Elena Gigli

• PostDoc Position at University of Florence

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispe...

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3–5]; and (2) multiple dispe...

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500-4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that d...

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier betwe...

Alignment of clone sequences. (PDF)

Description of primers used and their references. (DOCX)

Ancient and current populations used in comparative analysis. References corresponds to reference number in the manuscript. (DOC)

How samples should be collected.

NGS library preparation and sequencing chemistries. The material provided describes library preparation for the 454/Roche and Illumina platforms and their sequencing chemistries.

The « Golden criteria » by Cooper and Poinar 2000 [[10]].

In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution a...

The rapid accumulation of genetic data from Neandertals is gaining more and more scientific value, shedding light on different aspects of their evolution. This information allows testing of hypotheses previously generated with evidence from morphology, archaeology, paleoclimatology and chronology. The retrieval of six Neandertal complete mitochondr...

Background Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a char...

The remains of 12 Neandertal individuals have been found at the El Sidrón site (Asturias, Spain), consisting of six adults, three adolescents, two juveniles, and one infant. Archaeological, paleontological, and geological evidence indicates that these individuals represent all or part of a contemporaneous social group of Neandertals, who died at ar...

A text on a pyrographically decorated gourd dated to 1793 explains that it contains a handkerchief dipped with the blood of Louis XVI, king of France, after his execution. Biochemical analyses confirmed that the material contained within the gourd was blood. The mitochondrial DNA (mtDNA) hypervariable region 1 (HVR1) and 2 (HVR2), the Y-chromosome...

Neandertal skeletal remains are usually contaminated with modern human DNA derived from handling and washing of the specimens during excavation. Despite the fact that the distinct Neandertal haplotypes allow the design of specific primer pairs, for instance in most of the mitochondrial DNA (mtDNA) hypervariable region 1 (HVR1), the human contaminan...

The bitter taste perception (associated with the ability or inability to taste phenylthiocarbamide) is mediated by the TAS2R38 gene. Most of the variation in this gene is explained by three common amino-acid polymorphisms at positions 49 (encoding proline or alanine), 262 (alanine or valine) and 296 (valine or isoleucine) that determine two common...

Author Summary Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. However, ancient DNA studies are often based on DNA extracted from only one or a few individuals and, therefore, do not lend themselves to statisti...

Background Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic da...

All complete clone sequences obtained from PCRs in Reykjavik (R) and Barcelona (B). (0.51 MB XLS)

Initial cMAX candidate sequences and changes made as a result of the qualitative assessment procedure. (0.16 MB DOC)

Results from replication amplifications performed in Reykjavik. (0.08 MB DOC)

List of sampled skeletal remains with background information. (0.19 MB DOC)

Oligonucleotide primer sequences. (0.04 MB DOC)

List of sampled skeletal remains and overview of experiments performed in the Reykjavik lab. (0.44 MB DOC)

Published mtDNA sequences used in comparative analyses (sites 16055-16391). (0.13 MB DOC)

Results from replication amplifications performed in Barcelona. (0.05 MB DOC)

Rules for haplogroup classification of sequences. (0.30 MB DOC)

Primer pairs used for DNA amplifications. (0.04 MB DOC)

The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neande...

Clone sequences. Clone sequences generated for the ABO blood group gene and mtDNA fragments in Neandertals.

We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C-->T and G-->A miscoding lesions (the predominant manifestation...

We report the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca. The optimal preservation of the remains permitted the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth. MtDNA sequences from the tooth and rib were not identical, suggesting they belonged to different individua...

Summary of consistent mutations. Summarized distribution of mutations and examined PCR in a prototypal individual.

Distribution of consistent mutations in each Neandertal's mtDNA. Original distribution of mutations (only consistent substitutions) and examined PCRs for each mtDNA position between 16056 and 16375.

Nucleotide changes for each consistent mutation. Nucleotide changes for each consistent mutation in Neandertal's mtDNA.

Statistics used for estimating the damage distribution. Calculation of the expected probability of multiple (consistent) mutations per region in the mtDNA hypervariable region 1.

We report on the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca exhumed in November 2003, from the S. Maria Assunta church, in Arquà Padua (Italy) where he died in 1374. The optimal preservation of the remains allowed the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth a...