.
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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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