The geography of recent genetic ancestry across Europe

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.Comment: Full size figures available from http://www.eve.ucdavis.edu/~plralph/research.html; or html version at http://ralphlab.usc.edu/ibd/ibd-paper/ibd-writeup.xhtm

AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION

This dissertation is research in the domain of information science and specifically, the organization and representation of information. The research has implications for classification of scientific books, especially as dissemination of information becomes more rapid and science becomes more diverse due to increases in multi-, inter-, trans-disciplinary research, which focus on phenomena, in contrast to traditional library classification schemes based on disciplines.The literature review indicates 1) human socio-cultural groups have many of the same properties as biological species, 2) output from human socio-cultural groups can be and has been the subject of evolutionary relationship analyses (i.e., phylogenetics), 3) library and information science theorists believe the most favorable and scientific classification for information packages is one based on common origin, but 4) library and information science classification researchers have not demonstrated a book classification based on evolutionary relationships of common origin.The research project supports the assertion that a sensible book classification method can be developed using a contemporary biological classification approach based on common origin, which has not been applied to a collection of books until now. Using a sample from a collection of earth-science digitized books, the method developed includes a text-mining step to extract important terms, which were converted into a dataset for input into the second step—the phylogenetic analysis. Three classification trees were produced and are discussed. Parsimony analysis, in contrast to distance and likelihood analyses, produced a sensible book classification tree. Also included is a comparison with a classification tree based on a well-known contemporary library classification scheme (the Library of Congress Classification).Final discussions connect this research with knowledge organization and information retrieval, information needs beyond science, and this type of research in context of a unified science of cultural evolution

The Impact of Medieval and Early Modern Migrations on Dental Nonmetric Variation in Hungary

The Carpathian Basin has been a natural crossroads for expanding empires and populations migrating between Europe and Asia. During the medieval and early modern periods, three major migrations shaped the population history of the basin: 1) the migration of the Avars in the late 6th century; 2) the conquest of the Magyars in the late 9th century; and 3) the invasion of the Ottomans in the mid-16th century. While these migrations have been explored archaeologically and linguistically, their impact on biological variation is not well understood. In response to this disparity, this dissertation uses dental nonmetric data to address three aims: 1) to explore the impact of these migrations on dental variation, 2) to see if these migrations changed how Hungarians were related to other Eurasians, and 3) to determine whether or not the impact of these migrations differed by sex. Nonmetric dental data were collected from medieval and early modern bioarchaeological collections at the Magyar Természettudományi Múzeum, including individuals from eight medieval and early modern Hungarian sites that span the Carolingian through Ottoman periods (Dánszentmiklós-Tetveshalom, Fonyód-Fehérbézseny, Fonyód-Vár, Budapest-József nádor tér, Zalavár-Kápolna, Zalavár-Rezes, Zalavár-Vársziget Hadrianus templom, and Zsámbék-Premontrei templomrom). This sample was bolstered by Avar period data collected at the same institution and Szeged University and additional data collected from post-Magyar conquest medieval sites. The Avar, Carolingian, Magyar, and Ottoman period Hungarian samples were compared to a Byzantine sample from Çatalhöyük and Roman, medieval, early modern, and modern European and Central Asian samples of the Christy G. Turner II database. Trait frequencies, phenotypic diversity, and relatedness were assessed and compared across time periods to explore the impact of these migrations on dental variation. Analyses revealed relative consistency among post-Avar period Hungarian samples. This similarity supports historical records that indicate people of Slavic origin made up the bulk of the basin’s population during these periods, regardless of major demographic shifts. The consistency between the Carolingian and Magyar periods supports the elite dominance model of the Magyar conquest. The Ottoman period sample was the most dissimilar of the post-Avar group indicating major demographic shifts during this period. The distinctness of the Avar period sample is likely a reflection of their population history originating in Mongolia or Northern China and suggests that the collapse of the Avar empire was the event that most impacted biological variation in the basin. Some significant differences were observed in analyses of sex-separate samples indicating that these major migrations differentially impacted biological variation by sex. This study demonstrates the utility of dental nonmetric data as a genetic proxy to explore major migrations and contributes to the limited literature on the demography of the medieval Carpathian basin and the impact of Ottoman occupation in Europe. The results highlight the complex relationship between cultural and demographic change and give insight into dental variation at the crossroads between Europe and the rest of Eurasia. These relationships would be further clarified with additional data from medieval and early modern Eurasia

Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia

Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today

Ancient and Archaic Genomes

The development of high-throughput sequencing has triggered a revolution in the study of ancient DNA. In the last decade, methodological advances have allowed researchers to overcome some of the limits linked to the degradation and preservation of nucleic acids, improving the capacity of recovery and analysis of the ancient molecules. This fact, along with a wider accessibility to the next-generation sequencing platforms, has contributed to increase the number of genomic studies on ancient remains. This Special Issue, titled “Ancient and Archaic Genomes”, collects original research articles that present different methods and aspects of the paleogenetic research applied to anthropological, archaeological, and historic questions. Interestingly, specific regional contexts and cultural aspects previously poorly studied from a genetic point of view are here investigated. This Special Issue, presenting different methodological approaches and applications, will be a useful resource for both students and young researchers who are interested in ancient DNA studies

Using Gabmap

AbstractGabmap is a freely available, open-source web application that analyzes the data of language variation, e.g. varying words for the same concepts, varying pronunciations for the same words, or varying frequencies of syntactic constructions in transcribed conversations. Gabmap is an integrated part of CLARIN (see e.g. http://portal.clarin.nl). This article summarizes Gabmap's basic functionality, adding material on some new features and reporting on the range of uses to which Gabmap has been put. Gabmap is modestly successful, and its popularity underscores the fact that the study of language variation has crossed a watershed concerning the acceptability of automated language analysis. Automated analysis not only improves researchers’ efficiency, it also improves the replicability of their analyses and allows them to focus on inferences to be drawn from analyses and other more abstract aspects of that study

The TXM Portal Software giving access to Old French Manuscripts Online

Texte intégral en ligne : http://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdfInternational audiencehttp://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdf This paper presents the new TXM software platform giving online access to Old French Text Manuscripts images and tagged transcriptions for concordancing and text mining. This platform is able to import medieval sources encoded in XML according to the TEI Guidelines for linking manuscript images to transcriptions, encode several diplomatic levels of transcription including abbreviations and word level corrections. It includes a sophisticated tokenizer able to deal with TEI tags at different levels of linguistic hierarchy. Words are tagged on the fly during the import process using IMS TreeTagger tool with a specific language model. Synoptic editions displaying side by side manuscript images and text transcriptions are automatically produced during the import process. Texts are organized in a corpus with their own metadata (title, author, date, genre, etc.) and several word properties indexes are produced for the CQP search engine to allow efficient word patterns search to build different type of frequency lists or concordances. For syntactically annotated texts, special indexes are produced for the Tiger Search engine to allow efficient syntactic concordances building. The platform has also been tested on classical Latin, ancient Greek, Old Slavonic and Old Hieroglyphic Egyptian corpora (including various types of encoding and annotations)