Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies

Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy

The biological aspects of infancy within late Upper Palaeolithic populations and the role of southern refugia at the end of the Last Glacial Maximum are not yet fully understood. This study presents a multidisciplinary, high temporal resolution investigation of an Upper Palaeolithic infant from Grotta delle Mura (Apulia, southern Italy) combining palaeogenomics, dental palaeohistology, spatially-resolved geochemical analyses, direct radiocarbon dating, and traditional anthropological studies. The skeletal remains of the infant – Le Mura 1 – were directly dated to 17,320-16,910 cal BP. The results portray a biological history of the infant’s development, early life, health and death (estimated at ~72 weeks). They identify, several phenotypic traits and a potential congenital disease in the infant, the mother’s low mobility during gestation, and a high level of endogamy. Furthermore, the genomic data indicates an early spread of the Villabruna-like components along the Italian peninsula, confirming a population turnover around the time of the Last Glacial Maximum, and highlighting a general reduction in genetic variability from northern to southern Italy. Overall, Le Mura 1 contributes to our better understanding of the early stages of life and the genetic puzzle in the Italian peninsula at the end of the Last Glacial Maximum. © The Author(s) 2024

L'impatto del rumore antropico sui cetacei: aspetti scientifici e normativi

Per anni gli spiaggiamenti di massa di mammiferi marini hanno rappresentato un mistero per i ricercatori. A fronte dei numerosi quesiti tuttora senza risposta, è ormai scientificamente provato che il mondo subacqueo, e i cetacei in particolare, risentono del rumore antropico. La dissertazione esaminerà dapprima gli aspetti scientifici: i cetacei, le emissioni e la propagazione acustica in ambiente subacqueo e le correlazioni con il comportamento di tali mammiferi, presentando significativi case studies. Successivamente ne tratteggerà gli aspetti normativi e legislativi, mirati alla mitigazione del problema in prospettiva futura di conservazione del dominio subacqueo, dimensione strategica dal punto di vista ambientale, socioeconomico, tecnologico e geostrategico. I cetacei sono un ordine di mammiferi completamente adattatosi alla vita acquatica che, a differenza dell’uomo che ha come senso principale la vista, sfruttano l’elemento uditivo per lo svolgimento delle funzioni vitali, come navigazione, nutrizione e riproduzione. Se la presenza di cetacei nei nostri mari e oceani è un fatto attestato, la loro distribuzione è ancora oggetto di ricerca, grazie all’ausilio di sistemi rimorchiati e tag. Dal punto di vista ecologico, i mammiferi marini rappresentano un elemento vitale dell’ecosistema marino, in quanto ne garantiscono l’equilibrio. Si analizzerà poi la propagazione del suono in acqua ed i fenomeni fisici che la caratterizzano. In particolare, si rimarca la distinzione tra segnale, ossia il suono utile, e rumore (o disturbo), che è quella porzione di suono indesiderata, prodotta da processi naturali o dagli esseri umani. Ed è proprio il rumore, in particolare quello prodotto dalle attività antropiche, come emissioni con sonar militari ad alta potenza, attività industriali, rilevamenti sismici, traffico navale ed utilizzo di esplosivi, a rappresentare un pericolo per i mammiferi marini. Per eseguire il monitoraggio delle emissioni acustiche in acqua, è necessario utilizzare dei sistemi di registrazione acustica, ancora in fase di studio. La problematica principale riguarda l’individuazione dei parametri ed indici acustici più idonei e, soprattutto, una standardizzazione del metodo di misurazione. Quest’ultima è particolarmente importante perché permette di effettuare i confronti tra misurazioni diverse dal punto di vista temporale e spaziale. Si vedrà come, grazie alla loro flessibilità di impiego – che rappresenta il miglior compromesso tra il tempo di registrazione e la quantità di dati memorizzabili – i sistemi maggiormente utilizzati al momento sono i registratori acustici fissi ed autonomi per il monitoraggio acustico passivo (Autonomous Recorders – ARs), i quali forniscono una modalità economica per determinare la presenza, il numero relativo e la distribuzione spaziale e temporale dei cetacei vocalizzanti. Tra la fine degli Anni Novanta ed i primi Anni Duemila, si sono verificati diversi spiaggiamenti di massa “atipici”, in diverse aree geografiche e con diversi numeri di esemplari spiaggiati, il cui fattore comune è rappresentato da esercitazioni navali che prevedevano l’utilizzo di sonar navali nei giorni antecedenti. In particolare, gli esemplari su cui è stato possibile effettuare le necropsie mostravano tutti i sintomi della malattia di decompressione, la stessa che colpisce i sommozzatori quando non rispettano le tempistiche di emersione. Si rimanda agli specifici case studies. Dal 2004 non sono stati documentati altri eventi “atipici”. Tuttavia, probabilmente anche grazie all’impatto mediatico di questi eventi e al crescente interesse per questi fenomeni, la volontà di trovare un metodo di mitigazione dell’impatto del rumore antropico è stata sin da subito un elemento primario per le autorità militari, scientifiche e governative, che per questo motivo hanno attivato workshop, risoluzioni e studiato procedure da implementare per l’impiego di sonar. Sebbene non si siano più verificati spiaggiamenti, la ricerca non si è fermata: si stanno sviluppando nuovi sistemi di monitoraggio e nuove procedure per evitare che avvengano tragedie simili a quelle del passato. Si rende quindi necessario che le misure di mitigazione da mettere in atto a tutela dei mammiferi marini assumano un ruolo di primissimo piano per la conservazione e la salvaguardia dell’ambiente subacqueo. Se la dimensione subacquea è luogo di scavi minerari, trasporto di energia e teatro di attività di Difesa e Sicurezza, essa è anche riserva alimentare e ambientale imprescindibile per la vita del nostro Pianeta

Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291{ extendash}1329 {CE}) indicates the first known case of late-onset Pompe disease

Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard "clinical exome analysis" conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder

More data on ancient human mitogenome variability in Italy: new mitochondrial genome sequences from three Upper Palaeolithic burials

Background Recently, the study of mitochondrial variability in ancient humans has allowed the definition of population dynamics that characterised Europe in the Late Pleistocene and Early Holocene. Despite the abundance of sites and skeletal remains few data are available for Italy. Aim We reconstructed the mitochondrial genomes of three Upper Palaeolithic individuals for some of the most important Italian archaeological contexts: Paglicci (South-Eastern Italy), San Teodoro (South-Western Italy) and Arene Candide (North-Western Italy) caves. Subjects and methods We explored the phylogenetic relationships of the three mitogenomes in the context of Western Eurasian ancient and modern variability. Results Paglicci 12 belongs to sub-haplogroup U8c, described in only two other Gravettian individuals; San Teodoro 2 harbours a U2'3'4'7'8'9 sequence, the only lineage found in Sicily during the Late Pleistocene and Early Holocene; Arene Candide 16 displays an ancestral U5b1 haplotype already detected in other Late Pleistocene hunter-gatherers from Central Europe. Conclusion Regional genetic continuity is highlighted in the Gravettian groups that succeeded in Paglicci. Data from one of the oldest human remains from Sicily reinforce the hypothesis that Epigravettian groups carrying U2'3'4'7'8'9 could be the first inhabitants of the island. The first pre-Neolithic mitogenome from North-Western Italy, sequenced here, shows more affinity with continental Europe than with the Italian peninsula

Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes

Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre- Iron Age populations, that should be further investigated

The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations