This event is kindly supported by

CIBIO Research Center in Biodiversity and Genetic Resources, Porto University
Association Parisienne de Génétique des populations
The Municipal Council of the City of Porto
Human Biology - The International Journal of Population Genetics and Anthropology
Foundation for Science and Technology (Portugal)
 University of Porto
logos



Comparing Ancient and Modern DNA Variability
in Human Populations


International Conference -- Porto (Portugal), 23-25 November 2011

FINAL SCIENTIFIC PROGRAM vs. 2.1 (October 18, 2011)
Printable PDF version
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Wednesday, November 23, 2011
Venue: Almeida Garrett Municipal Library at the Crystal Palace Gardens
Biblioteca Municipal Almeida Garrett
Website



2.00pm – 4.00pm Registration
4.00pm – 4.30pm Franz Manni and Jorge Rocha
Welcome message
4.30pm – 5.00pm Nuno Ferrand
Scientific research in CIBIO
(Research Center for Biodiversity and Genetic Resources)

5.00pm – 6.00pm Wolfgang Haak
Invited talk: What can ancient DNA tell us about human history during the Holocene?
6.00pm – 8.00pm
Cocktail reception offered by
Human Biology
The International Journal of Population Genetics and Anthtropology




Thursday, November 24, 2011
Venue: Almeida Garrett Municipal Library at the Crystal Palace Gardens
Biblioteca Municipal Almeida Garrett
Website



First session: Comparing ancient and modern variability in sub-Arctica
9.30am – 10.15am Michael H. Crawford
Invited talk: Current developments in molecular and population genetics of contemporary and
ancient Aleut and Eskimo populations
10.15am – 10.40am

Maanasa Raghavan
Prehistoric migrations into the New World High-Arctic: A genetic perspective

10.40am – 11.15am Justin Tackney
Invited talk: Ancient and modern genetic diversity of Iñupiat populations from the Alaskan North Slope: insights into Paleo- and Neo-Eskimo origins
11.15am – 11.45am Coffee break



Second session: Comparing ancient and modern variability in Europe
11.45am – 12.10am

Maarten H. D. Larmuseau
Temporal differentiation across a West-European Y-chromosomal cline-genealogy as a tool in human population genetics

12.10am – 12.35am Eveline Altena
The Dutch medieval and post-medieval genetic landscapes
12.35am –2.30pm Lunch offered to all participants



Second session continued: Comparing ancient and modern variability in Europe
2.30pm – 2.55pm

Cristina Gamba
Comparing ancient and modern DNA variability in Northern Eastern Iberia: the Neolithic impact of first farmers

2.55pm – 3.20pm Esther J. Lee
Where are all the "WIX"? Rare European maternal lineages W, I, and X2 in the past and present



Third session: Methodology
3.20pm – 3.45pm

E. Andrew Bennett
Primer contamination with modern human DNA: problems and solutions

3.45pm – 4.10pm

Beatrice Kelemen
Usefulness of nanoparticles in enhancing aDNA extraction protocols

4.10pm – 4.40pm Coffee break



Third session continued: Methodology
4.35pm – 5.00pm

Martina Molak
Using ancient DNA in estimation of timeframes for evolutionary and demographic events

5.00pm – 5.25pm

Mannis van Oven
Global inference of uniparental biogeographic ancestry facilitated by a set of sensitive multiplex genotyping tools

5.25pm – 5.50pm

Martina Lari
Genomic selection and next generation sequencing for genetic characterization of ancient human remains from Italy



8.00pm – 10.00pm Conference dinner




Friday, November 25, 2011
Venue: Almeida Garrett Municipal Library at the Crystal Palace Gardens
Biblioteca Municipal Almeida Garrett
Website



Fourth session: Ancient DNA studies in organisms associated to humans
10.05am – 10.30am Silvia De Lima Guimaraes     NEW
Phylogeography of B. primigenius during the Holocene based on ancient mitochondrial DNA data
10.30am – 10.45am Simon J.M. Davis
Molecular and osteometric sexing of cattle metacarpals agree – evidence for
Christian improvement of cattle in Portugal
10.45am – 11.00am

F.Gabbianelli
Sex ratio of medieval livestock in a site of Central Italy

11.00am – 11.15am

F.Gabbianelli
Detecting genetic diversity in modern and ancient sheep (
Ovis aries)

11.15am – 11.40am Christos Economou
aDNA typing of leprosy cases in Medieval Scandinavia



Fifth session: Comparing ancient and modern variability in Asia and Americas
11.40am – 12.15am Phillip Endicott
Invited talk: The prehistory of the Andaman Archipelago within Southeast Asia, combining ancient and modern DNA research
12.15am – 12.40am

Timothy A. Jinam and Naruya Saitou
Evolutionary history of continental South East Asians: "Early Train" hypothesis based on complete mitochondrial DNA sequences

12.40am –2.00pm Lunch offered to all participants



Fifth session continued: Comparing ancient and modern variability in Asia and Americas
2.00pm – 2.25pm

Pontus Skoglund and Mattias Jakobsson
Archaic human ancestry in East Asia

2.25pm – 2.50pm

Monica Sans
Extermination or continuity? Mitochondrial DNA Native lineages in Uruguay

2.50pm – 3.10pm Paula Campos
The First Americans, DNA from Pre-Clovis Coprolites in Oregon, U.S.A.
3.10pm – 3.25pm Francesc Calafell
Can the Y chromosome in current men carrying the Colon or Colombo surnames be used to reveal the origin of Christopher Columbus



Sixth session: Concluding remarks
3.25pm – 3.50pm Giovanni Destro-Bisol
Mine, yours, ours? Sharing data on genetic variation in ancient and modern humans
3.50pm – 4.00pm

Franz Manni and Jorge Rocha
Concluding comments




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.ABSTRACTS


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What can ancient DNA tell us about human evolutionary history during the Holocene?

Wolfgang Haak

Australian Centre for Ancient DNA, The University of Adelaide, Australia
wolfgang.haak@adelaide.edu.au

Inferences about the genetic evolutionary past of anatomically modern humans have been based largely on data from modern-day populations. In theory, the time-travelling aspect of ancient DNA studies could help provide direct insight into past demographic events. However, despite initial excitement, issues surrounding contamination and the availability of samples suitable for ancient DNA analyses quickly became apparent and have plagued the field. Now, after more than a decade of establishing and optimizing strict scientific protocols alongside major technical and methodological innovations, the number of studies presenting reliable authentic data with special emphasis on ancient human DNA has increased. I will summarize and review important studies reporting ancient human DNA results and highlight the potential of such studies (as well as their shortcomings and pitfalls). In addition, I will present new high-resolution data from ancient human specimens that will both extend and complement the current map of ancient European populations. While recent technical advances allow the generation of extensive data from both authentic ancient and modern-day populations, I argue that a stronger emphasis on the informative value of ancient DNA studies is justified. It is also apparent that the suite of population genetic tools require adjustments to allow incorporation of the temporal information inherent in ancient human specimens.

Current Developments in the Molecular and Population Genetics of Contemporary and Ancient Aleut and Eskimo Populations

Michael H. Crawford

Kansas University, (USA)

Laboratory of Biological Anthropology, University of Kansas, Lawrence, Kansas
This presentation reconstructs the prehistoric settlement patterns of the Aleutian Islands and the Arctic regions of the Americas and Greenland on the basis of archaeological evidence, ancient DNA from skeletal remains and mt-DNA and NRY haplotypes. This unique integration of the Siberian origins of Aleuts and Eskimos, and their contemporary genetic structure comes from a collaboration (sponsored by the National Science Foundation) between the Universities of Kansas and Utah. In addition, a collaboration with Eske Willerslev of the University of Copenhagen provides whole genomic sequences of a 4,000 year old Paleo-Eskimo of the Saqqaq culture of Greenland. 
Based on the sampling of 11 Aleut populations of the Archipelago, contemporary Aleuts exhibit only A (primarily A2a1)  and D (D2a1) mt-DNA haplogroups. Mantel tests of genetic and geographic distances have produced a highly significant correlation of r=0.717 (p<0.0001) indicating that the genetic structure reflects the settlement patterns that are preserved in the maternal DNA. In contrast, there is no significant relationship between geography and genetics based on Y-chromosome haplotypes-since the gene flow from Europeans into the Aleut gene pool was unidirectional. Genetic barrier analysis of contemporary mt-DNA sequence distributions indicate genetic discontinuity, reflecting the expansion of the Aleuts from the eastern to the central islands stimulated by climatic changes 6,000 years ago.
Ancient DNA analyses of skeletal remains from three Aleutian regions (Mink Island, Port Moller and Brooks River) by Dennis O'Rourke (University of Utah) and his colleagues, reveals the presence of haplogroups A and D in two regions but B2 in one region. The presence of B is suggestive of prehistoric gene flow from Alaska and Kodiak Island populations. Whole genomic sequencing of the 4,000 year old PaleoEskimo, "Inuk," indicated that the Saqqaq sequences clustered with the Chukchi and Koryaks of Siberia-suggesting an earlier migration from Siberia along the northern slope of Alaska to Greenland. The mt-DNA sequences from the PaleoEskimo is D2a1, found primarily in Aleut populations. These data indicate that ancient DNA data provide significant insights into the evolution and migration of contemporary populations and vice versa.  

Prehistoric migrations into the New World High-Arctic: A genetic perspective

Maanasa Raghavan* and Eske Willerslev*

*Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Denmark
email: mraghavan@snm.ku.dk

Distinct cultural waves swept through the New World high-Arctic (Canada and Greenland), leaving behind well-preserved material and biological traces in the permafrost. This talk will focus on a major paleogenetic endeavor aimed at determining the genetic signatures of the three ancient high-Arctic cultures - Saqqaq, Dorset and Thule - and ascertaining any genetic relationships between them by analyzing bone, hair and teeth samples from individuals excavated from sites across the Canadian Arctic and Greenland. Current work constitutes the use of state-of-the-art next generation sequencing to identify genome-wide markers that would help resolve the phylogenetic relationships of the Saqqaq, Dorset and Thule with respect to each other as well as to modern Inuit and Native American populations. Results from this analysis will help disentangle issues surrounding the origins of the first humans in the region, the timing of these migrations, and provide some perspective on the extent to which they have individually contributed to the genetic history of the New World Arctic.

Ancient and Modern Genetic Diversity of Iñupiat Populations from the Alaskan North Slope: Insights into Paleo- and Neo- Eskimo origins

J Tackney1, JA Raff2, M Rzhetskaya2, DH O'Rourke1, MG Hayes2,3

1Department of Anthropology, University of Utah, Salt Lake City, UT
2Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL.
3Department of Anthropology, Northwestern University, Evanston, IL.

The first human colonization of the North American arctic is believed to be the result of Holocene migrations from residual populations of Beringia, a geographic region represented today by northeastern Siberia and Alaska, but constituting a much greater landmass during the lower sea levels of the late Pleistocene/Early Holocene.  The eastern Canadian arctic and Greenlandic archaeological record is characterized by at least two extinct Paleo-Eskimo material cultures (Independence I-Saqqaq and Independence II-Dorset).  Beginning around 1000 AD a cultural shift is evident across the arctic, potentially originating in northern Alaska.  This Neo-Eskimo (Thule) culture quickly occupied the region from Alaska to Greenland, and their descendents are modern Iñupiat/Inuit.
The source populations for both the Paleo-Eskimo and Neo-Eskimo are undetermined.  Iñupiat speaking populations of Canada and Greenland that have been investigated previously for mtDNA sequence diversity are uniquely homogenous when compared to southern Amerindian groups. They are characterized almost exclusively by 'Beringian-specific' mtDNA haplotypes A2a/A2b (95%) and D3 (5%).  However, very little is known genetically of Iñupiat populations from North Alaska, who currently occupy the most likely starting point for the Thule colonization of the North American arctic.  To better place these populations in the geographical and temporal context of North American arctic prehistory, their mitochondrial haplotype frequencies have been analyzed.
MtDNA hypervariable region sequences were determined from 178 consenting adults residing in all eight modern communities that span the Alaskan North Slope. We have also sequenced the same segment from ancient skeletal remains from Nuvuk, an Iñupiat village at Point Barrow, AK that was continuously inhabited for at least 1300 years until it was lost to coastal erosion in the last century.  Archaeologically recovered burials from Nuvuk, associated with the Thule tradition, have calibrated radiocarbon ages between 1187 and 1579AD.  While there was considerable variation in the pattern and frequencies of mtDNA haplogroups among the eight modern communities investigated, haplotypes A2a/A2b were the most common (88%), followed by haplogroup D3 (7%).  The ancient mtDNA results from Nuvuk at Point Barrow also reveal the expected A2a/A2b/D3 haplotypes, though with additional A2 sublineages not found in the modern samples.  Haplotype D2 (3%), found among modern Aleut and Siberian Eskimos, was identified at a low frequency in the modern samples but not the ancient.  This haplotype was recently identified in an ancient Paleo-Eskimo Saqqaq individual from western Greenland.
These results support the notions that only a subset of Beringian-specific mtDNA haplotypes were carried by the early Thule during their dispersal across the North American arctic and that the Alaskan North Slope might have served as a source region for the earlier Paleo-Eskimo migrations as well.  The late expansion and limited dispersal of arctic mtDNA haplotypes in the Americas emphasizes the need to assay the full mtDNA genome, the Y chromosome, and various autosomal markers in both the modern and ancient samples to better access their prehistory.

Temporal differentiation across a West-European Y-chromosomal cline - genealogy as a tool in human population genetics

Maarten H.D. Larmuseau1,2,3,*, Claudio Ottoni1,2,4, Joost A.M Raeymaekers3, Nancy Vanderheyden1, Hendrik F.M Larmuseau5 and Ronny Decorte1,2

1UZ Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, Kapucijnenvoer 33, B-3000 Leuven (Belgium)
2Katholieke Universiteit Leuven, Department of Human Genetics, Campus Gasthuisberg, Herestraat 49, B-3000 Leuven (Belgium)
3Katholieke Universiteit Leuven, Laboratory of Animal Diversity and Systematics, Ch. Deberiotstraat 32, B-3000 Leuven (Belgium)
4 Katholieke Universiteit Leuven, Center for Archaeological Sciences, Leuven (Belgium)
5Katholieke Universiteit Leuven, Faculty of Social Sciences, Centre of Sociological Research (CESO), Parkstraat 45 (3601), B-3000 Leuven (Belgium)
*Corresponding author: Dr. Maarten Larmuseau, Laboratory of Forensic Genetics and Molecular Archaeology, Kapucijnenvoer 33, B-3000 Leuven (Belgium). Email: maarten.larmuseau@bio.kuleuven.be. Phone: +3216336663. Fax: +3216345997.

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing in time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome genotyping to disentangle signals of historical population genetic structures due to the exponential increase of genetic genealogical data. To test this approach we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and The Netherlands (Northwest-Europe). Genealogical data of 881 individuals from Northwest-Europe were collected from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chromosome genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chromosome distribution was detected through a north-south gradient in the frequencies distribution of subhaplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-152). The gradient on R-U106 faded in time and became even totally invisible during the Industrial revolution in the first half of the 19th century. Therefore, genealogical data for at least 200 year are required to study small-scale 'autochthonous' population structure in Western-Europe.

The Dutch medieval and post-medieval genetic landscapes

Eveline Altena, Risha Smeding, Peter de Knijff.

Forensic Laboratory for DNA research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Since 2005 many archeological human skeletons have been sampled for DNA research under forensic conditions in The Netherlands. This enables us to perform a large scale genetic survey on reliable genetic data from the prehistory until the present. The majority of the available archaeological DNA samples, though, originate from medieval and post-medieval sites. Here we present preliminary autosomal and Y-chromosomal data from more then 500 archaeological human skeletons, excavated at several medieval and post-medieval sites. We also compare these historical genetic data with data from more then 2000 modern Dutch males.

Comparing ancient and modern DNA variability in North Eastern Iberia: the Neolithic impact of first farmers

Cristina Gamba, Eva Fernández, Mirian Tirado, Marie-France Deguilloux, Marie-Hélène Pemonge, Rita Rasteiro, Lounès Chikhi, Eduardo Arroyo-Pardo

Archaeological, anthropological and demographic hypotheses can be tested by comparing ancient and modern DNA from human samples in a diachronical context. In this case, it was possible to evaluate genetic continuity or discontinuity between different periods, and/or to infer ancient human migrations in a set of Iberian samples. We evaluated the demographic impact associated to the spread of the Neolithic in North Eastern Iberia. We recovered mitochondrial DNA from 13 Early Neolithic specimens from three archaeological sites: Can Sadurní, Chaves and Sant Pau. A bayesian simulation approach was performed to compare the obtained results with Middle Neolithic and modern samples from the same region. We tested different scenarios to determine which among them better explained the analyzed data. By comparing simulated and observed FST values, we observed genetic differentiation between Early Neolithic and Middle Neolithic populations, which suggests that at the beginning of the Neolithic, genetic drift played an important role.
Genetic differentiation was also observed between Early Neolithic and modern- day populations. These data are compatible with the arrival of small genetically-distinctive groups at the beginning of the Neolithic, suggesting a pioneer colonization of North Eastern Iberia by first farmers.

Where are all the "WIX"? Rare European maternal lineages W, I, and X2 in the past and present

Esther J. Lee1, Melanie Harder1, Ben Krause-Kyora1, Nicole von Wurmb-Schwark2, Almut Nebel3.

1Graduate School "Human Development in Landscapes", Christian-Albrechts-University of Kiel,
2Institute of Legal Medicine, Christian-Albrechts-University of Kiel,
3Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel.

Studies utilizing ancient DNA to examine past populations in Europe have increased dramatically in recent years. Specifically, mitochondrial DNA (mtDNA) sequences for over 100 individuals in prehistoric Europe have been sequenced and published. Scholars have intensively focused on the so-called Neolithic transition in Europe, the transformation from hunter-gatherer lifestyle to agro-pastoralism, and continue to debate whether the process was a result of population movement or cultural dispersion. Both hypotheses continue to be tested and genetics analyses from past and present populations have suggested a complex  movement of people and cultures across Eurasia. This work focuses on the mtDNA  haplogroups identified in past European populations that are rare in the present, haplogroups W, I, and X2. New data will be presented from Neolithic Funnel Beaker collective burials sites, a late Neolithic Bell Beaker site, and an Iron Age Halstatt site in Germany, in which the three maternal lineages are identified. Among the published European Neolithic data, haplogroup X2 appears in late Neolithic sites in Germany and France but not in the earlier LBK culture. Haplogroup X2 shows an intriguing phylogenetic landscape with a wide  geographical distribution at an overall low frequency, but on the other hand, pockets of high diversity and frequency among certain modern western Eurasian populations have been  described. The discussion focuses on whether the presence of the three haplogroups in the  past is a result of ascertainment bias or some viable population movement.

Primer Contamination with Modern Human DNA: Problems and Solutions

E. Andrew Bennett, Olivier Gorgé, Thierry Grange and Eva-Maria Geigl

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

Avoiding contamination by modern DNA while attempting to amplify genuine ancient molecules is one of most formidable challenges of the field. Contaminating DNA can enter the amplification reaction at multiple points, such as during excavation, museum handling, sample preparation, or it can be found within the amplification reagents themselves. Reagent-borne contaminants can be particularly dangerous when attempting to amplify ancient DNA from humans or the animals used today in commercial reagent production. This can manifest itself as occasional positives in blank controls, or worse, modern human sequence amplified from ancient extracts. These events will certainly lead to incorrect conclusions concerning human population migrations or continuity, population admixtures, or the geographic origins of individuals. We have systematically identified sources of reagent contamination and developed a method to decontaminate PCR reagents for use in ancient DNA and other sensitive amplifications (Champlot, et al. PLoS One 2010, 5(9): e13042), but removing contaminating DNA from DNA primers without damaging them has remained problematic. Using qPCR methods to investigate ancient human DNA, we have identified commercial primers as a major source of modern human DNA contamination and found batch-to-batch and provider-to-provider variation in the pattern of contaminating human DNA. To address this vital problem, we have developed and tested several strategies to decontaminate commercial primers of modern human DNA. We present a robust method to eliminate this significant contaminant from primers that will greatly benefit the reliability of future ancient human DNA data derived using traditional PCR and qPCR methods.
 
Usefulness of nanoparticles in enhancing aDNA extraction protocols

Kelemen Beatrice1, PONTA Oana2, BARBU-TUDORAN Lucian3, LUPAN Iulia1, ROMAN Delia4, SIMON Simion2, POPESCU Octavian1

1 Babes-Bolyai University, Interdisciplinary Research Institute on Bio-Nano-Sciences, Molecular Biology Center, Cluj-Napoca, Romania
2 Babes-Bolyai University, Interdisciplinary Research Institute on Bio-Nano-Sciences, … , Cluj-Napoca, Romania
3 Babes-Bolyai University, Faculty of Biology and Geology, Electron Microscopy Center, Cluj-Napoca, Romania
4 Corvin's Castle Museum, Hunedoara, Romania

Ancient human skeletal samples are known to preserve DNA in various degrees of preservation depending on age and burial conditions. Different sources and methods of extraction are used today for higher yield and high quality total DNA from ancient human skeletal samples. Even so, downstream applications, mainly PCR, are less successful compared with reactions involving fresh DNA sources, due to the degradation of the available DNA. Contamination by modern templates must be attentively and painstakingly monitored increasing thus time and resource allotted to sample processing.
In the present study we test a new total DNA extraction protocol which involves a step of positively charged nanoparticles addition during various phases of the DNA extraction in order to observe their effect on the quantity, quality and usefulness of the obtained DNA in downstream applications. Relative few studies have recently proposed nanoparticles based protocols for DNA extraction, and even fewer focus on aDNA. These papers try to promote methods circumventing Taq polymerase amplification of target sequences in order to avoid errors introduced by the polymerase and replication errors, whereas the present study tries to increase the yield of the DNA isolation protocol.
Combining nanotechnologies and classic DNA isolation protocols may prove a relatively economic solution for aDNA isolation to be used in Taq polymerase based amplification of targeted sequences.

Using ancient DNA in estimation of timeframes for evolutionary and demographic events in hominins

Martyna Molak and Simon YW Ho

School of Biological Sciences, University of Sydney, NSW 2006, Australia
corresponding author: martyna.molak@sydney.edu.au

Ancient DNA sequences are increasingly used in phylogenetic inference, both at the species and population levels. Although contamination poses a major problem for studies of human ancient DNA, the opportunity to explore the history of our own species makes this a very active area of research. This interest is reflected in the recent publication of a number of whole genomes of ancient humans and hominins [1-3].
One of the uses of ancient DNA in phylogenetics is the estimation of timeframes for evolutionary or demographic events. This is achieved by combining the genetic information carried by the sample with the information about its age, usually obtained by radiocarbon dating or from the stratigraphic/archaeological context. As with any other parameters that are estimated, the ages of the samples carry some amount of uncertainty. In this study we investigate how those uncertainties affect accuracy and precision when estimating the timescale of human evolution and migration. We also evaluate how the estimates are influenced by various characteristics of the data, such as the number and length of sequences, the timeframe spanned by the ancient samples, and the amount of genetic variation captured.
Our study focuses on Bayesian phylogenetic analysis, which allows the incorporation of prior knowledge, such as the ages of the samples and the distribution of associated uncertainty, when reconstructing the tempo and mode of evolutionary events. This makes the method highly suitable for analyses of data sets containing ancient DNA.
 The evaluation of factors affecting the power of using ancient DNA sequences is essential for assessing the reliability of previous studies of hominin evolution and human genetic diversity. Furthermore, it can provide guidance in the design of future research on the processes shaping the course of human populations over time.

1.    Reich, D., et al., Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 2010. 468: p. 1053-60.
2.    Rasmussen, M., et al., Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 2010. 463: p. 757-62.
3.    Green, R.E., et al., A draft sequence of the Neandertal genome. Science, 2010. 328: p. 710-22.

Global inference of uniparental bio-geographic ancestry facilitated by a set of sensitive multiplex genotyping tools

Mannis van Oven1*

*With: Mark Vermeulen1, Arwin Ralf1, Nathalie van den Tempel1, Kaye Ballantyne1,2, Mark Stoneking3, R. John Mitchell4, Roland A.H. van Oorschot2, and Manfred Kayser1.
1 Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
2 Forensic Services Department, Victoria Police, Macleod, Victoria, Australia
3 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
4 Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia

Abstract
Inferring bio-geographic ancestry from human DNA is of relevance in population genetic/anthropological studies including those involving ancient DNA. The two haploid genetic systems in humans, the paternally inherited Y chromosome and the maternally inherited mitochondrial DNA (mtDNA), carry informative signatures of patrilineal and matrilineal bio-geographic ancestry, respectively. Here we present a set of efficient genotyping assays for the hierarchical determination of haplogroup-defining SNPs on the Y chromosome and on mtDNA. In particular, we developed a global multiplex system for the detection of the major continental mtDNA haplogroups, including dedicated assays for the distinction of Eurasian and Native American haplogroups, as well as Australian Aboriginal and Near/Remote Oceanian haplogroups. For the Y chromosome, a system was established that allows the detection of the major worldwide Y haplogroups; in addition, we developed a supplementary assay devoted to the dissection of Y haplogroup O (the dominant Y haplogroup in East and Southeast Asia) into its most significant sublineages.
All assays make use of the single-base primer extension (SNaPshotTM) technology and were designed to provide high sensitivity in order to minimize template consumption and to allow the analysis of fragmented DNA. Across all assays, PCR amplicon sizes ranged between 45 and 237 bp, with an average of 116 bp. The use of short PCR amplicons, in combination with the sensitive primer extension technology, makes the assays expectedly suitable for application to ancient DNA (although this was not explicitly tested). Furthermore, the multiplexing potential, enabling multiple SNPs to be interrogated simultaneously, reduces the number of reactions needed as compared to singleplex genotyping, thereby limiting the consumption of template. In conclusion, the multiplex tools introduced here facilitate Y chromosome and mtDNA haplogroup inference at a global scale, using a sensitive and readily implementable technology.

Genomic Selection and Next Generation Sequencing for genetic characterization of ancient human remains from Italy

Martina Lari1, Ermanno Rizzi 2, Carlotta Balsamo2, Giorgio Corti1, Silvia Ghirotto3, Francesca Tassi3, Annamaria Ronchitelli4, Alessandra Fischetti5, Gianluca De Bellis1, Guido Barbujani3, David Caramelli2

1Dip. di Biologia Evoluzionistica, Laboratori di Antropologia, Università di Firenze, via del Proconsolo 12 , 50122 Firenze, Italy.
2Institute for Biomedical Technologies - National Research Council (ITB-CNR), Via F.lli Cervi 93, 20090, Segrate (MI) Italy.
3Dip. di Biologia ed Evoluzione Via Borsari 46, Università di Ferrara, 44100 Ferrara, Italy.
4Dip. di Scienze Ambientali "G. Sarfatti", UR: Ecologia Preistorica, Università degli Studi di Siena,Via T. Pendola n. 62, 53100, Siena  Italy.
5 TELTEC srl, Via Lecco n°4, Agrate Brianza (MI), 20041 Italy

The study of ancient nuclear DNA in humans has been severely limited by the difficulty to ascertain whether the DNA sequences obtained are really endogenous to the specimen. However, nuclear DNA sequences recovered from early modern humans could shed light on DNA diversity in the past, and could pave the ground for a deeper understanding of human evolutionary history.
The advent of next-generation sequencing methods (NGS), allowed in some cases to overcome these limitations. We applied a combined method of target enrichment by capture and subsequent NGS to a human specimen of the Upper Palaeolithic (Paglicci of the layer 23) previously successfully characterized.
Capture probes were synthesized as oligo-nucleotides using in-situ synthesis Customarray(TM) platform. Oligos were subsequently RNA transformed and biotinylationed to allow target enrichment collection. Customarray's enrichment pool has a high grade quality due to the use of classical phosphoramidite chemistry. The high quality chemistry process allows reliable and reproducible data and moreover long oligos synthesis (up 120 mer). The fast turnaround and the limited cost of the custom pool, allowed to design and optimize target enrichment experiments in few days, for big or small region of interest. Target region for probe design encompassed the entire human mitochondrial genome and several nuclear loci in order to provide a phylogenetic and phenotypic classification.  Genomic enrichment targeted several genes involved in the expression of features that may have played an important role in the evolution of humans such as skin and hair pigmentation, cognitive, cardiac and respiratory function, perception of different tastes. Enriched samples, after library preparation, were quantitated using quantitative PCR (qPCR), 454 pyrosequenced and analysed in order to identify endogenous sequences.

Phylogeography of B. primigenius during the Holocene based on ancient mitochondrial DNA data

Silvia De Lima Guimaraes1, Mélanie Pruvost1, Reinhard Schwarz1, Michael Hofreiter2, Bénédicte Bertrand1, Virginia Bessa Correia1, Marie Liouville1, Matthias Meyer2, Frantz Depaulis3, Mathieu Gautier4, Simon Ho5,  Rose-Marie Arbogast6, Sévérine Braguier7, Anne Bridault8, Hijlke Buitenhuis9, Simon Davis10, Lamys Hachem8, Hitomi Hongo11, Gülçin Ilgezdi12, Corina Liesau von Lettow-Vorbeck13, Denise Moser14, Mihriban Özbasaran15, Mehmet Özdogan15, Joris Peters16 Ingrid Wiechmann16, Antonio Taglioacozzo17, Hans-Peter Uerpmann14, Thierry Grange1 and Eva-Maria Geigl1
 
1, Institut Jacques Monod CNRS-Université Paris Diderot, 15, rue Hélène Brion, 75013 Paris, France. melpruvost@googlemail.com or delimaguimaraes.silvia@ijm.univ-paris-diderot.fr or thierry.grange@univ-paris-diderot.fr or geigl.eva-maria@ijm.univ-paris-diderot.fr
2, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany. michi@palaeo.eu or mmeyer@eva.mpg.de
3, Ecole normale supérieure UMR 7625 - Fonctionnement et Evolution des Systèmes Ecologiques, Laboratoire d'Écologie, Paris, France. depaulis@biologie.ens.fr
4, INRA, UMR de Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France. mathieu.gautier@jouy.inra.fr
5, Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, Australia. simon.ho@anu.edu.au
6, CNRS/UMR 7044/MISHA, Strasbourg. rose-marie.arbogast@misha.fr
7, severine.braguier@orange.fr
8, Institut National de Recherches Archéologies Préventives (INRAP), Pantin, France, and Maison de l'Archéologie et de l'Ethnologie, Nanterre, France. Maison de l'Archéologie et de l'Environnement, UMR 7041, Arscan, Protohistoire Européenne, Nanterre, France. lamys.hachem@inrap.fr or lamys.hachem@mae.u-paris10.fr
9, ARC Groningen, The Netherlands.  h.buitenhuis@arcbv.nl
10, Instituto Português de Arqueologia (IGESPAR), Lisboa, Portugal. simonjmdavis@gmail.com
11, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama, Miura, Kanagawa, Japan. hongouhm@soken.ac.jp
12, Prehistorya Middle East Technical University, ODTÜ, Ankara, Turkey. gilgezdi@yahoo.com
13, Dpto de Prehistoria y Arqueología, Facultad de Filosofía y Letras, Universidad Autónoma de Madrid, Madrid. liesau@uam.es
14, Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany. hans-peter.uerpmann@uni-tuebingen.de and Jeanise@web.de
15, Prehistorya Anabalim Dali, Edebiyat Fakultesi, Istanbul University, Istanbul, Turkey. mozdo@atlas.net.tr
16, Institut für Palaeoanatomie und Geschichte der Tiermedizin, Ludwig-Maximilians-Universität München, Munich, Germany. joris.peters@palaeo.vetmed.uni-muenchen.de
17, Soprintendenza al Museo Nazionale Preistorico Etnografico "Luigi Pigorini", Roma, Italy. antonio.tagliacozzo@beniculturali.it.

The domestication of the aurochs has been studied over the last ten years by both archaeozoologists and palaeogeneticists. It is still not entirely clear, however, which aurochs populations were initially domesticated and whether and where post-domestication events took place. In the framework of a close collaboration with archaeozoologists we performed a palaeogenetic study of remains of aurochsen and domesticated cattle from Europe and Southwest Asia (SWA) spanning the last 10,000 years to analyze the genetic diversity of B. primigenius in Eurasia during the Holocene and its impact on cattle domestication. This study is based on considerable methodological development to overcome the severe problems linked to reagent contamination with bovine DNA leading to erroneous results that biased published ancient DNA studies of cattle. Our recent results question current views of the domestication process and can explain some features of the population structure of extant cattle in Eurasia.

Molecular and osteometric sexing of cattle metacarpals agree - evidence for Christian improvement of cattle in Portugal

Simon JM Davis1, Emma Svensson2, Umberto Albarella3, Cleia Detry4, Anders Götherström2, Ana Elisabete Pires5,6, Catarina Ginja5,6

1Instituto de Gestão Património Arquitectónico e Arqueológico, IGESPAR, Lisboa, Portugal [sdavis@igespar.pt]
2Department of Evolutionary Biology, Evolutionary Biology Centre, University of Uppsala, Sweden [esvensson09@gmail.com & anders.gotherstrom@ebc.uu.se]
3Department of Archaeology, University of Sheffield, England [u.albarella@sheffield.ac.uk]
4UNIARQ - Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa, Portugal [cdetry@gmail.com]
5Grupo de Biologia Molecular, Instituto Nacional de Recursos Biológicos, I.P., Lisboa, Portugal
6Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Portugal [elisabete.pires@inrb.pt & catarinaginja@gmail.com]

In the course of a zooarchaeological survey of Holocene archaeological sites in southern Portugal, a substantial size increase of cattle teeth and bones was noted following the Christian reconquista (Davis 2008). In general a size increase in the course of time within a lineage of domestic livestock is considered to represent their improvement (Schlumbaum et al. 2003). However, several other factors, including sex, may influence the average size of a sample of mammal bones - cattle exhibit considerable sexual size dimorphism with bulls being larger than cows. A histogram of the distal metacarpal widths of a large sample (n=44) from 15th century Beja (Alentejo, Portugal) revealed a bimodal distribution. It was assumed that the large measurements belonged to males and the small to females. In order to rule out the possibility of a post-Moslem change in the sex ratio of cattle a subsample of 21 cattle metacarpals from Beja were analysed for a single nucleotide polymorphism (SNP) that identifies male and female cattle (Svensson et al. 2008). The ancient DNA sexing of all specimens agreed with the previously assumed sex determined osteometrically. We conclude that the two nearly separated peaks for the distal width measurements do indeed indicate sex. A similar bimodal distribution was obtained from another large but earlier sample of cattle metacarpals from Moslem Alcáçova de Santarém (9th-12th century AD). Although these have not been molecularly sexed and since osteometric sexing has now been validated, we conclude that both small (female) and large (male) peaks are smaller than the 15th century ones and that there was an overall size increase or improvement of cattle in this region. Why the Christians improved cattle is unclear, but a selection for larger beeves for meat is one possibility as is the selection of more robust cattle for power. The spread of the quandrangular or chariot plough in Iberia is known to have occurred at this time.

Davis, S.J.M. (2008) Zooarchaeological evidence for Moslem and Christian improvements of sheep and cattle in Portugal. Journal of Archaeological Science 35 (4), 991-1010
Schlumbaum, A.; Stopp, B. ; Breuer, G. ; Rehazek, A.; Blatter, R.; Turgay, M. & Schibler, J. (2003) Combining archaeozoology and molecular genetics: the reason behind the changes in cattle size between 150 BC and 700 AD in Northern Switzerland. Antiquity 77, Nº 298 (http://antiquity.ac.uk/ProjGall/schlumbaum/index.html)
Svensson, E. & Götherström, A. (2008) Temporal fluctuations of Y-chromosomal variation in Bos taurus. Biology Letters 4, 752-754.

Sex ratio of medieval livestock in a site of Central Italy

Gabbianelli F., Valentini A., Alhaique F., Mascelloni A., De Minicis E., Pariset L.

federica.gabbianelli@unitus.it -- Università della Tyscia, Italy

Sex determination in ancient livestock remains may be very helpful in reconstructing exploitation strategies adopted by ancient population, thus providing important insights on past human economies. However, in an archaeological faunal assemblage, usually only a few specimens may be confidently sexed on morphological or dimensional bases and wrong assignments are likely to occur because of animal size changes through time, low sexual dimorphism, presence of different breeds, etc.
The aim of the present research is to discriminate between male and female cattle remains in an assemblage from the medieval layers of Ferento (Viterbo, Italy). The study is particularly important because for large livestock age profiles are not as informative on the actual use of the animals (meat, milk or animal power) as for ovicaprines and the application of DNA analysis may represent an innovative approach.
Ferento is a site where cattle often occurs in high percentages and in some of the medieval layers it represents the most frequent animal. Sex information is therefore fundamental for assessing the employment of Bos taurus in this town shedding light on human economies in Central Italy during this period of human history.
We applied a method previously set up in our lab, allowing a fast and secure discrimination between male and female cattle bones,  based on the simultaneous amplifications of both ZFX/ZFY genes and the selective digestion of the same PCR products with two restriction enzymes.
The preliminary results show that, out of 10 specimens analysed, 8 are males and 2 females. Such prevalence of males may suggest that during the Middle Ages at Ferento cattle were exploited mainly for their meat. This hypothesis is in agreement with the archaeological and historical interpretation of the town as a center where handicraft activities, rather than agricultural ones, were mainly carried out.

Detecting genetic diversity in modern and ancient sheep (Ovis aries)

Gabbianelli F., Mariotti M., Valentini A., Alhaique F., Mascelloni A., De Minicis E., Pariset L.

federica.gabbianelli@unitus.it -- Università della Tyscia, Italy

The domestication of wild sheep occurred about 11,000 years ago in Southwestern Asia, as documented by archaeozoological and genetic evidences.
The mitochondrial DNA (mtDNA). of 16 medieval sheep (Ovis aries) bones retrieved in the archaeological site of Ferento (Viterbo, central Italy) was analyzed. These ancient samples were compared with modern ones from Europe and Middle East in order to identify similarities between them and reconstruct migration routes.
Preliminary data suggest that Ferento sheep belong to haplogroup B (typical of European sheep breeds) even if, surprisingly, one specimen belongs to haplogroup A (common in animals from the Middle East and Asia) suggesting hypothesis on ancient migration routes.

aDNA typing of leprosy cases in Medieval Scandinavia

Christos Economou

Leprosy has been one of the most talked-about diseases that have plagued mankind and the impact that it had to populations of the past can be deduced from the various references that can be found in texts dated as back as 600 BC in India, descriptions by ancient Greek and Roman physicians, the leprosaria that were founded in Europe during the Middle-Ages and the Biblical stories among others. Thought to have originated in Asia and reached the Mediterranean with the army of Alexander the Great returning from its campaign, it became prevalent in Europe in the 12th-13th centuries AD, with a subsequent decline in the continent but areas of Scandinavia where it persisted until the 19th century. After the initial stages the infection can even affect the skeleton leaving deformities that are indicative to the osteoarchaeologists. Ancient-DNA analysis have proven to be a powerful tool in the studies of palaeopathology as -apart from the actual presence of the microorganism- it can refer to its evolution and the phylogeography patterns that a disease follows.
In this study, M. leprae DNA sequences have been successfully extracted from human remains found in Medieval Sweden showing not only the existence of leprosy at that particular time and space but a type of the disease unique to what has been considered to be the case in Europe so far. Previous studies on the various genetic profiles of the bacterium around the world using modern, as well as ancient, samples, have shown the existence of a number of distinct types and sub-types of the pathogen, regarding its evolution and spatial distribution. Our results show the presence of a type of M. leprae that so far had only been found in Middle-East, implying that a transmission took place, affecting that population in Scandinavia.

The prehistory of the Andaman Archipelago within Southeast Asia, combining ancient and modern DNA research

Phillip Endicott

Musée de l'Homme, Paris

The prehistory of the Andaman archipelago is a topic of enduring interest within anthropology, due to the unusual phenotype and isolated languages of the indigenous groups, who displayed considerable linguistic and phenotypic diversity at the time of European contact. Unfortunately, the majority of the Greater Andaman populations did not survive the ravages of the Colonial experience, dictating that current genetic research conclusions are formulated on data from a small subset of the original population. A deeper understanding of the genetic structure and diversity of Andaman linguistic groups at the time of contact is a prerequisite to assessing whether the surviving populations are representative of the past, attempting to reconstruct the demographic prehistory of the archipelago, and resolving its relationship to the rest of Southeast Asia.
Mitochondrial DNA was extracted from 40 Museum samples designated as Northern and Southern Greater Andamanese, and genetic profiles obtained using multiplexed SNP genotyping and control region sequencing. These were combined with data from living populations to model the demographic history of the Andaman Islands. Additional 19th century individuals from Sentinel Island and the neighbouring Nicobars were included for comparison. Whole mitochondrial genomes were sequenced from surviving Greater Andamanese and maternally related individuals living throughout South and Southeast Asia to further investigate genetic connections within and between the regions and provide data for phylogenetic dating.
The results demonstrate hitherto unsuspected connections between the Nicobar and Andaman archipelagos that were not detectable using extant populations. Crucially, a rare mitochondrial DNA haplogroup, previously considered to be a recent intrusion to the Andamans is shown to reflect a deep separation from other regions of Southeast Asia. The geographic distribution and diversity of the haplogroup suggests that it may have been part of the early settlement of Island Southeast Asia and that a subsequent back migration took it to South Asia. Within the Andamans, there is clear overlap of linguistic and genetic boundaries, reflecting ancient divisions that are also observed in material culture. Overall, the study demonstrates the power and utility of combining high quality ancient DNA research with modern population genetics.

Evolutionary history of continental South East Asians: "early train" hypothesis based on complete mitochondrial DNA sequences

Timothy A. Jinam1,2, Lih-Chun Hong3, Maude E. Phipps4, Mark Stoneking5, Mahmood Ameen3, Juli Edo6, and Naruya Saitou2,1

1Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
2Division of Population Genetics, National Institute of Genetics, Mishima, Japan
3Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
4School of Medicine and Health Sciences, Monash University (Sunway Campus), Selangor, Malaysia
5Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
6Department of Anthropology, Faculty of Arts and Social Sciences, University of Malaya, Kuala Lumpur, Malaysia

The population history of the indigenous populations in Southeast Asia is generally accepted to have been shaped by two major migrations; the ancient 'Out of Africa' migration ~50,000 years before present (YBP) and the relatively recent 'Out of Taiwan' expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated from the ancient migration whereas the majority of Southeast Asians are associated with the Austronesian expansion. We determined 86 complete mitochondrial DNA (mtDNA) sequences and conducted an analysis to test the plausibility and impact of those migration models in four indigenous Malaysian populations. Mitochondrial haplogroup R21 was most frequent in the Negirots (Jehai), indigenous to West Malaysia and date back to the Pleistocene (~40,000 YBP). The three Austronesian groups (Bidayuh, Selatar and Temuan) showed high frequencies of haplogroups which originate from the Asian mainland dating to around 30,000 to 15,000 YBP while showing low frequencies of 'Out of Taiwan' markers. Principal Component Analysis differentiates the Negritos from the Austronesians while showed a dichotomy between continental and island Austronesian groups. Taken together, our results suggest an 'early train' migration originating from Indochina or South China around late-Pleistocene to early Holocene period which predates, but may not necessarily exclude, the proposed Austronesian expansion.

Archaic human ancestry in East Asia

Pontus Skoglund & Mattias Jakobsson

Department of Evolutionary Biology, Uppsala University, Norbyv. 18D, 75236 Uppsala,
Sweden

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We re-analyzed the signal of archaic ancestry in modern human populations and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. We show that genetic drift coupled with an ascertainment bias for common alleles can cause artificial, but largely predictable, differences in affinity to archaic genomes between descendants of an admixture event. In genotype data from non-African humans, this effect results in a biased genetic similarity to Neandertal with increasing distance from Africa. In addition to the two previously reported connections between non-Africans and Neandertals as well as between Oceanians and a Denisovan archaic human genome from Siberia, we found a significant affinity between East Asians (in particular Southeast Asians) and the Denisovan genome, a pattern that is not expected under a model of solely Neandertal-related admixture in the ancestry of East Asians. This observation could be explained either by substantial migration from Oceania into East Asia, or more common history between anatomically modern- and archaic populations than previously proposed.

Extermination or continuity? Mitochondrial DNA Native lineages in Uruguay.

M. Sans, G. Figueiro, P.C. Hidalgo

Departamento de Antropología Biológica, Facultad de Humanidades, Universidad de la República, Uruguay.

At the moment of the Iberian conquest, three or four Native ethnic groups lived in the present territory of Uruguay, South America. Several ethnohistorical sources refer to their extermination not later than the 19th Century. However, genetic studies of the modern Uruguayan population show a Native contribution of around 10% (nuclear DNA) and 30% maternal (mitochondrial DNA (mtDNA)). 
Our first aim was to analyze ancient DNA from two Uruguayan regions, namely East and West. Our second aim was to determine the existence of continuity between prehistoric or historic individuals and the present population, and third, to compare haplogroup frequencies and hypervariable region I (HVR I) sequences with those in the contemporary population.
To accomplish these aims, we analyzed the presence of the four major Amerindian mtDNA haplogroups by RFLPs as well as mtDNA-HVR I sequences in 14 prehistoric individuals from the East and 7 from the West, one historic individual (born ca. 1780), and around 400 individuals carrying Amerindian haplogroups taken from the present population living in different regions of the country.
We found some interesting facts: a) considering the sample as a whole, we found mtDNA haplogroups A, B, C, and D; b) at least one lineage, not detected in other populations out of Uruguay, appeared in prehistoric times at least 1610 years B.P and continues at present; this lineage is probably part of haplogroup C1d, but adds mutations at positions 16288 and, in more recent times, 16140; and c) no substructures were found in the present population regarding the haplogroup distribution that could be related with the original populations; B and C were the most frequent haplogroups while D had the lowest frequency. The results are discussed in relation to regional history and the distribution of mtDNA haplogroups in America.

The first Americans, DNA from Pre-Clovis human coprolites in Oregon, U.S.A.

Paula F. Campos1, Dennis L. Jenkins2, Thomas W. Stafford3, Jr., Eske Willerslev1

1Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
2Museum of Natural and Cultural History, 1224 University of Oregon, Eugene, OR 97403-1224, USA.
3 Stafford Research Laboratories, 200 Acadia Avenue, Lafayette, CO 80026, USA.

The timing, route and origin of the first human migration into the Americas are still heavily debated. The most widely accepted dates of occupation relate 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 technology that appears to have originated and spread throughout North America in as little as 200 to 300 years.
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). These coprolites are >1000 14C years older than the accepted dates for the Clovis complex.
Here we present new genetic, archaeological and stratigraphical data that further confirm
these results. Nothing is known about the genetic relationship between these Pre-Clovis
human remains and the Clovis culture or other modern humans. Our current work is lookingat using PEC (primer extension capture) coupled with state-of-the-art next generation sequencing (Illumina, Hi Seq) to target the complete mitochondrial genome of Clovis and Pre-Clovis people in order to help resolve the phylogenetic placement of these first Americans and possibly disentangle issues surrounding the origin of the first Americans and the timing and route of these migrations.

Can the Y chromosome in current men carrying the Colom or Colombo surnames be used to reveal the origin of Chistopher Columbus?

Francesc Calafell1, Luis Javier Martínez-González2, Esther Martínez-Espín3, Juan Carlos Álvarez4, Francesc Albardaner5, Olga Rickards6, Cristina Martínez-Labarga6, José Antonio  Lorente2,4

1. Institute of Evolutionary Biology (CSIC-UPF), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
2. GENYO - Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica y Oncología, Granada, Spain
3. LORGEN GP, S.L., Granada, Spain
4. Dept. of Legal Medicine. University of Granada, Spain
5. Centre d'Estudis Colombins, Òmnium Cultural, Barcelona, Catalonia, Spain
6. Centre of Molecular Antropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy

According to most historians, Christopher Columbus was born in Genoa, Italy. However, based on some key facts in the discoverer's biography, as well as in the linguistic analysis of his texts, some historians and linguists believe that Columbus could have been of Catalan origin. A Ligurian Columbus would have carried the Colombo surname, while he would have been called Colom if he were Catalan. In order to test whether it would be possible to discriminate between a Ligurian or a Catalan origin were Columbus' Y chromosome haplotype to be retrieved, we genotyped 17 Y-chromosome STRs in 238 Spanish (from Catalonia, Valencia, and the Balearic Islands) and French Colom men, 114 North Italian Colombo (from Liguria, Lombardy, and Piedmont). The Italian samples, and, in particular, the Lombard Colombos, were genetically as diverse as the general population, and we found little evidence of clusters of haplotypes that could indicate descent from a single founder. Colombo is actually the most frequent surname in Lombardy, where foundlings and orphans used to be given the surname Colombo. By contrast, Y chromosome diversity was reduced in the Iberian Colom, where most of the men had Y chromosomes belonging to a few lineages. This implies that a positive identification would be more likely if Columbus were of Catalan descent. In this study, we have shown how the study of present populations, in conjunction with ancient DNA studies, can be used to address very specific historical questions.

Mine, yours, ours? sharing data on genetic variation in ancient and modern humans

Nicola Milia1,2,§, Alessandra Congiu1,2,§, Paolo Anagnostou1,3, Francesco Montinaro3, Emanuele Sanna2 and Giovanni Destro Bisol1,3*

1 Università di Roma "La Sapienza", Dipartimento di Biologia Ambientale, Roma Italy
2 Università di Cagliari, Dipartimento di Biologia Sperimentale, Cagliari, Italy
3    Istituto Italiano di Antropologia, Roma, Italy
§ These authors contributed equally to the work
*destrobisol@uniroma1.it

The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. However, it has been argued that its possible advantages in terms of better exploitation of data and optimized use of resources may be counteracted by the time and economic costs required, underlying ethical concerns, and conflicts of interest with patenting discoveries. In this contrasting scenario, empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 410 mitochondrial and Y chromosomal datasets reported in 379 papers indexed in the Pubmed database from 2008 to 2010. A substantial portion of datasets (17.6%) was found to be withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 87%. Our results suggest that future strategies should view complete data sharing as a mandatory requisite before final publication, and consider possible differences in sharing behavior even among closely related research fields  such as evolutionary, medical and forensic genetics. Finally, we observed a 72.7% increase in citations for shared datasets compared to the withheld ones,  and estimated that 37% to 43% of total resources were used to generate withheld datasets. Making the scientific community and the public aware of these two important aspects, we may help popularize a more effective culture of data sharing. 
Using ancient DNA in estimation of timeframes for evolutionary and demographic events in hominins.


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