Eva-Maria Geigl

Institut Jacques Monod | IJM · Epigenome and Paleogenome

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more...

This volume originates in a conference session that took place at the 2018 International Council of Archaeozoology conference in Ankara, Turkey, entitled "Humans and Cattle: Interdisciplinary Perspectives to an Ancient Relationship." The aim of the session was to bring together zooarchaeologists and their colleagues from various other research fiel...

Before the introduction of domestic horses in Mesopotamia in the late third millennium BCE, contemporary cuneiform tablets and seals document intentional breeding of highly valued equids called kungas for use in diplomacy, ceremony, and warfare. Their precise zoological classification, however, has never been conclusively determined. Morphometric a...

Résumé Au milieu des années 1980, l’extraction et l’analyse de l’ADN préservé dans des vestiges biologiques du passé ont donné des premiers résultats, entérinant la naissance du domaine de la paléogénétique. C’est grâce à l’invention de la PCR que cette nouvelle discipline a pu évoluer et récolter ses premiers succès. Néanmoins, la nature dégradée...

Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic stu...

Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotype...

Northwestern Africa is today characterized by high geographical, climatic and ecological diversity; it is recognized as a hotspot of biodiversity and a major area for both human and faunal evolution. Studies of North African fossil microvertebrates have increased considerably in recent years, but they no longer just provide palaeontological descrip...

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yie...

The Gravettian technocomplex was present in Europe from more than 30,000 years ago until the Last Glacial Maximum, but the source of this industry and the people who manufactured it remain unsettled. We use genome-wide analysis of a ~36,000-year-old Eastern European individual (BuranKaya3A) from Buran-Kaya III in Crimea, the earliest documented occ...

It is the dream of all researchers working with ancient DNA to identify prior to DNA extraction from bone the specimens or specific zones within them that contain the highest proportion of endogenous DNA. As it impacts the sacrifice of precious ancient specimens and the financial support needed for the analyses, the question is of high importance t...

Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contra...

Neither genetics and genomics of modern cats nor archeology could so far reconstruct the domestication and dispersal process of the cat. It was only known that all domestic cats belong to the subspecies Felis silvestris lybica, that their genomes are close to the ones of wildcats, and that they were translocated to Cyprus by the Neolithic farmers w...

The genetic analysis of calcified remains of past organisms, mainly bones and teeth, enrich largely our knowledge of the evolution of animal and plant species and their domestication, the evolution of human lineages, the peopling of the continents, the admixture between different human lineages, the Neolithic diffusion, the composition of necropoli...

The site of Birgelsgaerten in Ostheim (Haut-Rhin, France) was excavated in 2008 by the Pôle d’Archéologie Interdépartemental Rhénan. This rural settlement is located on the edge of a terrace of loess and an alluvial area crossed by a palaeochannel. Around 2500 animal bones were retrieved from the stratigraphie layers attributed to the Early Middle...

The cat has long been important to human societies as a pest-control agent, object of symbolic value and companion animal, but little is known about its domestication process and early anthropogenic dispersal. Here we show, using ancient DNA analysis of geographically and temporally widespread archaeological cat remains, that both the Near Eastern...

Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine th...

All tables are presented as separate spreadsheets consolidated into a single Excel file. Table A Description of all samples analyzed Table B Primers used to amplify mitochondrial sequences Table C Description of published sequences used Table D Sample location and results of sPCA analysis Table E Summary statistics for the kiangs and dziggetais of...

Supplementary figures of the phylogenetic analyses followed by the detailed description of the archeological sites and the samples analyzed grouped in a single supporting document. Figure A: Global alignment of all sequences obtained and used for the various analyses Figure B: Diagnostic SNPs of the various clades Figure C: sPCA, distribution of th...

Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine th...

Coprolites are fossil scats and provide indirect witness of the activity of past animals of a given area, whether or not fossil bones of these animals are present in the site. The shape, size, inclusions and geo- and bio-chemical composition are criteria for identification of the animal that left the coprolite. Unit II from Azokh 1 has yielded two...

Background: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe’s megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is...

Background Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe’s megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is k...

The origin and dispersal of the domestic cat remain elusive despite its importance to human societies around the world. Archaeological evidence for domestication centers in the Near East and in Egypt is contested, and genetic data on modern cats show that Felis silvestris lybica , the subspecies of wild cat inhabiting at present the Near East and N...

Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe’s megafauna. Here we show that the emblematic European bison has experienced several waves of population expansion, contraction and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic dive...

We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyze many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotypin...

The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related...

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of in...

Pellets of raptors are an important source for the study of the taxonomy, phylogeography and ecological diversity of small vertebrates. Since birds of prey are efficient collecting agents for both rare species and those reluctant to enter traps, they offer an important complement to traditional trapping efforts in the field. The possibility of usin...

Seven centuries before the discovery of the African zebras by the Europeans, the names zebro and zebra were given to an enigmatic equid widely reported in the Iberian Peninsula during the Middle Ages. Roughly 150 toponyms deriving from the words zebro/a have been recorded in Iberia starting from the IX th century A.D. together with 65 Portuguese Fo...

Os et dents résistent au passage du temps et à la décomposition du corps. Ils deviennent alors des fossiles, témoins précieux de la vie du passé, des archives biologiques et environnementales, archives culturelles lorsqu’ils sont retrouvés dans un contexte archéologique... Ils sont porteurs d’autant de « messages » qui peuvent être décryptés par de...

Os et dents résistent au passage du temps et à la décomposition du corps. Ils deviennent alors des fossiles, témoins précieux de la vie du passé, des archives biologiques et environnementales, archives culturelles lorsqu’ils sont retrouvés dans un contexte archéologique... Ils sont porteurs d’autant de « messages » qui peuvent être décryptés par de...

Os et dents résistent au passage du temps et à la décomposition du corps. Ils deviennent alors des fossiles, témoins précieux de la vie du passé, des archives biologiques et environnementales, archives culturelles lorsqu’ils sont retrouvés dans un contexte archéologique... Ils sont porteurs d’autant de « messages » qui peuvent être décryptés par de...

The recent breathtaking progress in whole genome sequencing technology allows access to the genomes both of ancient organisms and populations, including those now extinct. Despite the heavy degradation and the extremely low quantities of ancient DNA, it is sometimes possible to sequence an entire genome from a fossil. This enterprise has been succe...

A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from di...

Palaeogenetic studies of faunal remains from archaeological sites can provide invaluable information if DNA is preserved. The quantity and quality of the genetic information that can be retrieved critically depends on the biomolecular preser-vation in the fossils. Here we report the assessment of the preservation state of DNA infaunal and human rem...

L'homme et l'animal unis à travers les âges

The Equidae have a long evolutionary history that has interested palaeontologists for a long time. Their morphology-based taxonomy, however, is a matter of controversy. Since most equid species are now extinct, the phylogenetic tree based on genetic data can be established only imperfectly via deduction of present day genomes and little is known ab...

Table S1 Mitochondrial fragments amplified for aDNA analysis Table S2 Comparisons of average numbers of alleles per locus and expected heterozygosities calculated from 15 microsatellite loci overlapping in four different felid species. Table S3 Population pairwise distances (RST) based on 18 polymorphic microsatellite loci. Fig. S1 Phylogenetic rel...

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000-12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA an...

Relationships between the numbers of NTCs performed and the PCR contamination level that can be excluded with a 95% confidence level. The exact binomial test [11] was used to calculate the one tailed probability that a certain number of NTCs performed is significantly lower than a certain theoretical proportion of contaminated PCR reactions. The si...

Supporting information as a single pdf file for printing or offline reading. (0.82 MB PDF)

Primers used for amplication of various target molecules. (0.02 MB DOCX)

Examples of significantly different distributions between sample and control PCRs. When sample and contaminating sequences are indistinguishable, to ensure authenticity of the sample amplification with a 95% confidence level it is necessary to demonstrate that the rate of success of sample amplification is significantly higher than the background o...

(0.09 MB DOC)

Genetic diversity of mitochondrial sequences contaminating PCR reagents. Median Joining networks [8] of products from negative PCR controls (NTCs) using primer pairs BB3/4 and BB1/2. A. Bos taurus sequences. The sequence distribution observed in the contaminant resembles that of the European bovine mitochondrial sequences: the bovine sequences show...

DNase I treatment. A. Effects of the DNase I treatment on the degradation of primers. Radio-labeled primers BR1 and BR2 had been incubated with DNase I for 10 minutes at 37°C at a concentration allowing complete degradation of a 103 bp fragment of plasmid pBR322, followed by 10 minutes of heat inactivation at 95°C prior to gel electrophoresis in a...

hl-dsDNase treatment of primers. PCR efficiency after treatment of DNase I-sensitive primers BR1/2 with hl-dsDNase. Blue diamonds = Control: PCR with untreated primers BR1/2; red squares = PCR with primers BR1/2 that were treated separately; green triangles = PCR with primers BR1/2 treated together. (0.05 MB TIF)

PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface...

Early diagenesis, spanning the time a few years after death, is crucial to later fossilization, because the former may determine the success of the latter. The external environment in which bones (and fossils) have been altered is critical to early diagenesis and fossilization processes. Alteration of bones by the former may determine the successfu...