Publications by authors named "David Caramelli"

64 Publications

The Illumina Sequencing Protocol and the NovaSeq 6000 System.

Methods Mol Biol 2021 ;2242:15-42

Department of Biology, University of Firenze, Firenze, Italy.

The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of sequencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.
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http://dx.doi.org/10.1007/978-1-0716-1099-2_2DOI Listing
January 2021

First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy).

Genes (Basel) 2021 Apr 25;12(5). Epub 2021 Apr 25.

Department of Cultural Heritage, University of Bologna, via Degli Ariani 1, 48121 Ravenna, Italy.

The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.
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http://dx.doi.org/10.3390/genes12050636DOI Listing
April 2021

Successful extraction of insect DNA from recent copal inclusions: limits and perspectives.

Sci Rep 2021 Mar 25;11(1):6851. Epub 2021 Mar 25.

Department of Animal Medicine, Production and Health, University of Padova, 35020, Legnaro, PD, Italy.

Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.
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http://dx.doi.org/10.1038/s41598-021-86058-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7994385PMC
March 2021

Archaeogenomic distinctiveness of the Isthmo-Colombian area.

Cell 2021 Apr 23;184(7):1706-1723.e24. Epub 2021 Mar 23.

Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain.

The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
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http://dx.doi.org/10.1016/j.cell.2021.02.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8024902PMC
April 2021

New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.

Front Genet 2021 18;12:619950. Epub 2021 Feb 18.

Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy.

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.
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http://dx.doi.org/10.3389/fgene.2021.619950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930628PMC
February 2021

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity.

Nat Plants 2021 02 8;7(2):123-128. Epub 2021 Feb 8.

Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations. Farmers selected desirable phenotypic traits (such as improved energy accumulation, palatability of seeds and reduced natural shattering) while leading domesticated populations through several more or less gradual demographic contractions. As a consequence, the erosion of wild genetic variation is typical of modern cultivars, making them highly susceptible to pathogens, pests and environmental change. The loss of genetic diversity hampers further crop improvement programmes to increase food production in a changing world, posing serious threats to food security. Using both ancient and modern seeds, we analysed the temporal dynamics of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) in the southern Andes. Here, we show that most domestic traits were selected for before 2,500 years ago, with no or only minor loss of whole-genome heterozygosity. In fact, most of the changes at coding genes and linked regions that differentiate wild and domestic genomes are already present in the ancient genomes analysed here, and all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable (at least as variable as modern genomes from the wild). Single seeds from modern cultivars show reduced variation when compared with ancient seeds, indicating that intensive selection within cultivars in the past few centuries probably partitioned ancestral variation within different genetically homogenous cultivars. When cultivars from different Andean regions are pooled, the genomic variation of the pool is higher than that observed in the pool of ancient seeds from north and central western Argentina. Considering that most desirable phenotypic traits are probably controlled by multiple polymorphic genes, a plausible explanation of this decoupling of selection and genetic erosion is that early farmers applied a relatively weak selection pressure by using many phenotypically similar but genetically diverse individuals as parents. Our results imply that selection strategies during the past few centuries, as compared with earlier times, more intensively reduced genetic variation within cultivars and produced further improvements by focusing on a few plants carrying the traits of interest, at the cost of marked genetic erosion within Andean landraces.
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http://dx.doi.org/10.1038/s41477-021-00848-7DOI Listing
February 2021

The first evidence for Late Pleistocene dogs in Italy.

Sci Rep 2020 08 7;10(1):13313. Epub 2020 Aug 7.

U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy.

The identification of the earliest dogs is challenging because of the absence and/or mosaic pattern of morphological diagnostic features in the initial phases of the domestication process. Furthermore, the natural occurrence of some of these characters in Late Pleistocene wolf populations and the time it took from the onset of traits related to domestication to their prevalence remain indefinite. For these reasons, the spatiotemporal context of the early domestication of dogs is hotly debated. Our combined molecular and morphological analyses of fossil canid remains from the sites of Grotta Paglicci and Grotta Romanelli, in southern Italy, attest of the presence of dogs at least 14,000 calibrated years before present. This unambiguously documents one of the earliest occurrence of domesticates in the Upper Palaeolithic of Europe and in the Mediterranean. The genetic affinity between the Palaeolithic dogs from southern Italy and contemporaneous ones found in Germany also suggest that these animals were an important common adjunct during the Late Glacial, when strong cultural diversification occurred between the Mediterranean world and European areas north of the Alps. Additionally, aDNA analyses indicate that this Upper Palaeolithic dog lineage from Italy may have contributed to the genetic diversity of living dogs.
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http://dx.doi.org/10.1038/s41598-020-69940-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414845PMC
August 2020

The mitogenome portrait of Umbria in Central Italy as depicted by contemporary inhabitants and pre-Roman remains.

Sci Rep 2020 07 1;10(1):10700. Epub 2020 Jul 1.

Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy.

Umbria is located in Central Italy and took the name from its ancient inhabitants, the Umbri, whose origins are still debated. Here, we investigated the mitochondrial DNA (mtDNA) variation of 545 present-day Umbrians (with 198 entire mitogenomes) and 28 pre-Roman individuals (obtaining 19 ancient mtDNAs) excavated from the necropolis of Plestia. We found a rather homogeneous distribution of western Eurasian lineages across the region, with few notable exceptions. Contemporary inhabitants of the eastern part, delimited by the Tiber River and the Apennine Mountains, manifest a peculiar mitochondrial proximity to central-eastern Europeans, mainly due to haplogroups U4 and U5a, and an overrepresentation of J (30%) similar to the pre-Roman remains, also excavated in East Umbria. Local genetic continuities are further attested to by six terminal branches (H1e1, J1c3, J2b1, U2e2a, U8b1b1 and K1a4a) shared between ancient and modern mitogenomes. Eventually, we identified multiple inputs from various population sources that likely shaped the mitochondrial gene pool of ancient Umbri over time, since early Neolithic, including gene flows with central-eastern Europe. This diachronic mtDNA portrait of Umbria fits well with the genome-wide population structure identified on the entire peninsula and with historical sources that list the Umbri among the most ancient Italic populations.
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http://dx.doi.org/10.1038/s41598-020-67445-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329865PMC
July 2020

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.

Nat Ecol Evol 2020 03 24;4(3):334-345. Epub 2020 Feb 24.

Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain.

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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http://dx.doi.org/10.1038/s41559-020-1102-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080320PMC
March 2020

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process.

Nat Ecol Evol 2020 03 24;4(3):324-333. Epub 2020 Feb 24.

School of Archaeology and Ancient History, Leicester University, Leicester, UK.

It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists and agropastoralists in western Eurasia that were up to 6,500 yr old. Despite the high genetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of 5,000 yr. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human-adapted S. enterica is linked to human cultural transformations.
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http://dx.doi.org/10.1038/s41559-020-1106-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186082PMC
March 2020

Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians.

Sci Rep 2019 04 1;9(1):5412. Epub 2019 Apr 1.

Department of Biology, University of Florence, Florence, Italy.

One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria - Shekerdja mogila, Gabrova mogila and Bereketska mogila - dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.
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http://dx.doi.org/10.1038/s41598-019-41945-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443937PMC
April 2019

Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.

Sci Rep 2019 03 5;9(1):3530. Epub 2019 Mar 5.

Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy.

Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.
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http://dx.doi.org/10.1038/s41598-019-39802-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401177PMC
March 2019

Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.

Sci Rep 2019 03 5;9(1):3530. Epub 2019 Mar 5.

Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy.

Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.
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http://dx.doi.org/10.1038/s41598-019-39802-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401177PMC
March 2019

A genetic perspective on Longobard-Era migrations.

Eur J Hum Genet 2019 04 16;27(4):647-656. Epub 2019 Jan 16.

Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy.

From the first century AD, Europe has been interested by population movements, commonly known as Barbarian migrations. Among these processes, the one involving the Longobard culture interested a vast region, but its dynamics and demographic impact remains largely unknown. Here we report 87 new complete mitochondrial sequences coming from nine early-medieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC). Population genetics analysis and demographic modeling highlighted a similarity between LC individuals, as reflected by the sharing of quite rare haplogroups and by the degree of genetic resemblance between Hungarian and Italian LC necropoleis estimated via a Bayesian approach, ABC. The demographic model receiving the strongest statistical support also postulates a contact between LC and NLC communities, thus indicating a complex dynamics of admixture in medieval Europe.
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http://dx.doi.org/10.1038/s41431-018-0319-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460631PMC
April 2019

From unknown to known: Identification of the remains at the mausoleum of fosse Ardeatine.

Sci Justice 2018 11 24;58(6):469-478. Epub 2018 May 24.

Department of Biology, University of Florence, Laboratory of Anthropology -Molecular Anthropology and Forensic Unit, Firenze, Italy.

During the Second World War, on 24th March 1944, 335 Italians were massacred near Rome by the occupying forces of Nazi Germany. Four months later forensic examination led to the identification of 323 out of 335 victims. After approximately 60 years, the identification of the remaining unidentified twelve victims began with anthropological and genetic analysis carried out by a team of Italian forensic experts. Anthropological analysis was performed in field in order to confirm the sex of each victim and verify the presence of only one individual in each grave for a correct sampling. Selected bone fragments for each individual were then collected and transferred to the laboratory for genetic analysis. Although the anthropological ante mortem information was limited, morphological and metrical data was collected for a possible future identification of the victims. Subsequently, the typing of autosomal loci, Y-STR and mtDNA D-loop region of all bone and available reference samples was conducted. LR and cumulative LRs obtained from autosomal STR and Y-STR results confirmed the alleged relationship between three victims and their relatives with values over 10 (one sample) and 10 (two samples). Therefore, the genetic analysis offered the families the possibility of replacing the number of the grave with the name of the victim.
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http://dx.doi.org/10.1016/j.scijus.2018.05.007DOI Listing
November 2018

Understanding 6th-century barbarian social organization and migration through paleogenomics.

Nat Commun 2018 09 11;9(1):3547. Epub 2018 Sep 11.

Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA.

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy.
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http://dx.doi.org/10.1038/s41467-018-06024-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134036PMC
September 2018

The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany.

Am J Phys Anthropol 2018 11 6;167(3):497-506. Epub 2018 Sep 6.

Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy.

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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http://dx.doi.org/10.1002/ajpa.23679DOI Listing
November 2018

Maternal DNA lineages at the gate of Europe in the 10th century AD.

PLoS One 2018 14;13(3):e0193578. Epub 2018 Mar 14.

Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania.

Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period. We successfully amplified and typed the mitochondrial control region of 10 individuals. For five of them, we also reconstructed the complete mitochondrial genomes using hybridization-based DNA capture combined with Next Generation Sequencing. We have portrayed the genetic structure of the Capidava medieval population, represented by 10 individuals displaying 8 haplotypes (U5a1c2a, V1a, R0a2'3, H1, U3a, N9a9, H5e1a1, and H13a1a3). Remarkable for this site is the presence of both Central Asiatic (N9a) and common European mtDNA haplotypes, establishing Capidava as a point of convergence between East and West. The distribution of mtDNA lineages in the necropolis highlighted the existence of two groups of two individuals with close maternal relationships as they share the same haplotypes. We also sketch, using comparative statistical and population genetic analyses, the genetic relationships between the investigated dataset and other medieval and modern Eurasian populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193578PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851556PMC
June 2018

The Beaker phenomenon and the genomic transformation of northwest Europe.

Nature 2018 03 21;555(7695):190-196. Epub 2018 Feb 21.

Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain.

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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http://dx.doi.org/10.1038/nature25738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973796PMC
March 2018

The genomic history of southeastern Europe.

Nature 2018 03 21;555(7695):197-203. Epub 2018 Feb 21.

Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy.

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
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http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018

Neither femur nor tooth: Petrous bone for identifying archaeological bone samples via forensic approach.

Forensic Sci Int 2018 Feb 24;283:144-149. Epub 2017 Dec 24.

Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Firenze, Italy.

One of the major challenges of molecular biology in anthropological analysis is the identification via DNA typing of bone or teeth samples that can be collected from archaeological site in order to investigate kinship relationships. Due to the difficulties of isolating and analysing DNA from such samples, several efforts have been made to solve these problems, but less work has been conducted to identify the proper type of bone samples for the DNA analysis. Therefore, following the promising results obtained from the DNA analysis of petrous bones by different groups of researchers, for the first time, here we investigated the possibility of using petrous bones as skeletal elements useful for short tandem repeat (STR) typing via capillary electrophoresis technique in ancient bone samples. In order to compare the results from petrous bone, femur and tooth samples, a total of 39 skeletal elements were collected from 13 different individuals excavated from Italian archaeological sites, dating from the sixth to seventh century C.E. The DNA was extracted, quantified, and subsequently amplified using two STR multiplex kits. The presence of a good amount of genetic material, despite high degradation, allowed us to quantify and subsequently identify STR profiles via CE analysis from ancient petrous bones that were complete for four out of thirteen samples and higher than 11 autosomal loci for all samples. Our results indicated that petrous bone is the best skeletal element with regard to DNA conservation and is a valuable element from which it is possible to obtain a complete STR profile also when analysing ancient bones. The STR results showed the possibility to use the petrous bones for identification and matching purposes in cases in which the biological material is poor and highly degraded such as in archaeological studies. Therefore, STR typing could represent a time-saving and cheap chance to verify kinship relationships in archaeological sites and evaluate sex when skeletal material is not suitable for morphometric estimate as in case of infants.
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http://dx.doi.org/10.1016/j.forsciint.2017.12.023DOI Listing
February 2018

Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages.

Proc Biol Sci 2017 Nov;284(1867)

Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy

It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.
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http://dx.doi.org/10.1098/rspb.2017.1540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719168PMC
November 2017

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Nature 2017 04 8;544(7650):357-361. Epub 2017 Mar 8.

Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK.

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.
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http://dx.doi.org/10.1038/nature21674DOI Listing
April 2017

Complete mitochondrial sequences from Mesolithic Sardinia.

Sci Rep 2017 03 3;7:42869. Epub 2017 Mar 3.

Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy.

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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http://dx.doi.org/10.1038/srep42869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335606PMC
March 2017

DNA Sequencing in Cultural Heritage.

Top Curr Chem (Cham) 2016 Feb 12;374(1). Epub 2016 Jan 12.

Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy.

During the last three decades, DNA analysis on degraded samples revealed itself as an important research tool in anthropology, archaeozoology, molecular evolution, and population genetics. Application on topics such as determination of species origin of prehistoric and historic objects, individual identification of famous personalities, characterization of particular samples important for historical, archeological, or evolutionary reconstructions, confers to the paleogenetics an important role also for the enhancement of cultural heritage. A really fast improvement in methodologies in recent years led to a revolution that permitted recovering even complete genomes from highly degraded samples with the possibility to go back in time 400,000 years for samples from temperate regions and 700,000 years for permafrozen remains and to analyze even more recent material that has been subjected to hard biochemical treatments. Here we propose a review on the different methodological approaches used so far for the molecular analysis of degraded samples and their application on some case studies.
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http://dx.doi.org/10.1007/s41061-015-0009-8DOI Listing
February 2016

Human identification by lice: A Next Generation Sequencing challenge.

Forensic Sci Int 2016 Sep 16;266:e71-e78. Epub 2016 May 16.

Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Viale Forlanini, 12, 27100 Pavia, Italy.

Rapid and progressive advances in molecular biology techniques and the advent of Next Generation Sequencing (NGS) have opened new possibilities for analyses also in the identification of entomological matrixes. Insects and other arthropods are widespread in nature and those found at a crime scene can provide a useful contribution to forensic investigations. Entomological evidence is used by experts to define the postmortem interval (PMI), which is essentially based on morphological recognition of the insect and an estimation of its insect life cycle stage. However, molecular genotyping methods can also provide an important support for forensic entomological investigations when the identification of species or human genetic material is required. This case study concerns a collection of insects found in the house of a woman who died from unknown causes. Initially the insects were identified morphologically as belonging to the Pediculidae family, and then, human DNA was extracted and analyzed from their gastrointestinal tract. The application of the latest generation forensic DNA assays, such as the Quantifiler(®) Trio DNA Quantification Kit and the HID-Ion AmpliSeq™ Identity Panel (Applied Biosystems(®)), individuated the presence of human DNA in the samples and determined the genetic profile.
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http://dx.doi.org/10.1016/j.forsciint.2016.05.006DOI Listing
September 2016

The genetic history of Ice Age Europe.

Nature 2016 06 2;534(7606):200-5. Epub 2016 May 2.

Instituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, 39005 Santander, Spain.

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.
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http://dx.doi.org/10.1038/nature17993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943878PMC
June 2016