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Assessing the Genetic Identity of Tuscan Sweet Chestnut (Castanea sativa Mill.). FORESTS 2022. [DOI: 10.3390/f13070967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The sweet chestnut (Castanea sativa Mill.) is an important species of European trees, studied for both ecological and economic reasons. Its cultivation in the Italian peninsula can be linked to the Roman period and has been documented, especially in the Tuscan region, for centuries. We sampled 131 grafted trees from three separate areas to determine the genetic variability between populations and assess genetic identity for different varieties of trees, which is useful for future breeding programs and propagation efforts. Molecular analyses were performed using eight microsatellite loci. A total of 98 alleles was detected with an average of 12.3 alleles per locus. We found high levels of genetic diversity within the varieties of the same area, ranging between He = 0.682–0.745. Of the eight loci, seven were found to be at Hardy-Weinberg equilibrium. (FST values Differentiation between cultivation areas was significant between 0.052–0.147) with the two Southern Tuscan areas showing the closest relationship as also indicated by Bayesian inference of the population structure, which revealed the existence of three ancestral gene pools of origin. Demographic events were detected by a coalescent-based approximate Bayesian computation in two of the homogeneous clusters. This work is a step forward for the conservation of this iconic species, albeit at a regional level, as chestnut varieties have never received the full attention of breeders.
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2
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Sarno S, Cilli E, Serventi P, De Fanti S, Corona A, Fontani F, Traversari M, Ferri G, Fariselli AC, Luiselli D. Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia). Ann Hum Biol 2021; 48:247-259. [PMID: 34459340 DOI: 10.1080/03014460.2021.1937699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea. AIMS The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events. SUBJECTS AND METHODS The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belvì (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples. RESULTS While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belvì cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals. CONCLUSION This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility.
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Affiliation(s)
- Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Patrizia Serventi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy
| | - Andrea Corona
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Università di Pavia, Pavia, Italy
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Mirko Traversari
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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3
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Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, Al-Asadi H, Dey K, Joseph TA, Liu CC, Der Sarkissian C, Radzevičiūtė R, Michel M, Gradoli MG, Marongiu P, Rubino S, Mazzarello V, Rovina D, La Fragola A, Serra RM, Bandiera P, Bianucci R, Pompianu E, Murgia C, Guirguis M, Orquin RP, Tuross N, van Dommelen P, Haak W, Reich D, Schlessinger D, Cucca F, Krause J, Novembre J. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun 2020; 11:939. [PMID: 32094358 PMCID: PMC7039977 DOI: 10.1038/s41467-020-14523-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/30/2022] Open
Abstract
The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.
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MESH Headings
- Archaeology/methods
- Body Remains
- Chromosomes, Human, X/genetics
- Chromosomes, Human, Y/genetics
- DNA, Ancient
- DNA, Mitochondrial/genetics
- Datasets as Topic
- Female
- Genetics, Population/history
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Human Migration
- Humans
- Italy
- Male
- Models, Genetic
- Sequence Analysis, DNA
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Affiliation(s)
- Joseph H Marcus
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA
- Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Anja Furtwängler
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Hussein Al-Asadi
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Kushal Dey
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Tyler A Joseph
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Clio Der Sarkissian
- Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse 3, Toulouse, France
| | - Rita Radzevičiūtė
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Megan Michel
- Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | - Patrizia Marongiu
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Daniela Rovina
- Soprintendenza Archeologia, belle arti e paesaggio delle province di Sassari e Nuoro, Sassari, Italy
| | - Alessandra La Fragola
- Departamento de Geografía, Historia y Humanidades Escuela Internacional de Doctorado de la Universidad de Almería, Almería, Spain
| | - Rita Maria Serra
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy
| | - Pasquale Bandiera
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy
| | - Raffaella Bianucci
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, 15121, Alessandria, Italy
- Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, 10126, Turin, Italy
| | - Elisa Pompianu
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Clizia Murgia
- Universitat Autònoma de Barcelona, Departament de Biologia Animal, Biologia Vegetal i Ecologia, 08193, Barcelona, Spain
| | - Michele Guirguis
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Rosana Pla Orquin
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Peter van Dommelen
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, 02912, USA
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy.
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany.
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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Abstract
The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA (aDNA) studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. We find Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland aDNA samples varies subtly across the island. Together, our results indicate within-island sub-structure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.
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Leonardi M, Sandionigi A, Conzato A, Vai S, Lari M, Tassi F, Ghirotto S, Caramelli D, Barbujani G. The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:497-506. [PMID: 30187463 DOI: 10.1002/ajpa.23679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/14/2018] [Accepted: 06/19/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast. MATERIALS AND METHODS We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups. RESULTS Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes. CONCLUSIONS The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation.
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Affiliation(s)
- Michela Leonardi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Anna Sandionigi
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Annalisa Conzato
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
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6
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Silva NM, Rio J, Currat M. Investigating population continuity with ancient DNA under a spatially explicit simulation framework. BMC Genet 2017; 18:114. [PMID: 29246100 PMCID: PMC5731203 DOI: 10.1186/s12863-017-0575-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples. RESULTS We first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500 years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes. CONCLUSIONS Here, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species.
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Affiliation(s)
- Nuno Miguel Silva
- AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Jeremy Rio
- AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- AGP lab, Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
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7
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Modi A, Tassi F, Susca RR, Vai S, Rizzi E, Bellis GD, Lugliè C, Gonzalez Fortes G, Lari M, Barbujani G, Caramelli D, Ghirotto S. Complete mitochondrial sequences from Mesolithic Sardinia. Sci Rep 2017; 7:42869. [PMID: 28256601 PMCID: PMC5335606 DOI: 10.1038/srep42869] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.
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Affiliation(s)
- Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Roberta Rosa Susca
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Ermanno Rizzi
- Fondazione Telethon, 20121 Milano, Italy.,Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Milano, Italy
| | | | - Carlo Lugliè
- LASP, Dipartimento di Storia, Beni Culturali e Territorio, Università di Cagliari, 09124 Cagliari, Italy
| | - Gloria Gonzalez Fortes
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
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8
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Barthe S, Binelli G, Hérault B, Scotti-Saintagne C, Sabatier D, Scotti I. Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield. Mol Ecol 2017; 26:1161-1174. [PMID: 27926985 DOI: 10.1111/mec.13949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Abstract
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.
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Affiliation(s)
- Stéphanie Barthe
- UMR EcoFoG ("Ecologie des forêts de Guyane"), UAG, Campus Agronomique, BP 709, 97387, Kourou, French Guiana.,UMR EcoFoG ("Ecologie des forêts de Guyane"), INRA, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Giorgio Binelli
- DBSV ("Dipartimento di Biotecnologie e Scienze della Vita"), Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Bruno Hérault
- UMR EcoFoG ("Ecologie des forêts de Guyane"), CIRAD, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Caroline Scotti-Saintagne
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
| | - Daniel Sabatier
- UMR AMAP ("Botanique et modélisation de l'architecture des plantes et des végétations"), IRD, Boulevard de la Lironde, Parc Scientifique 2, 34398, Montpellier, France
| | - Ivan Scotti
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
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9
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Guirao-Rico S, Sánchez-Gracia A, Charlesworth D. Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow. Mol Ecol 2017; 26:1357-1370. [PMID: 28035715 DOI: 10.1111/mec.13969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/02/2016] [Accepted: 12/12/2016] [Indexed: 01/16/2023]
Abstract
DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.
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Affiliation(s)
- Sara Guirao-Rico
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JN, UK
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JN, UK
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10
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Allentoft ME, Heller R, Holdaway RN, Bunce M. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site. Heredity (Edinb) 2015; 115:481-7. [PMID: 26039408 DOI: 10.1038/hdy.2015.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022] Open
Abstract
By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.
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Affiliation(s)
- M E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - R Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R N Holdaway
- Palaecol Research Ltd, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M Bunce
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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11
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Vai S, Ghirotto S, Pilli E, Tassi F, Lari M, Rizzi E, Matas-Lalueza L, Ramirez O, Lalueza-Fox C, Achilli A, Olivieri A, Torroni A, Lancioni H, Giostra C, Bedini E, Baricco LP, Matullo G, Di Gaetano C, Piazza A, Veeramah K, Geary P, Caramelli D, Barbujani G. Genealogical relationships between early medieval and modern inhabitants of Piedmont. PLoS One 2015; 10:e0116801. [PMID: 25635682 PMCID: PMC4312042 DOI: 10.1371/journal.pone.0116801] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.
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Affiliation(s)
- Stefania Vai
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Elena Pilli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy
| | | | - Oscar Ramirez
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain
| | | | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell’arte, Università Cattolica del Sacro Cuore, 20123 Milano, Italy
| | - Elena Bedini
- Anthropozoologica L.B.A. s.n.c., 57123 Livorno, Italy
| | | | | | | | | | - Krishna Veeramah
- Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794–5245, United States of America
| | - Patrick Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, New Jersey 08540, United States of America
| | - David Caramelli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
- * E-mail:
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12
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Bayesian inferences suggest that Amazon Yunga Natives diverged from Andeans less than 5000 ybp: implications for South American prehistory. BMC Evol Biol 2014; 14:174. [PMID: 25266366 PMCID: PMC4189748 DOI: 10.1186/s12862-014-0174-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/24/2014] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Archaeology reports millenary cultural contacts between Peruvian Coast-Andes and the Amazon Yunga, a rainforest transitional region between Andes and Lower Amazonia. To clarify the relationships between cultural and biological evolution of these populations, in particular between Amazon Yungas and Andeans, we used DNA-sequence data, a model-based Bayesian approach and several statistical validations to infer a set of demographic parameters. RESULTS We found that the genetic diversity of the Shimaa (an Amazon Yunga population) is a subset of that of Quechuas from Central-Andes. Using the Isolation-with-Migration population genetics model, we inferred that the Shimaa ancestors were a small subgroup that split less than 5300 years ago (after the development of complex societies) from an ancestral Andean population. After the split, the most plausible scenario compatible with our results is that the ancestors of Shimaas moved toward the Peruvian Amazon Yunga and incorporated the culture and language of some of their neighbors, but not a substantial amount of their genes. We validated our results using Approximate Bayesian Computations, posterior predictive tests and the analysis of pseudo-observed datasets. CONCLUSIONS We presented a case study in which model-based Bayesian approaches, combined with necessary statistical validations, shed light into the prehistoric demographic relationship between Andeans and a population from the Amazon Yunga. Our results offer a testable model for the peopling of this large transitional environmental region between the Andes and the Lower Amazonia. However, studies on larger samples and involving more populations of these regions are necessary to confirm if the predominant Andean biological origin of the Shimaas is the rule, and not the exception.
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13
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Fehren-Schmitz L, Haak W, Mächtle B, Masch F, Llamas B, Cagigao ET, Sossna V, Schittek K, Isla Cuadrado J, Eitel B, Reindel M. Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru. Proc Natl Acad Sci U S A 2014; 111:9443-8. [PMID: 24979787 PMCID: PMC4084453 DOI: 10.1073/pnas.1403466111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole.
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Affiliation(s)
- Lars Fehren-Schmitz
- Department of Anthropology, University of California, Santa Cruz, CA 95064;Historical Anthropology and Human Ecology, University of Göttingen, D-37073 Göttingen, Germany;
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Bertil Mächtle
- Geographisches Institut, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Florian Masch
- Historical Anthropology and Human Ecology, University of Göttingen, D-37073 Göttingen, Germany
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Elsa Tomasto Cagigao
- Departmento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Perú
| | - Volker Sossna
- German Archaeological Institute (DAI), Commission for Archaeology of Non-European Cultures (KAAK), D-53173 Bonn, Germany
| | - Karsten Schittek
- Seminar of Geography and Geographical Education, University of Cologne, D-50931 Cologne, Germany; and
| | - Johny Isla Cuadrado
- Centro de Investigación para la Arqueología y el Desarrollo (ANDES), Lima 11, Perú
| | - Bernhard Eitel
- Geographisches Institut, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Markus Reindel
- German Archaeological Institute (DAI), Commission for Archaeology of Non-European Cultures (KAAK), D-53173 Bonn, Germany
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14
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Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe. PLoS Genet 2014; 10:e1004353. [PMID: 24809476 PMCID: PMC4014435 DOI: 10.1371/journal.pgen.1004353] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/19/2014] [Indexed: 11/24/2022] Open
Abstract
Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture. The analysis of the genome of the Tyrolean Iceman, a 5,300 year old mummy from Central Europe, revealed a surprising recent common ancestry with modern Sardinians for this ancient genome. However, this study was limited both by the availability of data from Sardinians and by a lack of genomic data from other ancient European samples. Here, we use genomic data from modern Sardinians and from ancient European individuals from different geographic regions and cultural contexts, to demonstrate that this ancestry component is shared among individuals associated with the onset of agriculture in Europe. Our results thus suggest that the Iceman's Sardinian ancestry actually reflects a more widespread genetic component related to the migration of people during the Neolithic transition in Central Europe.
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15
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de Bruyn M, Pinsky ML, Hall B, Koch P, Baroni C, Hoelzel AR. Rapid increase in southern elephant seal genetic diversity after a founder event. Proc Biol Sci 2014; 281:20133078. [PMID: 24478305 PMCID: PMC3924085 DOI: 10.1098/rspb.2013.3078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 01/03/2014] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.
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Affiliation(s)
- Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, UK
| | - Malin L. Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA
| | - Brenda Hall
- Climate Change Institute and School of Earth and Climate Sciences, University of Maine, Orono, ME, USA
| | - Paul Koch
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - Carlo Baroni
- Dipartimento di Scienze della Terra, Università di Pisa, Pisa, Italy
| | - A. Rus Hoelzel
- School of Biological and Biomedical Sciences, University of Durham, Durham, UK
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16
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Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 2013; 342:257-61. [PMID: 24115443 DOI: 10.1126/science.1241844] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany.
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17
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Tassi F, Ghirotto S, Caramelli D, Barbujani G. Genetic evidence does not support an Etruscan origin in Anatolia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152:11-8. [PMID: 23900768 DOI: 10.1002/ajpa.22319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/20/2013] [Indexed: 01/22/2023]
Abstract
The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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18
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Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet 2013; 9:e1003296. [PMID: 23459685 PMCID: PMC3573127 DOI: 10.1371/journal.pgen.1003296] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022] Open
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Sergey Koshel
- Faculty of Geography, Moscow State University, Moscow, Russia
| | - Valery Zaporozhchenko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | - Eugen Kolpakov
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Vladimir Shumkin
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Kurt W. Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
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19
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Ghirotto S, Tassi F, Fumagalli E, Colonna V, Sandionigi A, Lari M, Vai S, Petiti E, Corti G, Rizzi E, De Bellis G, Caramelli D, Barbujani G. Origins and evolution of the Etruscans' mtDNA. PLoS One 2013; 8:e55519. [PMID: 23405165 PMCID: PMC3566088 DOI: 10.1371/journal.pone.0055519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022] Open
Abstract
The Etruscan culture is documented in Etruria, Central Italy, from the 8th to the 1st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.
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Affiliation(s)
- Silvia Ghirotto
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Erica Fumagalli
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Vincenza Colonna
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Institute of Genetics e Biophysics “Adriano Buzzati-Traverso”, National Research Council, Naples, Italy
| | - Anna Sandionigi
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Emmanuele Petiti
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Giorgio Corti
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - David Caramelli
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Guido Barbujani
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- * E-mail:
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20
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Batalha-Filho H, Cabanne GS, Miyaki CY. Phylogeography of an Atlantic forest passerine reveals demographic stability through the last glacial maximum. Mol Phylogenet Evol 2012; 65:892-902. [DOI: 10.1016/j.ympev.2012.08.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 07/17/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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21
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Pinhasi R, Thomas MG, Hofreiter M, Currat M, Burger J. The genetic history of Europeans. Trends Genet 2012; 28:496-505. [PMID: 22889475 DOI: 10.1016/j.tig.2012.06.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/16/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
Abstract
The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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22
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Pinhasi R, von Cramon-Taubadel N. A craniometric perspective on the transition to agriculture in Europe. Hum Biol 2012; 84:45-66. [PMID: 22452428 DOI: 10.3378/027.084.0102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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Kirsanow K, Burger J. Ancient human DNA. Ann Anat 2012; 194:121-32. [PMID: 22169595 DOI: 10.1016/j.aanat.2011.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/11/2022]
Abstract
The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements.
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Affiliation(s)
- Karola Kirsanow
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Germany
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Lander TA, Oddou-Muratorio S, Prouillet-Leplat H, Klein EK. Reconstruction of a beech population bottleneck using archival demographic information and Bayesian analysis of genetic data. Mol Ecol 2011; 20:5182-96. [PMID: 22097929 DOI: 10.1111/j.1365-294x.2011.05356.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Range expansion and contraction has occurred in the history of most species and can seriously impact patterns of genetic diversity. Historical data about range change are rare and generally appropriate for studies at large scales, whereas the individual pollen and seed dispersal events that form the basis of geneflow and colonization generally occur at a local scale. In this study, we investigated range change in Fagus sylvatica on Mont Ventoux, France, using historical data from 1838 to the present and approximate Bayesian computation (ABC) analyses of genetic data. From the historical data, we identified a population minimum in 1845 and located remnant populations at least 200 years old. The ABC analysis selected a demographic scenario with three populations, corresponding to two remnant populations and one area of recent expansion. It also identified expansion from a smaller ancestral population but did not find that this expansion followed a population bottleneck, as suggested by the historical data. Despite a strong support to the selected scenario for our data set, the ABC approach showed a low power to discriminate among scenarios on average and a low ability to accurately estimate effective population sizes and divergence dates, probably due to the temporal scale of the study. This study provides an unusual opportunity to test ABC analysis in a system with a well-documented demographic history and identify discrepancies between the results of historical, classical population genetic and ABC analyses. The results also provide valuable insights into genetic processes at work at a fine spatial and temporal scale in range change and colonization.
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Affiliation(s)
- Tonya A Lander
- UR627, UnitéÉcologie Forestière Mediterranéenne, INRA, Domaine Saint Paul, F-84914 Avignon Cedex 9, France
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Veeramah KR, Wegmann D, Woerner A, Mendez FL, Watkins JC, Destro-Bisol G, Soodyall H, Louie L, Hammer MF. An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data. Mol Biol Evol 2011; 29:617-30. [PMID: 21890477 DOI: 10.1093/molbev/msr212] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we resequenced a sample of San, Eastern, and Western Pygmies and non-Pygmy NKs individuals at 40 nongenic (∼2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ∼110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize "pseudo-observed" data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Arizona, USA
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Abstract
Approximate Bayesian computation (ABC) have become an essential tool for the analysis of complex stochastic models. Grelaud et al. [(2009) Bayesian Anal 3:427-442] advocated the use of ABC for model choice in the specific case of Gibbs random fields, relying on an intermodel sufficiency property to show that the approximation was legitimate. We implemented ABC model choice in a wide range of phylogenetic models in the Do It Yourself-ABC (DIY-ABC) software [Cornuet et al. (2008) Bioinformatics 24:2713-2719]. We now present arguments as to why the theoretical arguments for ABC model choice are missing, because the algorithm involves an unknown loss of information induced by the use of insufficient summary statistics. The approximation error of the posterior probabilities of the models under comparison may thus be unrelated with the computational effort spent in running an ABC algorithm. We then conclude that additional empirical verifications of the performances of the ABC procedure as those available in DIY-ABC are necessary to conduct model choice.
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Ghirotto S, Tassi F, Benazzo A, Barbujani G. No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:242-52. [DOI: 10.1002/ajpa.21569] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/10/2011] [Indexed: 11/06/2022]
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Liyanage KE, Burnett JR, Hooper AJ, van Bockxmeer FM. Familial hypercholesterolemia: epidemiology, Neolithic origins and modern geographic distribution. Crit Rev Clin Lab Sci 2011; 48:1-18. [DOI: 10.3109/10408363.2011.565585] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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von Cramon-Taubadel N, Pinhasi R. Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe. Proc Biol Sci 2011; 278:2874-80. [PMID: 21345869 DOI: 10.1098/rspb.2010.2678] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter-gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter-gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter-gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter-gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.
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Craniofacial morphometric variation and the biological history of the peopling of Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2010; 61:385-412. [PMID: 20979998 DOI: 10.1016/j.jchb.2010.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/17/2010] [Indexed: 11/22/2022]
Abstract
The aim of this work is to explore the pattern of craniofacial morphometric variation and the relationships among five prehistoric Sardinian groups dated from Late Neolithic to the Nuragic Period (Middle and Late Bronze Age), in order to formulate hypotheses on the peopling history of Sardinia. Biological relationships with coeval populations of central peninsular Italy were also analysed to detect influences from and towards extra-Sardinian sources. Furthermore, comparison with samples of contemporary populations from Sardinia and from continental Italy provided an indication of the trend leading to the final part of the peopling history. Finally, Upper Palaeolithic and Mesolithic samples were included in the analyses to compare the prehistoric Sardinians with some of their potential continental ancestors. The analysis is based on multivariate techniques including Mahalanobis D(2) distance, non-parametric multidimensional scaling (MDS) and principal component analysis (PCA). The results showed the tendency to progressive differentiation between Sardinian groups and peninsular Italian groups, with the possible exception of a discontinuity showed by the Bonnànaro (Early Bronze Age) Sardinian sample. Several aspects of the morphological results were found to agree with the current genetic evidence available for the present-day Sardinian population and a Nuragic sample: (1) biological divergence between the Sardinian and peninsular Italian populations; (2) similarity/continuity among Neolithic, Bronze Age and recent Sardinians; (3) biological separation between the Nuragic and Etruscan populations; (4) contribution of a Palaeo-Mesolithic gene pool to the genetic structure of current Sardinians.
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CAMPOS PAULAF, KRISTENSEN TOMMY, ORLANDO LUDOVIC, SHER ANDREI, KHOLODOVA MARINAV, GÖTHERSTRÖM ANDERS, HOFREITER MICHAEL, DRUCKER DOROTHÉEG, KOSINTSEV PAVEL, TIKHONOV ALEXEI, BARYSHNIKOV GENNADYF, WILLERSLEV ESKE, GILBERT MTHOMASP. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Mol Ecol 2010; 19:4863-75. [DOI: 10.1111/j.1365-294x.2010.04826.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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NAVASCUÉS MIGUEL, DEPAULIS FRANTZ, EMERSON BRENTC. Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol Ecol Resour 2010; 10:760-72. [DOI: 10.1111/j.1755-0998.2010.02895.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Cornuet JM, Ravigné V, Estoup A. Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinformatics 2010; 11:401. [PMID: 20667077 PMCID: PMC2919520 DOI: 10.1186/1471-2105-11-401] [Citation(s) in RCA: 321] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 07/28/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. RESULTS We used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit. CONCLUSIONS Our new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking computation within an ABC framework, hence filling up a gap of ABC analysis. The software DIYABC V1.0 is freely available at http://www1.montpellier.inra.fr/CBGP/diyabc.
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Affiliation(s)
- Jean-Marie Cornuet
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus international de Baillarguet, CS 30016, F-34988 Montferrier-sur-Lez cedex, France
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Bertorelle G, Benazzo A, Mona S. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 2010; 19:2609-25. [PMID: 20561199 DOI: 10.1111/j.1365-294x.2010.04690.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human-induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data-analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.
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Affiliation(s)
- G Bertorelle
- Department of Biology and Evolution, University of Ferrara, Via Borsari 46, 44100 Ferrara, Italy.
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Csilléry K, Blum MGB, Gaggiotti OE, François O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol 2010; 25:410-8. [PMID: 20488578 DOI: 10.1016/j.tree.2010.04.001] [Citation(s) in RCA: 588] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 04/01/2010] [Accepted: 04/06/2010] [Indexed: 11/26/2022]
Abstract
Understanding the forces that influence natural variation within and among populations has been a major objective of evolutionary biologists for decades. Motivated by the growth in computational power and data complexity, modern approaches to this question make intensive use of simulation methods. Approximate Bayesian Computation (ABC) is one of these methods. Here we review the foundations of ABC, its recent algorithmic developments, and its applications in evolutionary biology and ecology. We argue that the use of ABC should incorporate all aspects of Bayesian data analysis: formulation, fitting, and improvement of a model. ABC can be a powerful tool to make inferences with complex models if these principles are carefully applied.
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Affiliation(s)
- Katalin Csilléry
- Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité, Centre National de la Recherche Scientifique UMR5525, Université Joseph Fourier, 38706 La Tronche, France.
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