Biology subjects

Barbujani, G.

Publications and source records attributed to Barbujani, G..

5 recordsLinked to original sources

bioRxiv2025

Inference of human pigmentation from ancient DNA by genotype likelihood

Light eyes, hair and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic, and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in two high-coverage ancient samples, the Paleolithic Ust-Ishim from Russia and the Mesolithic SF12 from Sweden. We could thus compare three approaches to pigmentation inference, concluding that, for suboptimal levels of coverage (<8x), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye and hair color evolved over the past 45,000 years. The shift towards lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Copper and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.

genomics↗

bioRxiv2020

More rule than exception: Parallel evidence of ancient migrations in grammars and genomes of Finno-Ugric speakers

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method exclusively based on syntactic data, here we focus on the complex relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis supports three distinct clusters corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL-speakers. Therefore, our study indicates plausible secondary convergence in the syntax of languages of different families, providing evidence that such interference effects were accompanied, and possibly caused, by recognizable processes at the population level. In particular, based on the comparison of modern and ancient genomes, our analysis identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of the FU into Europe.

genomics↗

bioRxiv2018

A new Approximate Bayesian Computation framework to distinguish among complex evolutionary models using whole-genome data

Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analyzed, complex demographic processes can easily exceed computational constraints, and the procedures to evaluate the reliability of the estimates contribute to increase the computational effort. Here we present an Approximate Bayesian Computation (ABC) framework, based on the Random Forest algorithm, to infer complex past population processes using complete genomes. To do this, we propose to summarize the data by the full genomic distribution of the four mutually exclusive categories of segregating sites (FDSS), a statistic fast to compute from unphased genome data. We constructed an efficient ABC pipeline and tested how accurately it allows one to recognize the true model among models of increasing complexity, using simulated data and taking into account different sampling strategies in terms of number of individuals analyzed, number and size of the genetic loci considered. We tested the power of the FDSS to be informative about even complex evolutionary histories and compared the results with those obtained summarizing the data through the unfolded Site Frequency Spectrum, thus highlighting for both statistics the experimental conditions maximizing the inferential power. Finally, we analyzed two datasets, testing models (a) on the dispersal of anatomically modern humans out of Africa and (b) the evolutionary relationships of the three species of Orangutan inhabiting Borneo and Sumatra.

genetics↗

bioRxiv2018

A genetic perspective on Longobard-Era migrations

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 locations, we sampled necropolises characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found (NLC). Population genetics analysis and ABC modeling highlighted a similarity between LC individuals, as reflected by a certain degree of genetic continuity between these groups, that reached 70% among Hungary and Italy. Models postulating a contact between LC and NLC communities received also high support, indicating a complex dynamics of admixture in medieval Europe.

genetics↗

bioRxiv2018

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics

ABSTARCTDespite 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 was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

genetics↗