Valeria Mattiangeli

• Ph D
• Laboratory Manager at Trinity College Dublin

The relationship between humans and pigs has changed dramatically since their domestication in southwest Asia and subsequent human-induced introduction into Europe. Introgression between incoming southwest Asian pigs and European boar resulted in the gradual replacement of southwest Asian ancestry in European pigs. However, we currently lack genomi...

The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populati...

Roman writers found the relative empowerment of Celtic women remarkable¹. In southern Britain, the Late Iron Age Durotriges tribe often buried women with substantial grave goods². Here we analyse 57 ancient genomes from Durotrigian burial sites and find an extended kin group centred around a single maternal lineage, with unrelated (presumably inwar...

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia¹. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwe...

Background The Islamic influence on the Iberian Peninsula left an enduring legacy culturally and linguistically, however the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late Medieval period through ancient DNA. Results Our comprehensiv...

Brucella melitensis is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of Brucella in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.4...

Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etrusc...

Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputat...

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ances...

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ances...

A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: 1) the indigenous Jomon hunter-gatherers, 2) a Northeast Asian component that arrived during the agrarian Yayoi period, and 3) a major influx of East Asian ancestry in the imperial Kofun period. However,...

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumours consistent with the autosomal dominant condition multiple osteochondrom...

Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra spe...

Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched f...

A bstract Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple...

Significance The Orcadian Neolithic has been intensively studied and celebrated as a major center of cultural innovation, whereas the Bronze Age is less well known and often regarded as a time of stagnation and insularity. Here, we analyze ancient genomes from the Orcadian Bronze Age in the context of the variation in Neolithic Orkney and Bronze Ag...

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumors consistent with the autosomal dominant condition multiple osteochondroma...

The evolution of the genera Bos and Bison and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct Kouprey (Bos sauveli) and analysed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic sig...

Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Nor...

Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultur...

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole-genome sequences (3.94 X) of an approximately 1600-year-old naturally mummified sheep...

Significance Goats were among the first domestic animals and today are an important livestock species; archaeozoological evidence from the Zagros Mountains of western Iran indicates that goats were managed by the late ninth/early eighth millennium. We assess goat assemblages from Ganj Dareh and Tepe Abdul Hosein, two Aceramic Neolithic Zagros sites...

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole genome sequences (3.94X) of a~1600 year old naturally mummified sheep recovered from...

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ra...

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole genome sequences of a ~1600 year old naturally mummified sheep recovered from Chehrāb...

The nature and distribution of political power in Europe during the Neolithic era remains poorly understood¹. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the gre...

Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift...

Details to the shotgun and amplicon datasets, FastQScreen results, mapping statistics and detected variants.

Data S2: Additional Information to the Multi-omics Data and Elemental/Stable Isotope Analysis, Related to Figures 2–4 Details to the comparative modern animal samples used in this study and to the metabolite, glycan, stable isotope, elemental, protein, and lipid analysis results.

How humans got their goats Little is known regarding the location and mode of the early domestication of animals such as goats for husbandry. To investigate the history of the goat, Daly et al. sequenced mitochondrial and nuclear sequences from ancient specimens ranging from hundreds to thousands of years in age. Multiple wild populations contribut...

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1 • Fowler C. • Harding J. • Hofmann D. Defining th...

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one...

Electronic Supplementary Material - The York Gospels: a one thousand year biological palimpsest

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one...

The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic...

The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes samp...

Many archaeological bones display a heterogeneous degradation pattern. Highly degraded bones could contain pockets of well-preserved bone, harbouring good quality DNA. This dichotomy may explain why the relationships between global bone preservation parameters such as histological integrity, bone mineral crystallinity or collagen yield, and bulk DN...

A dogged investigation of domestication The history of how wolves became our pampered pooches of today has remained controversial. Frantz et al. describe high-coverage sequencing of the genome of an Irish dog from the Bronze Age as well as ancient dog mitochondrial DNA sequences. Comparing ancient dogs to a modern worldwide panel of dogs shows an o...

Admixture mapping affords a powerful approach to genetic mapping of complex traits and may be particularly suited to investigation in cattle where many breeds and populations are hybrids of the two divergent ancestral genomes, derived from Bos taurus and Bos indicus. Here we design a minimal genome wide SNP panel for tracking ancestry in recent hyb...

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 x) and seven...

More than 500 male-male interactions were recorded in a population of 560 fallow deer in order to evaluate the importance of fight duration as an index of risk and benefit. Fight duration was affected by rank, presence or absence of parallel walk in the fight sequence and, to a lesser extent, presence of females. Higher-ranking bucks fought for lon...

Allele frequencies at each microsatellilte locus

Microsatellite primer sequences and annealing temperatures

It has been postulated that gene function may influence the degree to which allele frequencies differ among populations. In order to evaluate this effect, genotypic data from resequencing studies of genes classified as cytokines, cytokine receptors, cell adhesion molecules, Toll-like receptors and coagulation proteins were analysed for genetic diff...

In this study we present a single population test (Ewens-Waterson) applied in a genomic context to investigate the presence of recent positive selection in the Irish population. The Irish population is an interesting focus for the investigation of recent selection since several lines of evidence suggest that it may have a relatively undisturbed gen...

The blue whiting, Micromesistius poutassou (Teleostei, Gadidae) is found between latitudes 26° and 82°N along the continental margin of the Northeast Atlantic, with smaller populations in the Northwest Atlantic and the Mediterranean. There is an annual spawning aggregation on the Porcupine Bank and Hebridean Shelf (west of Ireland and Scotland, res...

Genetic analysis of the four Trisopterus (Gadidae) taxa suggests that the interrelationships of the two morphs of poor cod (T. minutus minutus in the Atlantic and T. minutus capelanus in the Mediterranean) should be reconsidered. The Mediterranean poor cod T. m. capelanus is more closely related to bib T. luscus than to the Atlantic poor cod, so th...

Nine allozyme and two minisatellite loci were used to investigate potential genetic differentiation among three samples of Mediterranean poor cod, Trisopterus minutus capelanus, from the Gulf of Lion, the Tuscan Archipelago and the Aegean Sea. Both types of markers showed consistent results, with FST values of 0.0262 and 0.0296 (P < 0.0015, after B...

Nine samples of Atlantic poor cod, Trisopterus minutus minutus, collected from the Bay of Biscay to Trondheimsfjord, Norway, were analysed using three minisatellite DNA loci, amplified using PCR and screened with an automated sequencer. One focus was found to be polymorphic. F-ST analysis using the polymorphic locus indicated that 2.2% of the total...

Genetic analysis of the four Trisopterus (Gadidae) taxa suggests that the interrelationships of the two morphs of poor cod (T. minutus minutus in the Atlantic and T. minutus capelanus in the Mediterranean) should be reconsidered. The Mediterranean poor cod T. m. capelanus is more closely related to bib T. luscus than to the Atlantic poor cod, so th...

Competition between male fallow deer (Dama dama), during the breeding season was studied to determine if conflict strategies were consistent with the reduction of risk. Agonistic interactions between males were analysed in relation to age, dominance rank and availability of mating opportunities. The breeding season was divided into two main periods...

A population of 110 adult fallow deer kept in an enclosure under very intensive conditions (31.4 deer/ha) was observed for 12 h/d (from 0800 to 2000) for 17 d during the birth season in order to study social and feeding behavior under intensive management. Observations were carried out by a scan sampling technique. The feeding activity of all the d...