sara 1, TRANCUCCI Michela 1, GENTILINI Davide 3, DI BLASIO Anna Maria 3, CHILDS Geoff 4, CRAIG Sienna R. 5, BASNYAT Buddha 6, SHERPA Mingma G. 7, SHERPA Phurba 7, MARINELLI Giorgio 8, NATALI Luca 8-9, PELUZZI Davide 8, BEALL Cynthia 10, DI RIENZO Anna 2, PETTENER Davide 1, LUISELLI Donata 1, SAZZINI Marco 1

1 Laboratory of Molecular Anthropology & Centre for Genome Biology, Dept. of Biological, Geological and Environmental Sciences, University of Bologna, Italy

2 Department of Human Genetics, University of Chicago, United States

3 Center for Biomedical Research & Technologies, Italian Auxologic Institute IRCCS, Milan, Italy

4 Departement of Anthropology, Washington University in St. Louis, United States

5 Department of Anthropology, Dartmouth College, Hanover, United States

6 Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal

7 Mount Everest Summitter’s Club, Rolwaling, Dolakha, Nepal

8 Explora Nunaat International, Montorio al Vomano, Teramo, Italy

9 Italian Institute of Human Palaeontology, Rome, Italy

10 Anthropology Department, Case Western Reserve University, Cleveland, United States

Adaptation to high-altitude has been extensively studied in Himalayan populations by searching for signatures of natural selection on the Tibetan and, to a lesser extent, Sherpa genomes. Recent studies have also pinpointed how demographic processes (e.g. archaic introgression and/or population admixture) might have played a role in the spread of genetic variants favourable at high-altitude. Nepali populations from the Gaurishankar mountain range represent an intriguing case study to test such interplay between demography and natural selection in shaping the distribution of these adaptive traits. In fact, this region hosts populations belonging to three main ethnic groups distributed along a wide altitudinal range (900-4,900 m). People speaking Indo-Aryan languages are culturally related to Indian populations and live at low altitudes. Groups speaking Tibeto-Burman languages (i.e. Tamangs and Sherpas) are instead supposed to descend from Tibetan populations and to have moved to Nepal in historical times. While Tamangs have largely spread across Gaurishankar valleys up to medium altitudes, local Sherpa communities mainly settled in few high-altitude villages in the Rolwaling valley.

Patterns of population structure and genomic relationships of these groups with 1,152 additional Sherpa, Tibetan, South Asian and East Asian subjects belonging to 72 populations were inferred from genome-wide data generated for more than 700,000 SNPs on 75 individuals collected during three field expeditions.

Evidence of extensive admixture was found in low-altitude Indo-Aryan speaking groups, with East-Asian ancestry components presumably introduced by Tibeto-Burman migrants. These latter groups have instead experienced limited (or null in the case of Sherpas) gene flow from local Nepali populations, with Tamangs showing closer affinity to Tibeto-Burman people settled in Northeastern India than to high-altitude Rolwaling Sherpas or Tibetans. This picture suggests a more complex distribution of East Asian ancestry components in Nepali populations with respect to what previously thought.

Searching for shared or unique selective events underlying high-altitude adaptation in the Gaurishankar Tibeto-Burman groups was finally performed to further disentangle the differential role played by demography and natural selection in shaping the genomic background of these Himalayan populations.

This work was supported by ERC-2011-AdG295733 to DP?, NSF Award 1153911 to CMB, NSF Grant BCS-0924726 to ADR.

 

TALK PLENARY SESSIONS

132 microhaplotypes fully evaluated on 83 POPULATIONS (provisional title)

KIDD Kenneth K. et al.

University of Yale, USA

Abstract to be announced.

 

TALK PLENARY SESSIONS

The sea-nomad Bajo: Origin, dispersal, and adaptation.

KUSUMA Pradiptajati1,2, Nicolas Brucato1, Murray P. Cox3, Phillipe Grangé4, Thierry Letellier1, Herawati Sudoyo2,5, François-Xavier Ricaut1

1 Equipe de Médicine Evolutive, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR-5288, Université Paul Sabatier - Toulouse III, Toulouse, France

2 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia

3 Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

4 Institut Universitaire Asie-Pacifique, UFR des Lettres, Langues, Arts et Sciences Humaines, Université de la Rochelle, La Rochelle, France

5 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia

The Indonesian archipelago has been a home for sea-farer experts and sea nomads since the Austronesian expansion era, as late as 4,000 years ago. Among them, the sea-nomad Bajo occupy widely the coastal areas in a multitude of different islands until nowadays. The Bajo are known to be a mobile boat-dwelling people to do trading in distant places, and diving in the deep sea to fish to make living. Although many Bajo communities live in far-distanced locations, they share a common culture, notably marked by a unique language: The Sama-Bajaw, a language that belongs to the Malayo-Polynesian branch of Austronesian language family. Their relative cultural homogeneity tends to balance their constant interactions with diverse ethnic groups with which they live closely geographically (e.g. the Dayak and Banjar in Borneo, the Bugis in Sulawesi, etc.). This appears to be often assumed as inter-cultural marriages and integration of non-Bajo individuals into the community (“maritime creolization”), leading to a presumption that, despite a common cultural identity, the Bajo genetic diversity is heterogeneous. In addition to the absence of any archaeological and/or written history of the Bajo, this apparent complexity is the reflection of the absence of consensus on the geographical origin, as well as the scenario of the Bajo dispersal. To provide insights on these questions, here we present the autosomal genome-wide SNPs study on three Bajo communities (n=73, living in coastal area of 1 Kotabaru island, Southeast Borneo, 2 Derawan archipelago, Northeast Borneo, and 3 Kendari, Southeast Sulawesi, separated with minimum straight line distance of 690 km. We compared the data to an exhaustive dataset from published data and our newly generated data from ethnic populations of interest known to interact with Bajo communities (i.e. the Samihim and Banjar in southeastern Borneo, the Bugis and Mandar in Sulawesi, and North Maluku people), composed in total of 2,890 individuals. Our results show that the genetic diversity of the sea nomad Bajo, similar to linguistic evidence, reveal a nearly identical identity across far-distant communities, revealing a recent gene flow and/or common ancestry. Moreover, our analyses indicate a clear scenario of dispersal within the Indonesian archipelago. Finally, we examined whether their particular way of life, on the frequent sea-dwelling and long-period sea-fishing, have left genetic traces by selective pressure.

 

TALK PLENARY SESSIONS

Genes mirror migrations and cultures in prehistoric Europe
Jakobsson
Mattias
University of Uppsala, Sweden
Genomic information from ancient human remains is beginning to show its
full potential for learning about human prehistory. I review the last few years’ dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. The early times, the upper Paleolithic, appears to contain several population turn-overs followed by more stable populations after the Last Glacial Maximum and during the Mesolithic. Some 11,000 years ago the migrations driving the Neolithic transition start from around Anatolia and reach the north and the west of Europe millennia later. This event is followed by major migrations during the Bronze age. These findings show that culture and lifestyle were major determinants of genomic differentiation and similarity in pre-historic Europe rather than geography as is the case today.

 

TALK PLENARY SESSIONS

THE RISE AND FALL OF A POPULATION: GABON

MANNI Franz 12  and John Nerbonne 21

1 Musee de l’Homme, Paris, France

2 University of Groningen, The Netherlands.

Abstract to be announced.

 

TALK PLENARY SESSIONS

Human dispersal and inbreeding avoidance in Inner Asia

MARCHI Nina1, Tatiana Hegay2, Philippe Mennecier1, Tchodouraa Mikhaïlovna Dorjou3, Boris Chichlo1, Laure Ségurel1, Evelyne Heyer1

1: Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France

2: Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan

3: State University of Tuva Republic, Kyzyl, Russia

Inbreeding is the biological consequence of reproduction between closely related individuals. It results in an increase in the number of homozygous sites within genomes and a decrease in genetic diversity. This can reveal recessive deleterious alleles associated with genetic diseases, decrease fertility and impede the adaptive response of individuals. In humans, two strategies can limit inbreeding. First, individuals can migrate out of their native group and mate inside a new group, which corresponds to geographic exogamy. Second, in the absence of dispersal, individuals can mate within their groups according to specific matrimonial rules.

In Inner Asia, multiple human populations with contrasted social organisations and different levels of geographic exogamy cohabit. This area therefore represents an interesting opportunity to test for the presence of inbreeding avoidance strategies. In this study, we collected both ethnological and genomic data for 369 men and 177 women in 18 populations from Inner Asia (Uzbekistan, Tajikistan, Kyrgyzstan, Siberia and Mongolia). This allowed us to detect the presence of geographical exogamy for each couple and to estimate the genetic inbreeding of each individual.

First, based on genetic estimates, all populations are less inbred than under random mating, suggesting they all have some strategies to avoid inbreeding. Second, we found that the proportion of exogamous couples was highly variable between populations, from 0% to 72%. Furthermore, we found that the endogamous populations are less inbred than the exogamous ones. Moreover, mostly or entirely endogamous populations are organized under a cognatic society while mainly exogamous populations are patrilineal. Social organization (patrilineal or cognatic), correlated to differences in dispersal behaviours, seems to lead to different patterns of genetic inbreeding.

 

TALK PLENARY SESSIONs

Reconstructing the genetic and adaptive history of Bantu-speaking populations in Africa and North America

PATIN Etienne1,2,3, Marie Lopez1,2,3, Rebecca Grollemund4, Guillaume Laval1,2,3, Christine Harmant1,2,3, Hélène Quach1,2,3, Laure Lémée5, Béatrice Régnault5, Nathaniel J. Dominy6, George H. Perry7, Luis B. Barreiro8, Alain Froment9, Paul Verdu10, Evelyne Heyer10, Jean-Michel Dugoujon11, Luis Pereira12,13,14, Lolke Van der Veen15, Patrick Mouguiama-Daouda15, Jean-Marie Hombert15, Lluís Quintana-Murci1,2,3

1 Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France; 2 Centre National de la Recherche Scientifique URA3012, 75015 Paris, France; 3 Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France; 4 Evolutionary Biology Group, School of Biological Sciences, University of Reading, Reading RG6 6BX, England; 5 Eukaryote Genotyping platform, Biomics Pole, Institut Pasteur, 75015 Paris, France; 6 Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA; 7 Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA; 8 Université de Montréal, Centre de Recherche CHU Sainte-Justine, H3T 1C5 Montréal, Canada; 9 Centre National de la Recherche Scientifique UMR 208, Institut de Recherche pour le Développement, Muséum National d’Histoire Naturelle, 75005 Paris, France; 10 Centre National de la Recherche Scientifique UMR7206, Muséum National d’Histoire Naturelle, Paris 75005, France; 11 Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique FRE 2960/Université Paul Sabatier, Toulouse, France; 12 Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal; 13 Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal; 14 Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS), Porto 4050-313, Portugal; 15 Centre National de la Recherche Scientifique UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France

The Bantu language family includes ~310 million speakers in Africa, yet the genetic and adaptive history of Bantu-speaking populations remains largely unexplored. We genome-wide genotyped 1,318 individuals from 35 populations of central Africa, covering the homeland of Bantu language expansions.

We demonstrate that Bantu-speaking populations of eastern and southern Africa originate from the south of central Africa, supporting a southward migration of early Bantu speakers across the equatorial rainforest. We show that rapid adaptation of Bantu-speaking populations to newly colonized environments has been facilitated by gene flow from autochthonous populations, particularly at the HLA region.

We estimate that Bantu-speaking populations contributed to 30% of the African ancestry of African Americans, whose genomes present no evidence of positive selection since admixture with European Americans. Our results broaden our knowledge of the complex evolutionary history of sub-Saharan Africa, which will help identifying genetic risk factors for disease in Africans and African Americans.

 

TALK PLENARY SESSIONs

Bringing it all together: ancient DNA provides biological foundation for hypothesized population replacement in the California Channel Islands.
SCHEIB Christiana L., Tori Randall, Jay Stock, Susan Kerr, Amiee Potter, Luca Pagani, Zuzana Faltyskova, John R. Johnson, Joe Lorenz, Phillip Endicott, Toomas Kivisild.
Various affiliations
In the direct path of any Pacific coastal migration into the Americas, there is evidence of human occupation of the California Channel Islands from 13,000 years BP until the early-19th century when local populations were relocated to Spanish missions on the mainland. At the time of contact the southern islands were inhabited by Uto-Aztecan speaking peoples and the northern islands by Chumash speaking people. Patterns of change in the material record and in the morphology of human remains has led to speculation of an Uto-Aztecan expansion from the mainland between 1500 and 3000 years BP replacing earlier Chumash or Hokan speaking groups.
Samples were taken from skeletal remains spanning the last 8,000 years from San Nicolas Island (n=36, San Clemente Island (n=7, Santa Catalina Island (n=2, San Miguel Island (n=2, Santa Cruz Island (n=1, Point Sal (n=17, Santa Barbara (n=1, Baja California, Mexico (n=4, and greater San Diego area (n=17. DNA was extracted from skeletal material and nuclear genomes were shotgun sequenced to an average coverage of 0.01 - 15X per sample. All ancient samples exhibit novel mitochondrial lineages within the known Native American haplogroups A, B, C, and D. All ancient male California samples belong to Y-chromosome haplogroup Q1-L53, the main lineage present in modern Native Americans.
Principal Component analyses based on autosomal markers map all the ancient Californian samples near to a cluster of modern day Native American samples from Central and South America. At finer resolution, autosomal as well as mtDNA analyses allow us to detect in Channel Islanders two distinct clusters that likely correspond to early and recent periods. We use ADMIXTURE, f3, f4, and D statistics to determine the extent of continuity between past and present populations structures and to examine the extent of admixture between the ancient populations in the region.

 

TALK PLENARY SESSIONs

Unraveling the genomic landscape of hominin interaction in Island Southeast Asia.

TUCCI Serena1,2, Benjamin Vernot3, Samuel Vohr4, Joshua Schraiber1, Gludhug Ariyo Purnomo5, Herawati Sudoyo5,6, Guido Barbujani2, Joshua M. Akey1, Richard Edward Green4

1 Department of Genome Sciences, University of Washington, Seattle, Washington, USA

2 Department of Life Sciences and Biotechnologies, University of Ferrara, Italy

3 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

4 Department of Biomolecular Engineering, University of California, Santa Cruz 95064, USA

5 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia,

6 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia

Neandertal and Denisovan sequences have been identified in several populations in Eurasia and Oceania. However, very little is known about the legacy that these archaic species might have left in the genomes of present-day populations in Island Southeast Asia – the region that likely represented the crossroad for modern human migrations into Oceania.

We produced 10 high coverage genomes (>40x) from a population living in the Indonesian Island of Flores; these data represent, to date, the first complete genomes from Indonesia. We used formal tests of admixture, and a newly developed statistical framework ( Vernot et al. 2016, Science) to detect traces of admixture with archaic hominins, that might still be lingering in the Indonesian genomes. We recovered, on average, 225 Mbp of putative archaic haplotypes per individual, and estimated that the Indonesian genomes, in addition to ancestry from Neandertals, might harbor small traces (0.7-1.5%) of ancestry inherited from a Denisovan-related group, likely as consequence of admixture with New Guineans.

Our results contribute to provide new interesting insights into the landscape of hominin interaction, in this part of the world that plays a key role in the understanding of our evolutionary history.

Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., … Akey, J. M.

(2016. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Science 10.1126/science.aad9416

 

TALK PLENARY SESSIONs

The non-paradoxical paradox of recombination hotspots

Úbeda de Torres, Francisco

Reader in Mathematical Biology, School of Biological Sciences

Royal Holloway University of London

Egham TW20 0EX

United Kingdom

Recombination hotspots are small chromosomal regions, where meiotic crossover events happen with high frequency. Due to the nature of the recombination process alleles that prevent recombination are over-transmitted rendering recombination hotspots transient and overall recombination difficult to explain. How is it possible that recombination hotspots (and recombination) persists over evolutionary time when recombination hotspots are self-destructive? This fundamental question is known as the recombination hotspot paradox and has attracted much attention in recent years. Yet, that attention has not translated into a fully satisfactory answer. No existing model adequately explains what maintains the allelic variability in recombination hotspots while permitting over-transmission of the recombination resistant alleles. Here, we formulate a population genetics model for recombination hotspots finding a chaotic dynamic of allele frequency that maintains variability over time. This dynamic accounts for all empirical observations regarding the molecular mechanisms of recombination hotspots. Thus providing a fully satisfactory answers.

 

TALK PLENARY SESSIONs

Interpreting Human Genomic Regions Depleted of Neandertal and Denisovan Ancestry

WOLF Aaron B.1, Benjamin Vernot1,2, Joshua M. Akey1

Department of Genome Sciences, University of Washington, Seattle,

Washington, USA. 2Department of Evolutionary Genetics, Max-Plank-Institute for

Evolutionary Anthropology, Leipzig, Germany

Background: Anatomically modern humans overlapped in time and space with archaic

hominins like Neandertals and Denisovans. It is now established that admixture occurred such that non-African genomes contain ~2% introgressed Neandertal sequence and Oceanians contain an additional ~2%-4% introgressed Denisovan sequence. Strikingly, the distribution of surviving archaic sequence is very heterogeneous, with large regions depleted of it. Such regions are interesting because they may represent loci where archaic sequence was strongly deleterious and rapidly purged from modern human populations. However, depletions of archaic sequence could be due to other factors, such as random genetic drift.

Methods/Results: To better understand the origins of depleted regions we performed extensive coalescent simulations under a wide variety of neutral demographic models and find that demographic history alone is unlikely to explain large (>10Mb) depletions of archaic sequence. We also find significant overlap of regions depleted of Neandertal sequence and those depleted of Denisovan sequence, suggesting depletions at these loci originate from common processes such as recurrent selection against archaic sequence. Furthermore, we show that the largest regions depleted of archaic sequence are significantly enriched for genes expressed in the brain. Interestingly, one region depleted of archaic sequence contains the FOXP2 gene, which is associated with speech and language and carries a regulatory change unique to modern humans.

Significance: Understanding the formation and characteristics of regions depleted of archaic introgressed sequence in modern humans will help interpret how archaic admixture influenced human evolution and what genes may play a role in unique human behaviours.

 

LATE SUBMISSION -- PRESENTATION FORMAT STILL UNDECIDED

Dynamics of clans in human unilineal populations: a genetic approach

ALARD Bérénice1, Ly Goki1, Laurent Romain1, Evrard Olivier2, Bourdier Frédéric3, Lafosse Sophie1, Pavard Samuel1, CHAIX Raphaëlle1.

1 Eco-anthropologie et Ethnobiologie, UMR 7206, MNHN, France

2 Patrimoines Locaux et Gouvernance, UMR 208, IRD, MNHN, Paris, France

3 Développement et Sociétés, UMR 201, Panthéon Sorbonne, IEDES, IRD, Paris, France

Traditional societies are often organized into descent groups, such as clans. In matrilineal populations, the affiliation to a clan is transmitted by the mother and in the patrilineal populations it is transmitted by the father.

In this context, uniparental DNA can be particularly useful for the study of the dynamics of the clans. Indeed, the Y-chromosome is paternally transmitted similarly as the descent group affiliation in patrilineal populations and the mitochondrial DNA is maternally transmitted similarly as the descent group affiliation in matrilineal populations. Thus, if the descent rule is strictly respected, we expect individuals from the same descent group to be genetically related when we look at their Y chromosome (patrilineal populations) or their mitochondrial DNA (matrilineal populations).

We tested this hypothesis in four matrilineal and four patrilineal populations from Southeast Asia. We sequenced the HVS-1 sequence of the maternally inherited mitochondrial DNA (465 individuals), in addition to 17 STRs loci of the paternally inherited Y-chromosome (334 individuals).

We show that women from the same matrilineal clan tend to be more related through their mitochondrial DNA than are men from the same patrilineal clan through their Y chromosome. In other words, in matrilineal populations, there is a strict application of the descent rules compared to patrilineal populations in which the transmission of the affiliation to a clan is more flexible.Thus, genetic data unveil contrasted dynamics for matrilineal and patrilineal clans in South-East Asia.

 

LATE SUBMISSION -- PRESENTATION FORMAT STILL UNDECIDED

Reassessing the influence of social organization on genomic diversity: the case of Austroasiatic populations of South-East Asia

LY Goki, Raphaelle Chaix et al.

1 Musee de l’Homme, Paris, France

Ethnologists have described the impressive complexity of social organizations in human populations, and in particular the complex rules of alliance (which determine mate choice), rules of descent (which affiliate individuals to kin groups), and rules of residence (which indicate where married couples should settle down). The social organization of a population should be of particular interest to population geneticists since it conditions when, where and with whom individuals reproduce and raise their children, and thus impacts gene pool evolution. For the past ten years, geneticists have intended to understand how these rules affect the uniparental diversity of human populations. However, recent studies have found contradictory results and no consensus on the influence of social organizations on genetic diversity exists.

This lack of consensus may result from an approach of social organization focused on rules, that may or may not be followed, rather than on the actual patterns of residence, descent and alliance which are more likely to influence genetic diversity.

We tackled this issue by using a quantitative approach which allow us to delve into the actual patterns of residence, descent and alliance. We investigated the influence of these three components of social organization on uniparental and autosomal diversity in 12 ethnic groups from South-East Asia which exhibit different social organizations. We estimated quantitative variables associated with social organization from ethno-demographic data collected in 535 households and calculated genetic estimators from genomic data of more than 400 individuals for uniparental data and 800 individuals for autosomal data.

As expected, mitochondrial diversity was lower in matrilineal and matrilocal populations than in cognatic populations or in patrilineal and patrilocal populations and was correlated with female migration rates estimated from ethno-demographic data. Unexpectedly, Y chromosome diversity was not different across social organizations. Quantified male migration rates were also similar across social organizations which allow us to understand the lack of difference of Y chromosome diversity. In addition, we detected an influence of descent group structure on uniparental genetic diversity. Consanguinity levels estimated on autosomal data were higher in matrilineal and matrilocal populations than in cognatic populations or patrilineal and patrilocal populations. These higher levels were associated with a higher proportion of within village alliances in matrilineal and matrilocal populations.

Our study highlights the importance of quantifying social organization to better understand its influence on genetic diversity.

 

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Comparing population history inferred from genetic and linguistic data in Central Asia

AUSTERLITZ Frédéric1, Philippe Mennecier1, Remco Bouckaert2, Franz Manni1, Phillip Endicott1, Russell Gray3, Quentin D. Atkinson3, Evelyne Heyer1.

1Unité d'Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS/MNHN/Université Paris Diderot, Paris, France.

2Department of Computer Science, University of Auckland, Auckland , New Zealand

3School of Psychology, University of Auckland, Auckland , New Zealand

Genetic and linguistic contribute to the understanding of the biological and cultural history of human populations. We compared the diversity of Central Asian populations as it is mirrored by this kind of data. These human groups belong to two distinct linguistic families: Indo-Iranian and Turkic. Concerning the linguistic data, we used a modified Swadesh lists of concepts concerning basic vocabulary. Words were classified into cognates, i.e. homologous words related by common ancestry. For genetic polymorphism data, we used mitochondrial DNA sequences, Y-chromosome and autosomal microsatellites. To infer the genealogical tree of the populations the program starBeast has been used for both datasets. We compared the two trees obtained and found that the autosomal microsatellite tree had the best congruence with the linguistic tree. This may reflect the information gained by using many independent loci. Furthermore, the mitochondrial tree shows more congruence with the linguistic tree than the Y-chromosome tree, an interesting result in these populations known to be patrilineal. Finally, we find several populations from one linguistic group to genetically cluster with the other linguistic group, which might reflect specific linguistic replacements.

 

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THE COEVOLUTION OF LANGUAGES AND GENES: TRACKING DOWN MATCHES AND MISMATCHES

Chiara BARBIERI, Russell Gray

Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany

The coevolution of languages and genes represents the ultimate Darwinian paradigm for the reconstruction of population dynamics in time and space, and is still one of the most evoked parallels between cultural and biological diversity. In recent years, scholars have focused on the congruence of linguistic and genetic histories to shed light on population origin, diversification and contact. Popular case studies include the diffusion of major language families, such as Indo-European and Austronesian, but smaller, regional cases of population contact have also been examined.

Mismatches between linguistic and genetic variation are usually disregarded as an exception to the general pattern. But how often do these mismatches actually occur? Can we estimate the incidence of language shift and reconstruct more realistic models of cultural evolution? And which circumstances drive such discontinuities in cultural transmission? To answer these questions we will assemble genetic databases for different regions and we will match the population data collected with relevant linguistic and cultural information. We will correlate these data while controlling for ecological factors and geographic proximity, which are natural constrains on cultural exchange and gene flow.

Preliminary analysis on Europe suggest that language shift could have occurred in 10 or 30% of the populations considered, depending on the genetic dataset used. Cases of genetic discontinuity over regions where the same language is spoken might be associated with the state policies of the past centuries.

Our final aim is to develop a more realistic understanding of the complex mechanisms behind cultural transmission. The change of cultural features through time not only impacts our ability of tracing back human prehistory, but also influences the definition of “population” as the unit of research.

 

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Genetic history of southern African Khoisan populations reveals time dependent intensity of sex-biased gene flow

Vladimir BAJIĆ 1, Arturo Anaya VILLALOBOS 1, Mark STONEKING 1 and Brigitte PAKENDORF (1,2 

1 MPI for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany

2 Laboratoire « Dynamique du Langage », CNRS & Université Lyon 2, 14 avenue Berthelot, Lyon, France

The genetic history of southern African populations is characterized by interactions between indigenous hunter-gatherers and a range of populations that moved into the region in the past 2000 years. The relationships among these populations show different patterns for the paternally inherited non-recombining region of the Y chromosome (NRY), maternally inherited mtDNA, and autosomes, suggesting a complex scenario of sex-biased admixture and population interactions. Here we synergistically use all three lines of evidence (mtDNA, NRY, and genome-wide genetic data) to elucidate the genetic history of Khoisan populations. Our analysis reveals a complex history of multiple admixture events with immigrant food-producing populations. We find high levels of discrepancy between estimates of Khoisan-related ancestry based on the NRY vs. mtDNA as a consequence of heavily male-biased gene flow between the immigrant and autochthonous populations. Furthermore, we demonstrate that populations that experienced more recent admixture also show more heavily sex-biased gene flow.  Finally, we propose a method for uniparental haplogroup ancestry assignment based on autosomal and mtDNA/NRY data. This method can potentially increase the precision of ancestry assignments for haplogroups that are currently uninformative regarding the place of their geographic origin; it can thus be of use in forensics as well as human population studies.

 

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Ancient DNA bares its teeth: What ancient dental calculus can tell us about past populations

BENNET Andrew E., Olivier Gorge, Samantha Brunel, Thierry Grange, Eva-Maria Geigl, Melanie Pruvost

Jacques Monod Institute, Paris, France

The discovery of well-preserved DNA in dental calculus of ancient humans has opened a rich frontier in the reconstruction of past oral microbiomes.  This information has been used to trace the evolution of oral pathogens, origins of antibiotic resistance, and to begin to understand the impact regional variation and dietary practices have had on our oral microbiota over the millennia.

We present a comparative study of metagenomic data from dental calculus recovered from multiple archeological sites in France at various time points from the Neolithic to Middle Ages. We will also discuss the special insights and limitations that accompany this new perspective in the study of past populations.

 

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Genetic diversity and demographic history of Sub-Saharan human populations based on genome- wide markers

BRETON Gwenna, Carina Schlebusch, Lluis Barreiro, Barry S Hewlett, Evelyne Heyer, Alain Froment, George Perry, Himla Soodyall, Paul Verdu, Mattias Jakobsson

Various affiliations

Human evolutionary history is studied in many fields: archeology, linguistics, anthropology, ethnology. Recent developments in molecular biology allowed this field to become essential for the study of the human past. Our understanding of human evolutionary history has greatly improved; for example, it is now accepted that modern humans evolved in Africa before spreading to the rest of the world. One evidence for this is the decrease of genetic diversity along the hypothesized “out of Africa” routes. In this project, we focus on genome-wide variation in Sub-Saharan African populations. We expect to observe high genetic diversity in these populations (compared to the rest of the world). We want to address open questions about human evolution in Africa, like 1-deep population structure within Africa (before the “out of Africa” event – that is, in the order of 50,000 to 200,000 years ago), or 2-more recent events (1,000 to 10,000 years ago), for example the spreading of lifestyles (pastoralism and agriculture) to southern Africa, or the interactions between neighboring populations.

To that end, we are using modern DNA from several Central and Southern Africa populations: rainforest hunter-gatherers and neighboring farming populations, as well as Khoe-San populations, who are either hunter-gatherers or pastoralists. The ancestral populations of the rain forest hunter-gatherers and of the Khoe-San were the first to diverge from the rest of the tree of modern humans (Schlebusch et al 2012, Patin et al 2009. We obtained a dataset of genome-wide markers for these populations. We will apply a range of tools to this dataset, for example to describe diversity and infer potential ancestral populations. Approximate Bayesian Computation approaches will allow us to compare different potential demographic models. For some analyses, we combine our dataset to data from other human populations across the world.

First we will describe genetic diversity in our dataset. This will give us indications about how the populations relate to each other and allow us to make hypotheses about their past that we will then be able to test using model-based approaches. We are also interested in how well different categories – for example based on population identification, on geography or on subsistence pattern – correlate with the genetic diversity.

We will later focus on several precise demographic events: timing of divergence events between these populations and other modern humans, as well as old admixture events. We will also study more recent events that can be linked to a change of lifestyle and correlated with evidence in other fields; for example, we found evidence for admixture from an East African group into Khoe-San populations, that might be associated with the spread of pastoralism (Breton et al 2014. Concerning the Central African samples, one question of particular interest is the nature of the relationships between the hunter-gatherers and their neighbors; indeed, there is evidence of recent sex-biased admixture (Verdu et al 2013, that can be explained by the current organization of these societies.

This project will allow us to deepen our understanding of human evolutionary history in Africa, the cradle of modern humans. It combines events at different time scales, from the oldest divergence

events to historical and contemporary times. Finally, we can combine evidence based on molecular data with cultural evidence, which makes it particularly exciting.

 

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Genetic legacy of the Indian Ocean trading network

BRUCATO Nicolas1, Pradiptajati Kusuma1,2, Denis Pierron1, Murray P Cox3, Thierry Letellier1, Herawati Sudoyo3,4 and François-Xavier Ricaut1.

1 Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse. France, Toulouse, France

2 Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

3 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia

4 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia

For over 4000 years, the maritime routes of the Indian Ocean trading network favored the interactions between far-distanced human populations. As one of the earliest proto-globalization processes, it put into contact populations with highly differentiated genetic backgrounds such as Southeast Asians (various Austronesian-speaking groups), East Africans (ex: Swahili), and South Asians (ex: Indians). Eventually it led to the emergence of particular admixed groups. The best example of extensively admixed population, resulting from overseas historical trading activity, is the Malagasy, the descendants of a unique admixture event between South African Bantu and Southeast Borneo individuals. Although Malagasy is a clear result of gene flow between distant geographical areas of the Indian Ocean rim, the extent of the diverse gene flows along the dense trading network of maritime routes, remains to be examined. We gathered an exhaustive genome-wide SNP dataset of 3057 individuals from 189 populations along the Indian Ocean rim - including data generated by our group for 302 Island Southeast Asians and 100 East Africans. Using both SNP-based and haplotype-based analyses, we quantified and dated several gene flows that can be linked to anthropologically and/or archaeologically documented maritime trading routes. In addition to the Malagasy case study, we will discuss the important Austronesian input detected in Northeast India and the South African legacy in the Middle East and South Asia. We will also enlighten the absence of detectable gene flow in areas with documented interactions between groups, such as the absence of Austronesian genetic trace in East Africa, or Middle East influence in Southeast Asia. Considering historical and archaeological data, our study sheds a new light on the complexity of interactions that took place in the Indian Ocean.

 

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Genetic diversity during the Neolithic: what about France?

BRUNEL Samantha, E. Andrew Bennett, Laurent Cardin, Damien Garraud, Diyendo Massilani, Eva-Maria Geigl, Thierry Grange, Mélanie Pruvost

Institut Jacques Monod, CNRS UMR 7592, University Paris Diderot Paris 7, Paris, France --

samantha.brunel@ijm.fr

Methodological and technical advances in ancient DNA studies make it possible to have an ever deeper look into the genomes of individuals who lived several thousands of years ago.

Benefits from this are two­fold : on one hand, we can directly address questions about the diversity of genomes and their evolution through time, and on the other hand relate this information to modern genetic variability.

Despite a rich archaeological record, little is known about how the multiple migrations that punctuate the history of present­day France have shaped its modern population. To tackle this question, our current project uses targeted enrichment to study informative SNPs and alleles in a wide panel of individuals from periods ranging from the Neolithic to the Middle Ages, sampled from various sites across France. In this talk, we will discuss the preliminary results obtained for samples dating to the Neolithic.

 

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PREVALENCE OF HAEMOGLOBINOPATHIES IN UPPER ASSAM, INDIA

DAS Bhaskar

Assistant Professor, Department of Anthropology, DHSK College, Dibrugarh, 786001, Assam, India -- Email: bd_das2002@yahoo.co.in

Haemoglobinopathies are the most common inherited disorders of globin, the protein component of haemoglobin and poses a major public health problem in many countries including India. The hereditary disorders of haemoglobin may be classified into two broad groups – the haemoglobinopathies and the thalassaemias. Haemoglobinopathies are generally common in malarial regions of the world and North-East India in general and the state of Assam in particular are no exception to this.

The present paper focusses on the prevalence of haemoglobinopathies in three population groups of upper Assam namely the Mishing (N = 318, Ahom (N = 238 and the tea garden communities (N = 397. It is found that the prevalence of haemoglobin E (HbE) is very high among the Mishing and Ahom. The migrant tea garden workers of Assam show moderate presence of sickle cell haemoglobin (HbS) in them besides beta thalassaemia trait (BTT), S-thal and HbE.

Key words: Inherited disorders; HbE; HbS; BTT; S-thal

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Cross Continent Contact between China and Kenya as early as 1400s: Evidence from ancient mtDNA analysis of human remains

DONG Yu1, Tiequan Zhu2, Mohamed Mchulla3, Janet Monge4, Yinqiu Cui5, Hui Zhou5, and Chapurukha Kusimba6 and Sloan R Williams7

1 School of History and Culture, Shandong University, Jinan, Shandong 250100, China

2 School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China

3 Fort Jesus, National Museums of Kenya, Mombasa 82412, Kenya

4 Museum of Archaeology and Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA

5 School of Life Sciences, Jilin University, Changchun, Jilin 130012, China

6 Department of Anthropology, American University, Washington, DC 20016, USA

7 Department of Anthropology, University of Illinois, Chicago, Illinois 60607, USA

Zheng He (1371–1433, a famous general during China's early Ming dynasty, commanded seven expeditionary voyages to Southeast Asia, South Asia, Western Asia, and East Africa from 1405 to 1433. It has long been suspected that some of Zheng He’s crew members stayed behind or left descendants in Africa. Recent excavations undertaken at Manda, Kenya, revealed several human burials that dated between AD 1436 and AD 1643. At least one of the skeletons carry morphological characteristics typical of East Asians. In order to confirm their ethnic identity, the first hypervariable region (HVSI) of mtDNA of ten individuals was amplified and sequenced. The haplogroup SNPs in corresponding coding region were also sequenced to further confirm the mitochondrial haplogroup. In total, we found 3 individuals carrying typical Asian mitochondrial haplogroups, and at least one of them dated 100 years later than Zheng He’s last visit. While the “Polynesian motif” has been previously identified in modern Malagasy and Comoros Island populations, our research raises the possibility that the Asian mtDNA haplotypes at Manda may have been contributed by Chinese women, perhaps travelling aboard merchant vessels or in Zheng He’s fleet. Y chromosome and whole genome analysis could potentially contribute to better understanding this complex history.

 

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GENETIC ANALYSIS AND EVOLUTION OF RH BLOOD GROUP SYSTEM IN BASQUES

André FLORES-BELLO, David Mas, Miruna Rosu, David Comas

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Departament de Ciencies Experimentals i de la Salut, Barcelona, 08003, Spain.

Basque people have been in the limelight of many studies in the last decades due to their specific characteristics that have placed them as an isolated and unique population within Europe, highlighting their own non-Indo-European language, Euskara. They have been historically distributed along the West Pyrenees, between the Spanish and the French territories, which acted as one of the most important European glacial refugia during the Last Glacial Maximum [1]. One of the most striking characteristic is related to the Rhesus (Rh) blood group system, presenting very high frequencies of Rh-negative [2]. A variant that is expected to be selected against as consequence of the Hemolytic Disease of the Newborn (HDN) [3]. Nevertheless, the causes of this high Rh-negative frequency in Basques still remain unclear since it could be explained due to demographic or adaptive processes round the flanking regions of the Rh genes [4]. Most of the previous studies have been focused in serological and genotyping analyses.

In the present project, we carried out a genotyping analysis of the most important variants of the system: Rh+/Rh-, E/e and C/c; in our samples from Basque Country and other populations (Catalans, Moroccans, CEU, YRI and CHB) with a standard Rh-negative frequency. Then, haplotype-based analyses were performed for both the upstream and downstream flanking regions of the RHD gene and the upstream region of the RHCE gene by direct sequencing and phasing.

Our phylogeographic results do not show any special differentiation or evidence of selective pressure on flanking regions between Basques and the other populations. Instead, haplotypes grouped according to geography, with more diversity in Africans. Furthermore, two differentiated Rh+ and Rh- groups were identified among populations, being the Rh- mainly represented by Basques and less diverse than the Rh+. This observation is the expected as the Rh- variant derived from the ancestral Rh+ form [5]. We show that frequencies of Rh+/Rh-, E/e and C/c genotypes in populations are in agreement with previous data [6] as well as evidence of a correlation between C allele and Rh+ in non-African populations [4].

Thus, our results suggest that the origin of such high frequency of Rh-negative in Basques is the result of a demographic process, probably a bottleneck during the settlement of the glacial refugia in the Last Glacial Maximum, and then a subsequent drift by isolation.

[1] Behar D. M. et al. 2012. “The Basque paradigm: Genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-neolithic times”, Am. J. Hum. Genet., vol. 90, no. 3, pp. 486–493.

[2] Van Der Heide H. M. et al. 1951. “Blood group distribution in Basques”, Am. J. Hum. Genet., vol. 3, no. 4, pp. 356–361.

[3] Anstee D. J. 2010. “The relationship between blood groups and disease”, Blood, vol. 115, no. 23, pp. 4635–4643.

[4] Perry G. H. et al. 2012. “Evolutionary genetics of the human Rh blood group system”, Hum. Genet., vol. 131, no. 7, pp. 1205–1216.

[5] Flegel W. A. 2007. “The genetics of the Rhesus blood group system” Blood Transfusion, vol. 5, no. 2, pp. 50–57.

[6] Carritt B. et al. 1997. “Evolution of the human RH (rhesus) blood group genes: A 50 year old prediction (partially) fulfilled”, Hum. Mol. Genet., vol. 6, no. 6, pp. 843–850.

 

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A simple overview of musics throughout Gabon

GARDENT Jeremy and Sylvie Le Bomin

Eco-anthropologie et Ethnobiologie UMR 7206 CNRS/MNHN, Paris

Musics in Gabon share a number of common features, but reveals a great intrinsic diversity. Most of previous studies on these musics were focused on monographical description or small-scale comparisons. However, increasing knowledge about these musics, as well as intensive fieldwork throughout Gabon now allow a broader comparison of these musics.

We collected first-hand musical and contextual data in 20 ethnonymo-geographical units. These represent 10 ethnonymical groups, distributed in 7 different provinces of Gabon. About 250 pieces were recorded, from which 191 were transcribed and analysed thanks to musical systematics tools. The pieces recorded were all rhythmical-instrumental, typically with two or three vocal parts and two or three instrument parts played by drums or idiophones (stroken beam or wood board). In this region, pieces can be grouped according to their context of performance, the 'repertoires', which have been shown of cultural and musical relevance. Most of time, in each population, two different pieces of each repertoire has been recorded.

We compared three categories of data, concerning the internal organization of the sound produced. Metrical and rhythmical organization were identified from instrumental parts. We studied the diversity of metric organization through the number of beats per period and the type of subdivision of the pulsation. Rhythmical organization were studied through it segmentation in elementary rhythmic cells. Given the known relation between rhythmic figures and repertoires, rhythmic cells diversity were studied both globally and in each repertoire. Scales were identified from transcription of vocal parts. Scales diversity was studied through their interval sequence, the number of degrees and the number of half-tones they contain.

These data were compared by simple descriptive tools such as graphical representations and map plotting. This gives a first global overview and quantitative assessment of the diversity of Gabonese musics. Concerning metrics, we observed a neat geographical organization, whith ternary subdivision being more frequent on the east of the country, and binary subdivision more frequent on the west. Rhythmic cells repartition were found to be non homogeneous, neither inside a population nor at the country level. A wide variety of scales has been found, most of them being found in only one or two populations, whereas three of them are widespread.

 

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Impact of non-LTR retrotransposons in the differentiation and evolution of the Homo genus

GUICHARD Etienne*1, Lucia Abitante1, Margherita Musella1, Jimmy Caroli2, Valentina Peona1, Marco Ricci1, Davide Pettener1, Cristian Taccioli3, Alessio Boattini1

1 Department of Biological, Geological and Environmental Sciences – University of Bologna, Bologna (Italy)

2 Department of Life Sciences, University of Modena and Reggio Emilia, Modena (Italy)

3 MA.P.S Department, University of Padova, Padova (Italy)

* for further information contact: etienne.guichard2@unibo.it

Transposable Elements (TEs) have generated at least 46 % of the human genomic material. Although these elements have often been dismissed as "selfish", "parasites" or simply "junk", the advent of whole genome DNA sequencing, in conjunction with molecular genetic, biochemical, genomic and functional studies, is revealing that TEs are biologically important components of eukaryote genomes. In modern humans, only some TE subfamilies of the non LTR-retrotransposon sub-class have recently been active. These elements often contain internal promoters and Transcription Factor Binding Sites, are able to drive adjacent gene expression, can produce alternative transcripts for existing genes and have generated both new genes and pseudogenes. These characteristics make them one of the primary sources for genomic mutations and variability.

Despite all the evidence, the effects and implications of retrotransposon activity throughout the evolution of the human lineage are still understudied.

This study aims at the identification of the role of such retrotransposons in the differentiation and evolution of the genus Homo, by comparing insertions in the genome of modern humans with those of our closest extinct relatives, Neanderthals and Denisovans.

Because of the fragmentation of Ancient DNA (as well as the reads length limits implicit in NGS sequencing), plus the inability to work with assembled genomes due to the difficulties that occur while aligning repetitive genomic regions, a new in silico methodology for identifying species-specific insertions was developed.

The procedure hereby presented only relies on the BLAST+ package and custom R scripts; it operates on a modern reference genome and the raw reads of archaic DNA sequencing. Briefly, the retrotransposons’ 3’ ends and flanking sequences are identified in both the compared genomes, then the putative species-specific insertions 3’ portions are isolated by comparing the flanking sites in the two species. All the putative species-specific insertions are confirmed via the identification of the empty site in the other species’ genome, which in turn allows finding the 5’ portion of the insertion. Only insertions of which both 3’ and 5’ portions are present and have confirmed empty (pre-insertion) sites in the other species’ genome are kept.

The precise annotation of the species-specific retrotransposon insertions, the characterization of their genomic surroundings and the comparison of the site’s activity and functionality both with and without the inserted elements further clarifies the impact and role of retrotransposons in recent Homo evolution.

 

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EXPLORING THE POPULATION HISTORY OF VIETNAM

MACHOLDT Enrico1, ARIAS Leonardo1, NGUYEN Van Phong2, NGUYEN Thuy Duong2, NGUYEN Dang Ton2, NONG Van Hai2, PAKENDORF Brigitte3, STONEKING Mark1

1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

2 Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam.

3 Laboratoire Dynamique du Langage, UMR5596, CNRS & Universite Lyon Lumiere 2, Lyon, France.

The country of Vietnam, situated in Mainland Southeast Asia, is characterized by great ethnolinguistic diversity.  In particular, there are 54 official ethnic groups speaking languages that belong to five major language families: Austronesian, Austro-Asiatic, Hmong-Mien, Sino-Tibetan, and Tai-Kadai. In combination with the distribution of these groups within the heterogeneous geographical profile of Vietnam - lowland river deltas in the east and south, and high altitude mountain areas in the northern and central regions -'' the ethnolinguistic diversity indicates a potential importance in human migrations through the region. However, no comprehensive study of genetic diversity in Vietnam was conducted to date.

In this study we are focusing on Vietnam as one of the enigmatic parts of Mainland Southeast Asia. Current knowledge about the genetic history and composition of Vietnam is based on very limited data; in order to fully understand Vietnam's population history we investigate Vietnam's genetic diversity and structure on a broad scale. Based on a DNA sample set of 600 male individuals from various regions in Vietnam and representing all five language families, we are analyzing multiple lines of evidence: uniparental markers, namely full mitochondrial genomes and about 2.3 mb sequence data from the non-recombining portion of the Y chromosome, and single nucleotide polymorphism data typed on the Axiom Genome-Wide Human Origins 1 Arrays.

Preliminary analyses on the uniparental markers indicate high heterogeneity in the distribution of both mitochondrial and Y chromosome haplogroups among populations that does not correlate with geography or language, suggesting isolation and drift effects. The structure within the shared haplotypes and genetic distances among populations resemble a potential signals of post-marital residence patterns and sex-biased genetic contact.

Our aim is to investigate the demographic and historical processes that have shaped the history of Vietnam and Mainland Southeast Asia.

 

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Palaeogenetic analysis of Bronze Age/Iron Age transition in Southern Central Asia

MONNEREAU A., Lhuillier, J., Bendezu-Sarmiento, J.,Bon, C.

Musee de l’Homme, Paris, France

At the end of the Bronze Age, the proto-urban Oxus Civilisation in Southern Central Asia (Uzbekistan, Turkmenistan) disappeared and was replaced by Iron Age Yaz Cultures.Environmental changes such as aridification and geopolitical reasons are called for to explain this cultural transition. However, evidences of settlements from Andronovo populations during the late Bronze Age suggest that this transition was associated with migrations from northern steppe populations. Indeed, palaeogenetic studies (Allentoft et al., 2015; Haak et al., 2015 have already shown that gene flow from Yamnaya steppe populations occurred in Europe and Altai at the end of the Neolithic, suggesting that the steppe inhabitants spoke indo-european langages.

To investigate the role of migrations in the Bronze Age/Iron Age transition in Southern Central Asia, we turned to palaeogenetic studies. DNA was extracted from 17 skeletons excavated in Ulug Depe (Turkmenistan) archaeological site. The hypervariable region I of the mitochondrial (mt) genome was sequenced for 6 individuals from the Bronze Age and 4 from the Iron Age.

Criteria of authentication for ancient DNA were met: experiments were done in a clean room dedicated to ancient DNA analysis, and blank DNA extraction and PCR controls were performed. Indeed, we observed DNA damages specific for ancient DNA and an inverse correlation between the efficiency of the PCR and the length of the amplified DNA fragment. Thus, we first evidenced the preservation of ancient DNA in Southern Central Asia. After sequencing and assignment of individuals to human mitochondrial haplotypes, a high diversity of haplotypes at Ulug Depe was observed. All the haplogroups found in Ulug Depe belong to modern western Eurasian populations.

Haplogroups shared between steppe populations and Ulug Depe were evidenced, suggesting gene flow between Southern Central Asia and the Steppe. Genetic data suggest a close relationship between Yamnaya related populations and Iron Age Ulug Depe population. However, no significant genetic discontinuity between Bronze and Iron Age was shown, that may be due to a limited sample dataset and calls for nuclear DNA analysis.

Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., … Willerslev, E. (2015. Population genomics of Bronze Age Eurasia. Nature, 522(7555, 167–172. doi:10.1038/nature14507

Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., … Reich, D. (2015. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. doi:10.1038/nature14317

 

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COMPLEX ANCIENT GENETIC STRUCTURE AND CULTURAL TRANSITIONS IN SOUTHERN AFRICA POPULATIONS

MONTINARO Francesco1, George BJ Busby2, Miguel Gonzalez-Santos1, Ockie Oosthuitzen3, Erika Oosthuizen3,Paolo Anagnostou45, Giovanni Destro-Bisol 45,Vincenzo Pascali6,and Cristian Capelli1.

1 Department of Zoology,University of Oxford, South Parks Road, Oxford,OX1 3PS, UK

2 Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK

3 School of Medicine, University of Namibia, Windhoek, Namibia

4 Dipartimento di Biologia Ambientale, Università “La Sapienza”, Rome, Italy

5 Istituto Italiano di Antropologia 00185, Rome, Italy

6 Institute of Public Health, Catholic University,  Largo Francesco Vito 1 00168 Roma

The characterization of the structure of southern Africa populations has been the subject of numerous genetic, medical, linguistic, archaeological and anthropological investigations.

Current diversity in the subcontinent is the result of complex episodes of genetic admixture and cultural contact between the early inhabitants and the migrants that have arrived in the region over the last 2,000 years, with some of the variation present in the past being now lost as the result of cultural and demographic assimilation by surrounding populations. Here we analyze 1,856 individuals from 91 populations, comprising novel and available genotype data to characterize the genetic ancestry profiles of  631 individuals from 51 southern African populations. Combining local ancestry and allele frequency analyses we identify a tripartite, ancient, Khoesan-related genetic structure, which correlates with geography, but not with linguistic affiliation or subsistence strategy, and probably originated in pre-historical times (~30 Kya).

The fine mapping of these components in southern African populations reveals admixture dynamics and episodes of cultural reversion involving several Khoesan groups and highlights different mixtures of ancestral components in Bantu speakers and Coloured individuals, probably reflecting different historical scenarios.

 

POSTER

Confrontation of Red Cell Blood Groups distribution to environmental data

PETIT Florence1,2, Jacques Chiaroni2,3, Bérengère Saliba-Serre2

1 Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397, Marseille, France

2 Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916, Marseille, France 3

3 Etablissement Français du Sang Alpes Méditerranée

In Humans, thirty-five Red Cell Blood Group (RBG) systems have been defined and some susceptibilities to infectious diseases have been highlighted. Examples include interactions between the Knops system and tuberculosis, glycophorins and babesiosis, P antigen and parvovirus B19, the ABO system and cholera, the Duffy protein and malaria, or the RBG ABO-A and Rhesus-D negativity and West Nile virus. Some erythrocyte surface antigens would act as “anchor points” or “gateways” for viruses, parasites or bacteria. Moreover, for some RBG systems usually less known, geographical distribution similarities exist between their genetic diversity and the repartition of some pathogens. This may suggest potential interactions. Broadly, environmental constraints can influence the distribution of antigens, and can drive their retention or removal over several generations within human populations that express them. This natural selection process may let genomic signatures that we aim to highlight.

This project aims to confront the distribution of systems of high transfusional (ABO, Rhesus...) or anthropological (Indian, Diego...) interest, with potentially aggressive environments for red blood cell: climate, altitude, pathogen agents. The study is carried out by analyzing (with population genetics tools and statistic methods) genome-wide genetic data obtained in populations spread over the five continents and evolving in various environmental conditions associated with specific habitats. An original reading strategy, with selection detection related to the environment by genome scans, of the information contained in the loci encoding, or in connection with the RBG systems, can thus be validated.

The objective is to reveal an environment footprint on the distribution of genetic polymorphisms of RBG between human populations evolving in different ecosystems. Our study will be able to contribute to the improvement of blood safety of populations and takes as such a strong interest for the Établissement Français du Sang, which supports the project.

Keywords: Red Cell Blood Group Systems, Human Populations, Selection, Environment, Pathogens, Population Genetics, Single Nucleotide Polymorphims, Genome-wide Data.

 

POSTER

GENOMIC ANCESTRY OF SOUTHERN ITALY: INSIGHTS INTO A COMPLEX HISTORY OF ADMIXTURE

SARNO Stefania 1, BOATTINI Alessio 1, PAGANI Luca (1,2, SAZZINI Marco 1, DE FANTI Sara 1, QUAGLIARIELLO Andrea 1, GNECCHI RUSCONE Guido 1, GUICHARD Etienne, BORTOLINI Eugenio 1, BARBIERI Chiara 3, CILLI Elisabetta 4, PETRILLI Rosalba 1, MIKEREZI Ilia 5, SINEO Luca 6, VILAR Miguel 7, WELLS Spencer 7, LUISELLI Donata 1, PETTENER Davide 1

1 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

2 Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK.

3 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.

4 Department of Cultural Heritage, University of Bologna, Bologna, Italy.

5 Department of Biology, University of Tirana, Tirana, Albania.

6 Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy.

7 National Geographic Society, Washington, District of Columbia, USA.

Assessing the genetic impact of different migration processes on present-day populations is challenged by the extent of admixture layers involving ancestral groups. The cross-cultural gateway linking Southern Italy with the Balkans and Aegean islands has represented the theater of multi-layered migrations of peoples and cultures both in pre-historical and historical times. However, their relationship patterns are largely unexplored from a high-resolution genomic perspective.

In this study, we genotyped 511 samples from 23 populations of Sicily, Southern Italy, Greece and Albania with the Illumina GenoChip Array (~150,000 SNPs). New remarkable samples from Albanian- and Greek-speaking ethno-linguistic minorities of Southern Italy were also included. In order to disentangle admixture layers and assess recent cultural heritages, we compared our data with a large collection of modern and ancient Euro-Mediterranean individuals. 

Our results reveal that Sicily and Southern Italy belong to a vast Mediterranean genetic continuum, extending from Sicily to Cyprus, through Crete and Anatolian Greek Islands. Besides a predominant Neolithic heritage, these populations show significant impacts of Post-Neolithic Caucasus- and Levant-related ancestries. In addition, further historical genetic contribution from North-Central Balkans and Eastern Europe characterize the continental Southern Balkan groups of Greece and Albania.

The detected genetic texture helps clarifying some cultural changes associated to the spread of Italian Arbereshe and Grecani ethno-linguistic minorities during classical and medieval times. Albanian-speaking Arbereshe trace their recent heritage to Southern Balkans. On the other hand, the substantial genetic resemblance of Greek-speaking Grecani with the populations of the continuum and particularly their Italian neighbors suggest a longer history of presence in Southern Italy.

While contributing new details from both genetic and cultural viewpoints, our results emphasize the importance of considering complementary scales of investigations and detailed population panels to assess processes involving tightly related ancestries that repeatedly interacted at different times in the past.

 

POSTER

Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC)

SERVENTI Patrizia1,2, Chiara Panicucci1, Roberta Bodega1,2, Sara De Fanti2, Antonino Vazzana1, Chiara Delpino3, Stefania Sarno2, Manuel Fondevila Alvarez4, Francesca Brisighelli5, Beniamino Trombetta6, Donata Luiselli2, Giorgio Gruppioni1, Elisabetta Cilli1.

1 Department of Cultural Heritage, University of Bologna, Ravenna, Italy.

2 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

3 Superintendence of Archaeological Heritage of Marche region.

4 Instituto de Ciencias Forenses "Luis Concheiro", University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.

5 Sezione di Medicina Legale - Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy.

6 Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy.

During the Iron Age, in Italy, the archaeological data provide documentary evidence of the appearance of the first communities with a strong and well defined cultural identities.

At the moment, only few studies report genetic data about the Italian populations of this period and, in particular, the Piceni have never been studied. The traditional ethnogenesis describes the “Picenum Culture” as a pre-Roman population who lived in the northern Adriatic coastal plain of Italy.

A pilot research project, based on both genetic and archaeological approaches, has been started in the Novilara necropolis (dated at 8th-7th century BC) localized in the Marche region (central Italy). This archaeological site represents an exceptional evidence due to the presence of more than 300 graves excavated so far, characterized by abundance of grave goods and also a good conservation status of the skeletal remains. To shed light on the ancient genetic diversity of Italy of this period, the HVS-1 region of mitochondrial DNA (mtDNA) in a first set of 27 individuals from Novilara necropolis was examined by high-coverage next-generation sequencing (NGS). Typical ancient DNA damage pattern in the analysed sequences and their comparison with those of the researchers involved in this project confirm the authenticity of the obtained data. Moreover, we performed a forensic analysis on these same individuals obtaining partial profiles for both autosomal STRs (Globalfiler PCR Amplification kit and Powerplex ESX 17 System) and Indels (Investigator DIPplex Kit).

With the combination of these data, we used genetic tests in order to establish the possible kinship relationships among the individuals here analysed. By these analyses, we will try to be validate the archaeological technique of seriation based on the analysis of the material culture, and to understand the contribution of the Piceni population in shaping the modern Italian gene pool.

Keywords: human population genetics, ancient DNA, mtDNA, STRs, NGS, Iron Age, Piceni

 

POSTER

GENETIC MAPPING OF HISTORICAL ARMENIA

YEPISKOPOSYAN Levon        

Ethnogenomics Laboratory, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia (e-mail: lepiskop@yahoo.com)

The origins of Armenians are difficult to reconstruct due to several reasons. The vast majority of historical evidence has been destroyed or lost during numerous invasions and earthquakes. Further, the modern political division of historical Armenia among neighbouring states has made archaeological, anthropological and archival research a sensitive and difficult task. Though most of historical Armenian provinces were forcibly depopulated during the last few centuries, fortunately, the descendants of these refugees retain information providing the possibility of reconstructing the genetic legacy of their ancestors.

Here, we present the first ever attempt to create a genetic map of historical Armenia that reproduces the rich spacial mosaic of the Armenian gene pool. Our primiry findings show that the Armenian paternal genetic legacy displays immence diversity of lineages, indicating a large number of "founding fathers". The vast majority of Y chromosomes belongs to the haplogroups originated and expanded during or following the Neolithic. The modern Armenian gene pool, studied by genome-wide SNP data, consists of traces of an origin from a mixture of various populations taking place from 3000 to 2000 BCE, with dramatic decrease of admixture signals after 1200 BCE. Armenians had no significant mixture with other populations also in their recent history. Of the primary reasons that have impeded genetic contact of Armenians with foreigners, the highland geography, early adoption of Christianity, strong ethnic and cultural identity can be considered the most likely.

Recently, the origins of Armenians have been examined based on ancient DNA. A strong genetic continuity between the Bronze Age population and modern Armenians has been revealed. Further aDNA studies will cover time span from the Neolithic to the Middle Ages while addressing other principal questions on the Armenian genetic history.

 

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