Genetic variation related to the adaptation of humans to an agriculturalist lifestyle

Die vorliegende Arbeit befasst sich mit dem Einfluss von Klimaregionen und Lebensweisen auf die genetische Variabilität pre-historischer Menschen in Europa. Um diese Einflüsse zu analysieren wurde ein Datensatz aus über 100 pre-historischen Individuen erstellt, von denen 27 speziell für diese Studie sequenziert wurden. Der Datensatz umfasst einen Zeitraum von über 10,000 Jahren und enthält genomische Daten von Menschen die vor sowie während und nach dem Beginn des Neolithikums in Zentraleuropa gelebt haben. Für die Erstellung des Datensatzes wurde ein speziell entwickeltes nukleäres Capture Array in Kombination mit next-generation-sequencing verwendet um vordefinierte genomische Regionen aus alter DNA (aDNA) zu gewinnen. Diese Regionen bestehen aus 486 funktionellen Markern, einschließlich nicht-rekombinanter Y Marker, zusätzlich zu über 5,000 funktionell neutralen Regionen, welche die populationsgenetischen Analysen ermöglichen. Der Datensatz wurde durch genomweite Daten von drei modernen Referenzpopulationen komplettiert. Diese ermöglichten haplotyp- und frequenzbasierte Neutralitätstests wie den integrated haplotype score oder Tajima‘s D zu berechnen und damit Spuren von vergangenen Selektionsereignissen aufzeigen zu können. Unter Verwendung der Allelefrequenzdaten des aDNA Datensatzes konnten mögliche Selektionsereignisse zeitlich eingegrenzt werden. Die Analysen befassten sich schwerpunktmäßig mit drei Themengebieten: 1.) Die Entstehung der in Europa vorkommenden Haut-, Augen- und Haarfarbenphenotypen; 2.) Die Entwicklung der in Europa vorliegenden Prädisposition von Typ 2 Diabetes und dem Metabolischen Syndrom; und 3.) Die Entwicklung des Immunsystems im Hinblick auf Autoimmunkrankheiten. Der Hauptfokus lag bei den Analysen auf dem Einfluss der Sesshaftwerdung und der Hinwendung zum Ackerbau auf die beschriebenen Eigenschaften. Die Ergebnisse deuten darauf hin dass ein großer Teil der genetischen Variation in mit dem Energie- und Fettstoffwechsel assoziierten Genen durch Anpassungen an das lokale Klima in Mitteleuropa beeinflusst wurde. Des Weiteren wurden deutlich Hinweise darauf gefunden, dass auf Grund der verringerten UV Strahlung eine Abnahme der Hautpigmentierung bereits vor Beginn des Mesolithikums stattgefunden hat. Auf Grundlage der vorliegenden Daten kann angenommen werden dass durch die Umstellung der Lebens- und Ernährungsweise zum Teil bestehende Selektionsdrücke noch verstärkt wurden. Seit Beginn des Neolithikums konnte ein deutlicher Anstieg von mit helleren Pigmentierungsphenotypen im Zusammenhang stehenden Allelen verzeichnet werden, welcher wahrscheinlich auf den verringerten Vitamin D Gehalt in der Nahrung zurück zu führen ist. Weiterhin wurden Hinweise gefunden die auf eine Anpassung des Stoffwechsels an eine pflanzenreiche Ernährungsweise hindeuten. Für den Zeitraum des späteren Neolithikums und der Bronzezeit wurde ein Anstieg von Allelefrequenzen in Genen gefunden die den Schutz vor Infektionskrankheiten erhöhen. Ein Zusammenhang mit der steigenden Bevölkerungsdichte und einer sesshaften Lebensweise ist hier sehr wahrscheinlich.This study investigates the influence of climate and subsistence on the genetic variation of prehistoric individuals of Europe. Partial genomes from more than 100 individuals were analyzed, originating from a region spanning from north-western Anatolia, over Germany to Lithuania. The data is spread over a period of more than 10,000 years and thus covers the phases before and after people started to become sedentary. To fill temporal and geographical gaps, 27 individuals were sequenced specifically for this study. For this purpose, a hybridization-based enrichment process was used in combination with next-generation sequencing to obtain predefined genomic segments from ancient DNA (aDNA). These regions consist of over 400 functional markers, 68 non-recombinan Y markers, and more than 5,000 neutral regions of 1kb in length. The data set was completed b genomes of three modern reference populations. These made it possible to calculate haplotype- and frequency-based neutrality tests such as the integrated haplotype score or Tajima’s D and thus to be able to detect signals of past selection events. Using the allele frequencies of the ancient genomes, the timing of possible selection processes could be narrowed down. The analyzes focused on three main topics: 1.) the development of skin, eye and hair color phenotypes in Europe; 2.) The development of Europe’s predisposition to type 2 diabetes and the metabolic syndrome; and 3.) The development of the immune system with respect to autoimmune diseases. The historical focus was on the influence of subsistence and the transition to farming on the evolutionary processes. The results suggest that a high proportion of the genetic variation in genes associated with the energy and fat metabolism has been affected by adaptations to the local climate in Central Europe. Furthermore, clear indications were found that due to the reduced UV radiation in Central and Northern Europe, depigmentation of the skin had already begun before the onset of the Mesolithic. On the basis of the available data, it can be assumed that the the shift in diet and lifestyle that accompanied the transition to farming partially reinforced already existing selection pressures. Thus, with the Neolithic, a significant increase in allele frequencies associated with lighter pigmentation phenotypes was found. This is probably due to the reduced vitamin D content in the diet. Furthermore, evidence was found that indicates a metabolic adaptation to a plant-rich diet. For the later Neolithic and Bronze Age periods, an increase in allele frequencies has been found in genes that enhance protection against infectious diseases. A connection with the increasing population density and a sedentary lifestyle is very likely here.v, 206 Seite

Was the fishing village of Lepenski Vir built by Europe’s first farmers?

It is now widely accepted that agriculture and settled village life arrived in Europe as a cultural package, carried by people migrating from Anatolia and the Aegean Basin. The putative fisher-forager site of Lepenski Vir in Serbia has long been acknowledged as an exception to this model. Here, the Mesolithic–Neolithic transition—possibly inspired by interaction with the new arrivals—was thought to have taken place autochthonously on site. Our reinterpretation, based on ancient genomes, as well as archaeological and isotopic evidence, indicates that here, too, house construction, early village society and agriculture were primarily associated with Europe’s first farmers, thus challenging the long-held view of Lepenski Vir as a Mesolithic community that adopted Neolithic practices. Although aspects of the site's occupation, such as the trapezoidal houses, were inspired by local Mesolithic traditions, it is far from certain that the village was founded by Iron Gates foragers. A detailed timeline of population changes at the site suggests that Aegean incomers did not simply integrate into an established Mesolithic society, but rather founded new lineages and households. Iron Gates foragers and their admixed descendants largely appear to have been buried separately, on the fringes of the settlement. The diet of those buried outside in pits shows no major shift from aquatic to terrestrial food resources

Investigating the prehistory of Luxembourg using ancient genomes

This project examines the local impact of Neolithic and Steppe population dispersals on archaeological cultures west of the Rhine, using new high-coverage ancient genomes from present-day Luxembourg. In addition, we sampled the Beaker-period grave of Dunstable Downs in England, which offers close parallels to the grave of Altwies in Luxembourg

Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent. Therefore, we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago

Bewertung von Vogelarten bei der Zulassung von Pestiziden in Europa

Es wird eine Übersicht zur Vorgehensweise der Risikobewertung von Vögeln zu potentiell durch Pflanzenschutzmittel auftretenden akuten und reproduktiven Effekten gegeben. Grundlage einer solchen Risikobewertung ist die aktuelle Richtlinie (EFSA 2009) der europäischen Behörde für Lebensmittelsicherheit, EFSA. Nach kurzer Einleitung über die Veränderungen der Zulassungsbestimmungen für Vögel der Agrarlandschaft und Erläutern des grundsätzlichen Prozedere, wird an einem Beispiel eines fiktiven Fungizids eine Risikobewertung exemplarisch aufgezeigt. Grundlagen der derzeitigen Risikobewertung und deren Bewertung durch die Richtlinie werden kurz diskutiert.Stichwörter: Risikobewertung, Pflanzenschutzmittel, VögelAssessing bird species in the registration process of pesticides in EuropeAbstractWe provide an overview and discussion of the methodology currently used to assess the acute and chronic (i.e. reproductive) risk posed by plant protection products to birds. The methodology follows guidance published by the European Food Safety Authority, EFSA (EFSA, 2009). Our overview begins with a short introduction including a brief discussion of recent changes to the regulations on which the EFSA Guidance is based. The standard risk assessment procedure is then explained using the example of a hypothetical fungicide. This is followed by a discussion of the basis, weighting and evaluation of the current risk assessment methodology for birds.Keywords: risk assessment, plant protection products, bird

The genomic origins of the world’s first farmers

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Early farmers from across Europe directly descended from Neolithic Aegeans

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia