Biology subjects

Coppa, A.

Publications and source records attributed to Coppa, A..

6 recordsLinked to original sources

bioRxiv2025

Genetic admixture between East and West European Gravettian-associated populations in Western Europe before the Last Glacial Maximum

Modern humans first settled in Europe at least 45,000 years ago. However, limited genomic data from individuals dating between 45,000 and 20,000 years ago still restricts our understanding of population dynamics and admixture during the Upper Palaeolithic. Before the Last Glacial Maximum (LGM, 26.5-19 cal kya), Gravettian culture-associated populations were widespread and genetically diverse, comprising at least two distinct genetic groups, referred to as the Fournol and V[e]stonice clusters. We present genome-wide data from three Gravettian-associated individuals: two from cave sites in the Franco-Cantabrian region (Chufin and Isturitz) and one from Italy (Ostuni1b). These data reveal previously undetected gene flow linking the ancestry of 34,000-year-old individuals from Sungir (Russia) to Gravettian individuals from Western Europe, challenging the prevailing model of population continuity from the Aurignacian to the Solutrean. As osseous remains are scarce for this time period, DNA from sediments deposited by ancient humans opens a new possibility to obtain genomic data. We thus examine sedimentary DNA from Solutrean Layer 122 at El Miron Cave (Cantabria, [~]22,000 cal BP), recovering approximately 16,000 human SNPs, among the highest yields reported from a Palaeolithic context. Generating these data required over 1.15 billion sequencing reads, illustrating both the potential of sediment DNA for autosomal analysis and the technical challenges of the approach.

genomics↗

bioRxiv2022

A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean

The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. To investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia, and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbors together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.

genomics↗

bioRxiv2020

A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Ancient DNA sampling methods--although optimized for efficient DNA extraction--are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

evolutionary biology↗

bioRxiv2020

Population dynamics in pre-Inca human groups from the Osmore Valley, the Azapa Valley and the coast of the south central Andes

The present study applies a dental morphological perspective to the understanding of the complex population history of pre-contact South-Central Andes, the detection of the underlying dynamics, and the assessment of the biological ties among groups. It takes into account 1665 individuals from 16 sites that date from the Archaic to the Late Intermediate located along the coast, on the altiplano, and in the coastal valleys of both Chile and Peru. The results obtained highlight the need for wider perspectives capable of taking into account both the different micro-regional realities and the region in its ensemble. The population dynamics and mobility patterns detected indicate the widely accepted interpretations and distinctions based on cultural affiliations might be insufficient to comprehend the complex population history of the region, especially because the results obtained in the present study indicate the presence of a general and widespread common morphological background for the inhabitants of some of these cultures (i.e., Moche and Wari) and that the interactions they had throughout time must have been far from inconsequential.

evolutionary biology↗

bioRxiv2019

Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

genomics↗

bioRxiv2018

The Genomic Formation of South and Central Asia

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia--consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC--and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.\n\nOne Sentence SummaryGenome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

genomics↗