Ancient DNA: applications in human evolutionary history

Organiser and Chair

Professor Erika Hagelberg, University of Oslo, Norway

Pleistocene humans in the Americas/ East Asia and their environment

Dr Paula F Campos, Natural History Museum, Denmark

Abstract

The timing, route and origin of the first human migration into the Americas are still heavily debated. The most widely accepted dates of occupation are still the ones related to the Clovis complex, ~11,000 to 10,800 14C years before the present (yr B.P.) (13.2–13.1 to 12.9–12.8 ka), a distinct culture that appears to have originated and spread throughout North America in as little as 200 to 300 years, and that has been blamed for the extinction of several genera of megafaunal mammals approximately 10,000 years before present.

However, human mitochondrial DNA recovered from coprolites found at the Paisley 5 Mile Point Caves, in south-central Oregon, suggest human presence as early as 12,300 14C years B.P (coprolites were directly dated by accelerator mass spectrometry). Here we present genetic, archaeological and stratigraphical data that further confirm these results.

Impacts of colonization in the Americas

Professor Anne Stone, Arizona State University, USA

Abstract

European contact in the Americas resulted in major social changes to Native American societies. In addition, biological impacts, including changes in population size and patterns of diversity, admixture, and disease introduction, have left lasting signatures today. Genetic analyses of ancient populations (both pre and post contact) can provide insight into these changes. Here, we will present mitochondrial DNA data obtained from people from pre-contact archaeological sites, including Norris Farms in the Midwestern United States and Chen Chen in southern Peru, as well as at a contact period mission site in southern Argentina in order to highlight aspects of population diversity and continuity as well as, more recently, admixture. In addition, we will report initial results from attempts to characterize ancient disease strains including mycobacterial strains from cases of disseminated bone TB and Leishmania strains from facial lesions in order to understand the phylogenetic relationships between strains of these pathogens prior to and after contact.

Where are the Caribs ? Ancient DNA from ceramic period human remains in the Lesser Antilles.

Marie-France Deguilloux, Université Bordeaux 1

Abstract

When Europeans reached the Caribbean archipelago, in the late 15th century, they described four distinct human groups: Ciboneys and Tainos in Greater Antilles, Arawaks and Caribs in Lesser Antilles. Genetic analyses of extant populations from the Caribbean region have clearly confirmed high levels of genetic admixture with West African populations, and illustrated the limitations of working with modern Caribbean populations to unravel ancient populations’ origin and dynamics. We therefore developed a palaeogenetic project aiming to characterize the gene pool of the extinct Caribs, in order to ascertain the genetic affinities between Caribbean extinct populations. Carib human remains, originating from Guadeloupe, Marie-Galante and La Désirade were analysed for mtDNA and Y chromosome variation. The results obtained provide persuasive arguments concerning the origin of this human group in South America. They also permit to point out clear genetic differentiation between human groups from Greater and Lesser Antilles, furthermore clearly differentiated in front of social organization and archaeological cultures. Nevertheless, we also highlight the necessity to investigate the identity of individuals under study in palaeogenetic analyses (assessed through different funerary practices in our case), to propose reliable evolutionary scenarios for ancient populations. This task necessitates a real collaboration between archaeology and ancient DNA research.

Kinship analysis of ancient human remains based on Y-chromosomal, autosomal and mitochondrial DNA.

Professor Yinqiu Cui, Jilin University, China

Abstract

Yuan dynasty was the first foreign dynasty to rule all of China, and lasted more than 200 years. The Mongol rulers were a minority among the Han majority, and most of the cemeteries that have been discovered belong to the Han. Cemeteries belonging to Mongolian nobles have been rarely found, due to the special burial customs and absence of historical records.

Archaeological excavations in Shuzhuanglou at Hebei province of China led to the discovery of 13 skeletons in 6 separate tombs, currently assumed to be of Mongol nobles or Korgis. A multidisciplinary approach including archaeology, anthropology, isotope analysis and ancient DNA methods was applied to confirm the identity of the cemetery owners, and resolve the kin relationships between individuals. Data from autosomal, mitochondrial, and Y-chromosomal markers permitted the identification of genetic kin relationships between some of the individuals. A combination of archaeological information, stable isotope data and molecular evidence allowed the cemetery owners to be tentatively identified. We demonstrate that a multidisciplinary approach is useful for the identification of individuals and kinship relationships using bone specimens from old historic sites

Chair

Dr Anders Götherström, Uppsala University, Sweden

Assessing the authenticity of clonal sequence reads from ancient samples: A case study from Iceland

Dr Agnar Helgason, deCODE Genetics, University of Iceland

Abstract

The Viking age witnessed the expansion of Norse invaders across much of Northwestern Europe, with a particularly long-lasting cultural and genetic impact on the populations in the North Atlantic –particularly in Iceland and the Faroes, where there were no pre-existing human populations. In my talk, I will summarize the outcome of ancient DNA research that helps shed some light on the origin of the Icelandic population and the activities of the Norse invaders in the North Atlantic region

Genomic analysis of prehistoric populations in Europe: authentication and population history

Pontus Skoglund, Uppsala University, Sweden

Abstract

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. I will describe a novel statistical framework for isolating endogenous ancient DNA sequences from contaminating sequences using postmortem degradation patterns, and demonstrate using both published and novel large-scale sequence data that this approach is able to reduce high contamination fractions to negligible levels. This approach thus opens up the possibility of authenticating genome-wide sequence data from human remains. In an application for this, we have generated ancient genomic sequence data from several Scandinavian individuals associated with foraging and agricultural groups. We show that the Neolithic Scandinavian individuals show remarkable population structure corresponding to their cultural association, and that comparison with southern European ancient individuals as well as modern-day variation suggests a model where initial colonization by agricultural populations was followed by later admixture with hunter-gatherer populations and/or gene flow from other regions.

The Neolithic transition in the Cantabrian fringe (Peninsula Iberica)

Professor Concepción de la Rúa, University of the Basque Country, Spain

Abstract

The variability of mitochondrial DNA from different prehistoric populations of the Northern Iberian Peninsula (from the Magdalenian to the Bronze Age) was analyzed. The results obtained were validated using the authentication criteria proposed by the scientific community. The analysis of the mitochondrial variability in this study together with the ancient and present-day populations studied so far, indicates the differentiation of the hunter-gatherer groups regarding both Neolithic and present populations. As for Neolithic European groups, within the heterogeneity observed two groupings can be appreciated: on one side, the Neolithic sites that present haplogroup N (proposed as a marker for the spread of the Neolithic in Central Europe) and on the other side those lacking such haplogroup (Mediterranean sites and sites from the Cantabrian fringe). DNA analysis from ancient groups indicates that the diffusion of the Neolithic had different genetic impact in different European prehistoric populations, highlighting the complex biological patterns resulting from Neolithization in contrast with the simpler and more evident cultural patterns.

Human ancient DNA from the ancient city of Sagalassos (Turkey): a diachronic view of mtDNA variation from Roman to Byzantine time.

Dr Claudio Ottoni, Center for Archaeological Sciences, KU Leuven, Belgium

Abstract

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of an ancient urban settlement in all its features. The rise of the ancient city of Sagalassos can be likely placed at the end of 5th BC. At the crossroad between Europe and Southwest Asia, over the centuries the study region of Sagalassos experienced the domination and the influence of several empires and civilizations (Phrygians, Persians and Romans just to mention some). The city was eventually abandoned in the mid Byzantine time (13th century AD), after the Seljuk invasion.

The main goal of our study is to describe the maternal genetic variation in Sagalassos across a wide temporal frame of its human occupation and to reconstruct potential demographic dynamics in relation to historical events documented in the Anatolia region (e.g. a plague epidemic in the 6th century AD). For this purpose, we have analysed bone and teeth samples of 45 skeletons dated to the Classic-Hellenistic up to Roman Imperial times. By means of coalescence simulations and multivariate analyses, the novel mtDNA sequences will be compared with Byzantine (12th-13th century AD) sequences previously analysed in order to detect potential significant changes in the maternal genetic pools of Sagalassos dwellers across time and to envisage demographic scenarios which may have affected the region.

Co-authors: Rita Rasteiro, Dept of Genetics, School of History, University of Leicester, UK

Reyhan Yaka, METU Department of Biological Sciences, Turkey

Katrien Van de Vijver, Center for Archaeological Sciences, University of Leuven, Belgium

Rinse Willet, Sagalassos Archaeological Research Project, University of Leuven, Belgium

Jeroen Poblome, Sagalassos Archaeological Research Project, University of Leuven, Belgium

Lounés Chikhi, Laboratoire Evolution et Diversité, Biologique (UMR 5174, CNRS/UPS), University Paul Sabatier, Toulouse, France & Instituto Gulbenkian de Ciência, Oerias, Portugal

Organiser and Chair

Professor Michael Hofreiter, University of York, UK

Palaeogenomic analysis of ancient humans: methodological issues

Dr Eva-Maria Geigl, Université Paris Diderot/CNRS, France

Abstract

The analysis of genomes retrieved from archaeological material offers unprecedented new and detailed views of human evolution and the history of ancient human populations, as recent research has demonstrated. So far, however, these analyses were possible only in the cases of exceptionally well preserved specimens, ie either preserved in the permafrost or under particularly favorable taphonomic conditions in caves. To access the genomes of the majority of anthropologically important specimens where DNA is only poorly preserved, our approach to DNA retrieval and sequencing methods must be improved and fine tuned. Genomic analysis of this material, even when aseptically excavated and handled, is also particularly prone to contamination with modern DNA originating either from reagents and oligos or from previous analyses. We will show which lessons can be learned from our NGS experiments on human and animal bones and teeth.

Co-authors: E. Andrew Bennett and Thierry Grange, Institut Jacques Monod, CNRS, University Paris Diderot, Paris, France

Shall we still worry about contamination?

Professor Erika Hagelberg, University of Oslo, Norway

Abstract

For many years, studies on ancient human DNA were haunted by the spectre of contamination, and some of the most contentious discussions in the field concerned contamination and the authenticity of DNA sequences from human remains. Studies on human DNA were even held to be impossible by some researchers, and standards were imposed to try to weed out “suspect” research. It is interesting to note, however, that despite the prominent role of DNA contamination, none of the studies presented at this meeting on ancient human DNA focuses chiefly on contamination. This is a heartening development, and suggests researchers are now more interested in the outcome of research than in the obstacles to research. A few questions remain: do the standards for ancient DNA research still stand, shall we still worry about contamination with the advent of next generation sequencing, and how shall we address the issues of contamination constructively as a research community?

Next generation sequencing solutions to unidentified human remains cases

Abstract

One of the missions of the Armed Forces DNA Identification Laboratory (AFDIL) is to assist the Joint POW/MIA Accounting Command in the identification of missing service members from past military conflicts. Until recently, specimens submitted for testing from a specific set of 800 service members buried as unknowns have been surprisingly recalcitrant to the standard DNA identification methods employed by AFDIL. The reason for this lies in the extensive post-mortem treatment performed on these remains which included, among other things, immersion in formaldehyde for a several days. These aggressive mortuary practices caused severe damage to the endogenous DNA, generally leaving fragments of only 80 bp or less.

Using Illumina technology paired with hybridization capture, we are now able to produce sequence data for these highly degraded specimens. The first phase of our study has focused on individuals who were identified based on physical and circumstantial evidence and for whom “known” DNA from a maternal relative is available. The reference sequences are being employed to authenticate data, optimize bioinformatics parameters, and characterize the features of the NGS sequences generated from the degraded specimens. Most importantly, the reference samples are serving to demonstrate that the NGS methods being applied are indeed yielding authentic sequence data from these particularly recalcitrant specimens, and that these methods have the potential to aid in the identification of missing U.S. service members.

Co-authors: Alice Chung, Suzanne Barritt-Ross, Jodi Irwin, Timothy McMahon

Increasing the resolution - new molecular methods improve access to archaic human DNA

Dr Matthias Meyer, Max Planck Institute for Evolutionary Anthropology, Germany

Abstract

Improvements to ancient DNA extraction and library preparation techniques have enabled the reconstruction of genome sequences from Late Pleistocene archaic human groups at an unprecedented level of resolution, most prominently those of Neanderthals and Denisovans. Recent success in sequencing Middle Pleistocene animal remains indicates that these methods may also make it possible to retrieve DNA sequences from human fossils of much greater age in the future. However, if DNA is present in such fossils, it is even more degraded and present in smaller quantities than in any other ancient human fossil that has produced meaningful genetic data to date. My presentation will summarize the progress of our work on extremely poorly preserved ancient human DNA and the technical difficulties that are faced, both in the laboratory and with sequence analysis.

Chair

Professor Sir Paul Mellars, University of Cambridge, UK

Paleogenomics and the Mesolithic-Neolithic transition in Europe

Dr Carles Lalueza-Fox, Instituto de Biología Evolutiva (CSIC-UPF), Spain

Abstract

Neandertal remains at El Sidrón cave (Asturias, North Western Spain) were accidentally discovered in 1994 by cave explorers. The systematic excavations started in the year 2000 and have continued ever since. The remains of thirteen Neadertal individuals have been retrieved with a pioneer excavation protocol designed to prevent contamination of the remains with modern human DNA; moreover, the stable and cold temperatures within the cave have favoured endogenous DNA to be preserved for all the specimens. Different archaeological and geological evidences indicate that El Sidrón is a synchronic assemblage of a Neandertal family group cannibalized in the surface by other Neandertals and thus offer a unique opportunity to study intragroup genetic diversity, mating behaviour and kinship structure in these archaic humans. Since 2005, different paleogenetic studies -some of them in collaboration with the Max Planck Institute at Leipzig- have uncovered crucial phenotypic aspects of these individuals, including information about the hair pigmentation, the language and the ABO blood group. Moreover, new technological approaches have started unraveling patterns of genomic diversity among the individuals of this unique site

The landscape of Neandertal ancestry in present-day humans

Professor David Reich, Harvard Medical School, USA

Abstract

We inferred the locations of DNA sequences that derive from Neandertals in 1,004 present-day humans. We find regions of millions of base pairs that are nearly devoid of Neandertal ancestry and that are significantly enriched in functional elements showing that they owe their origin in part to rapid selection to remove Neandertal-derived gene material. The Neandertal-devoid regions are significantly enriched in genes expressed in testis compared with other tissues, and the greatest deficiency of Neandertal ancestry in the genome is on chromosome X where it is about a fifth of that on the autosomes; these two patterns can be parsimoniously explained if Neandertals carried alleles that conferred hybrid sterility when moved to a modern human genetic background. Neandertal alleles continue to shape human biology. We find 24 regions in Europeans and 22 in East Asians that harbor more Neandertal ancestry than can be explained by genetic drift. We also find that regions of high Neandertal ancestry are significantly enriched for genes affecting keratin filaments, sugar metabolism, oocyte meiosis, and vascular smooth muscle contraction, suggesting that mutations in these biological pathways may have helped modern humans to adapt to non-African environments. Finally, we show that multiple alleles that affect risk for disease entered present-day humans from Neandertals.

Ancient DNA studies: new perspectives on old samples

Elena Gigli, University of Florence, Italy

Abstract

Twenty years ago an exceptionally preserved archaic human skeleton was discovered inside a karstic cave (Lamalunga Cave) in the Altamura countryside in Southern Italy (Bari, Apulia). First observations, pointed out that the remains belonged to “Anteneanderthals”; with the exception of some photographic documentations, no direct examinations were carried out on the skeleton, until 2009 when in a new survey in the cave we remove a skeletal fragment to be used for high-quality investigations. In this study, we report the first results obtained from dating, paleogenetic and morphometric analyses. Overall, our data show that the skeleton from Altamura belonged to a Neanderthal, with some interesting peculiar features. Dating results show that Altamura skeleton is the most ancient Neanderthal from which endogenous DNA has been retrieved so far. Due to the very special conditions of preservation, it may be considered a good candidate for genome-wide analyses

Evolutionary consequences of the past pandemics

Abstract

In historical times epidemics and pandemics killed large proportions of the European population, with likely consequences for the human genome as a result of positive selection acting on protective alleles. Pathophysiological evidence has suggested, for example, that cystic fibrosis mutations may confer resistance to cholera or other chloride-secreting diarrhoeas, whereas a high incidence of the CCR5-Delta32 mutation, which nowadays plays a substantial role in immunity against HIV-I infection, has been proposed to have provided some immunity against plague.

To test these and other hypotheses of selection directly on ancient DNA from cholera and plague victims of the past we developed a multilocus analysis, which simultaneously assays up to 17 genetic loci for single nucleotide polymorphisms (SNPs) or deletions, by means of minisequencing or NGS analysis. Beyond polymorphisms hypothesised to be under selection, we investigated simultaneously five neutral SNPs which enable the individualisation of each analysed skeleton and the identification of contamination. Here we presented some preliminary results obtained from the analyses of about 300 skeletons.

Co-authors: Stephanie Hänsch, Magdalena Bogus, Anja Meister, Claudio Ottoni, Antonella Lannino, Joachim Burger, Mark G. Thomas