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

Abstract

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. Due to its acknowledged potential, archaeogenetics is broadly applied to study ancient civilizations, demographic histories and migration events. Markedly, advances in high-throughput genotyping technology have highlighted how the present-day genetic variation of human populations is the outcome of past population movements. In prehistoric times, the Mediterranean area experienced three significant migration waves whose legacy is retrieved in the mitochondrial pool of modern and ancient populations: the Paleolithic hunter-gatherers who survived and re-expanded from glacial refuges, the Neolithic farming societies that moved from the East, and the herders from the Pontic-Caspian steppes inaugurating the Bronze Age 1-13 .

Archaeogenomic distinctiveness of the Isthmo-Colombian area

“…Mitochondrial DNA capture was also performed at the University of Florence for four individuals (PAPV27, PAPV53, PAPV93, PAPV109), as in ( Modi et al., 2020 ).…”

Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

“…Carver Biotechnology Center of the University of Illinois. Mitochondrial DNA capture was also performed at the University of Florence for four individuals (PAPV27, PAPV53, PAPV93, PAPV109), as in (Modi et al, 2020). Libraries were sequenced at the National Neurological Institute C. Mondino in Pavia using an Illumina MiSeq instrument (paired-end reads 150x2).…”

“…After automated DNA extraction with Maxwell® RSC Instrument in the lab of Genomics of Human and Animal Populations at the University of Pavia, the samples were genotyped with the Affymetrix Human Origin 600K chip at the Institute of Healthcare Research in Santiago de Compostela (CEGEN). As for the mitogenome sequencing, the entire mtDNA was amplified in two overlapping fragments (Modi et al, 2020). Libraries were prepared using the Illumina Nextera XT DNA preparation kit and sequenced at the National Neurological Institute C. Mondino in Pavia on an Illumina MiSeq instrument (paired-end reads 150x2).…”

“…As for the mitogenome sequencing, the entire mtDNA was amplified in two overlapping fragments (Modi et al, 2020). Libraries were prepared using the Illumina Nextera XT DNA preparation kit and sequenced at the National Neurological Institute C. Mondino in Pavia on an Illumina MiSeq instrument (paired-end reads 150×2).…”

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

“…In many studies on ancient samples, mitochondrial DNA (mtDNA) has been preferred as a target because of its high number of copies in each cell and consequently its higher availability with respect to nuclear DNA. It represents also a useful marker for evolutionary and population genetics analysis extensively applied on ancient samples ( Modi et al, 2017 ; Chyleński et al, 2019 ; Ehler et al, 2019 ; Modi et al, 2019 , 2020a , b ; Översti et al, 2019 ; Vai et al, 2019 ; Juras et al, 2020 ; Yang et al, 2020 ). However, besides contamination by exogenous DNA samples, another source of artifacts generally affecting mtDNA analysis is represented by nuclear sequences of mitochondrial origin (NumtS), barely explored in aDNA ( den Tex et al, 2010 ; Samaniego Castruita et al, 2015 ).…”