Publications by authors named "Anna Linderholm"

20 Publications

  • Page 1 of 1

Dire wolves were the last of an ancient New World canid lineage.

Nature 2021 Mar 13;591(7848):87-91. Epub 2021 Jan 13.

School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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http://dx.doi.org/10.1038/s41586-020-03082-xDOI Listing
March 2021

Origins and genetic legacy of prehistoric dogs.

Science 2020 10 29;370(6516):557-564. Epub 2020 Oct 29.

Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
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http://dx.doi.org/10.1126/science.aba9572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116352PMC
October 2020

Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.

Nat Commun 2020 06 2;11(1):2770. Epub 2020 Jun 2.

Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.

Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.
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http://dx.doi.org/10.1038/s41467-020-16502-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265304PMC
June 2020

A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.

Proc Biol Sci 2020 06 3;287(1928):20200690. Epub 2020 Jun 3.

Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.

Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F hybrids are able to produce Fs through matings with Fs. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F offspring can produce Fs. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.
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http://dx.doi.org/10.1098/rspb.2020.0690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341909PMC
June 2020

Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland.

Sci Rep 2020 04 14;10(1):6885. Epub 2020 Apr 14.

Centre for Palaeogenetics, 10691, Stockholm, Sweden.

During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.
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http://dx.doi.org/10.1038/s41598-020-63138-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165176PMC
April 2020

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Proc Biol Sci 2019 12 27;286(1916):20191929. Epub 2019 Nov 27.

Institut des Sciences de l'Evolution-Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, Occitanie, France.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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http://dx.doi.org/10.1098/rspb.2019.1929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939252PMC
December 2019

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Authors:
Laurent A F Frantz James Haile Audrey T Lin Amelie Scheu Christina Geörg Norbert Benecke Michelle Alexander Anna Linderholm Victoria E Mullin Kevin G Daly Vincent M Battista Max Price Kurt J Gron Panoraia Alexandri Rose-Marie Arbogast Benjamin Arbuckle Adrian Bӑlӑşescu Ross Barnett László Bartosiewicz Gennady Baryshnikov Clive Bonsall Dušan Borić Adina Boroneanţ Jelena Bulatović Canan Çakirlar José-Miguel Carretero John Chapman Mike Church Richard Crooijmans Bea De Cupere Cleia Detry Vesna Dimitrijevic Valentin Dumitraşcu Louis du Plessis Ceiridwen J Edwards Cevdet Merih Erek Aslı Erim-Özdoğan Anton Ervynck Domenico Fulgione Mihai Gligor Anders Götherström Lionel Gourichon Martien A M Groenen Daniel Helmer Hitomi Hongo Liora K Horwitz Evan K Irving-Pease Ophélie Lebrasseur Joséphine Lesur Caroline Malone Ninna Manaseryan Arkadiusz Marciniak Holley Martlew Marjan Mashkour Roger Matthews Giedre Motuzaite Matuzeviciute Sepideh Maziar Erik Meijaard Tom McGovern Hendrik-Jan Megens Rebecca Miller Azadeh Fatemeh Mohaseb Jörg Orschiedt David Orton Anastasia Papathanasiou Mike Parker Pearson Ron Pinhasi Darko Radmanović François-Xavier Ricaut Mike Richards Richard Sabin Lucia Sarti Wolfram Schier Shiva Sheikhi Elisabeth Stephan John R Stewart Simon Stoddart Antonio Tagliacozzo Nenad Tasić Katerina Trantalidou Anne Tresset Cristina Valdiosera Youri van den Hurk Sophie Van Poucke Jean-Denis Vigne Alexander Yanevich Andrea Zeeb-Lanz Alexandros Triantafyllidis M Thomas P Gilbert Jörg Schibler Peter Rowley-Conwy Melinda Zeder Joris Peters Thomas Cucchi Daniel G Bradley Keith Dobney Joachim Burger Allowen Evin Linus Girdland-Flink Greger Larson

Proc Natl Acad Sci U S A 2019 08 12;116(35):17231-17238. Epub 2019 Aug 12.

The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3TG, United Kingdom;

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
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http://dx.doi.org/10.1073/pnas.1901169116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717267PMC
August 2019

The evolutionary history of dogs in the Americas.

Science 2018 Jul;361(6397):81-85

The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.

Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
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http://dx.doi.org/10.1126/science.aao4776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116273PMC
July 2018

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events.

Proc Biol Sci 2018 04;285(1876)

The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
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http://dx.doi.org/10.1098/rspb.2017.2566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904307PMC
April 2018

A novel allele for black coat colour reveals the Polynesian ancestry and hybridization patterns of Hawaiian feral pigs.

R Soc Open Sci 2016 Sep 7;3(9):160304. Epub 2016 Sep 7.

The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology , University of Oxford , Dyson Perrins Building, South Parks Road, Oxford OX1 3QY , UK.

Pigs () have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly the descendants of those originally introduced during Polynesian settlement, though there is evidence for some admixture. As such, extant Hawaiian pigs represent a unique historical lineage that is not exclusively descended from feral pigs of European origin.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043315PMC
http://dx.doi.org/10.1098/rsos.160304DOI Listing
September 2016

Genomic and archaeological evidence suggest a dual origin of domestic dogs.

Science 2016 06 2;352(6290):1228-31. Epub 2016 Jun 2.

The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.

The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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http://dx.doi.org/10.1126/science.aaf3161DOI Listing
June 2016

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.

Philos Trans R Soc Lond B Biol Sci 2015 Jan;370(1660):20130373

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden.

The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.
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http://dx.doi.org/10.1098/rstb.2013.0373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275881PMC
January 2015

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.

Proc Natl Acad Sci U S A 2014 Apr 17;111(13):4826-31. Epub 2014 Mar 17.

Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia.

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.
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http://dx.doi.org/10.1073/pnas.1320412111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977275PMC
April 2014

The role of humans in facilitating and sustaining coat colour variation in domestic animals.

Semin Cell Dev Biol 2013 Jun-Jul;24(6-7):587-93. Epub 2013 Apr 5.

Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham, United Kingdom.

Though the process of domestication results in a wide variety of novel phenotypic and behavioural traits, coat colour variation is one of the few characteristics that distinguishes all domestic animals from their wild progenitors. A number of recent reviews have discussed and synthesised the hundreds of genes known to underlie specific coat colour patterns in a wide range of domestic animals. This review expands upon those studies by asking how what is known about the causative mutations associated with variable coat colours, can be used to address three specific questions related to the appearance of non wild-type coat colours in domestic animals. Firstly, is it possible that coat colour variation resulted as a by-product of an initial selection for tameness during the early phases of domestication? Secondly, how soon after the process began did domestic animals display coat colour variation? Lastly, what evidence is there that intentional human selection, rather than drift, is primarily responsible for the wide range of modern coat colours? By considering the presence and absence of coat colour genes within the context of the different pathways animals travelled from wild to captive populations, we conclude that coat colour variability was probably not a pleiotropic effect of the selection for tameness, that coat colours most likely appeared very soon after the domestication process began, and that humans have been actively selecting for colour novelty and thus allowing for the proliferation of new mutations in coat colour genes.
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http://dx.doi.org/10.1016/j.semcdb.2013.03.015DOI Listing
October 2014

Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.

Mol Biol Evol 2013 Apr 22;30(4):824-32. Epub 2012 Nov 22.

Center for Archaeological Sciences, Department of Earth and Environmental Sciences, University of Leuven, Leuven, Belgium.

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.
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http://dx.doi.org/10.1093/molbev/mss261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603306PMC
April 2013

The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox.

Proc Biol Sci 2012 Nov 12;279(1747):4568-73. Epub 2012 Sep 12.

Department of Archaeology, Durham Evolution and Ancient DNA, Durham University, South Road, Durham DH1 3LE, UK.

Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.
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http://dx.doi.org/10.1098/rspb.2012.1796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479732PMC
November 2012

High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe.

BMC Evol Biol 2010 Mar 30;10:89. Epub 2010 Mar 30.

Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden.

Background: Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture.

Results: Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%).

Conclusions: We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.
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http://dx.doi.org/10.1186/1471-2148-10-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862036PMC
March 2010

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses.

Mol Ecol 2010 Jan 25;19(1):64-78. Epub 2009 Nov 25.

Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, 28029-Madrid, Spain.

Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.
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http://dx.doi.org/10.1111/j.1365-294X.2009.04430.xDOI Listing
January 2010

Cryptic contamination and phylogenetic nonsense.

PLoS One 2008 May 28;3(5):e2316. Epub 2008 May 28.

Archaeological Research laboratory, Stockholm University, Stockholm, Sweden.

Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002316PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2384008PMC
May 2008