Biology subjects

Ghirotto, S.

Publications and source records attributed to Ghirotto, S..

8 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↗

bioRxiv2024

Low-ABC: a robust demographic Inference from low-coverage whole-genome data through ABC

The reconstruction of past demographic histories relies on the pattern of genetic variation shown by the sampled populations; this means that an accurate estimation of genotypes is crucial for a reliable inference of past processes. A commonly adopted approach to reconstruct complex demographic dynamics is the Approximate Bayesian Computation (ABC) framework. It exploits coalescent simulations to generate the expected level of variation under different evolutionary scenarios. Demographic inference is then performed by comparing the simulated data with the genotypes called in the sampled individuals. Low sequencing coverage drastically affects the ability to reliably call genotypes, thus making low-coverage data unsuitable for such powerful inferential approaches. Here, we present Low-ABC, a new ABC approach to infer past population processes using low-coverage whole-genome data. Under this framework, both observed and simulated genetic variation are not directly compared using called genotypes, but rather obtained using genotype likelihoods to consider the uncertainty caused by the low sequencing coverage. We first evaluated the inferential power of this procedure in distinguishing among different demographic models and in inferring model parameters under different experimental conditions, including a wide spectrum of sequencing coverage (1x to 30x), number of individuals, number, and size of genetic loci. We showed that the use of genotype likelihoods integrated into an ABC framework provides a reliable inference of past population dynamics, thus making possible the application of model-based inference also for low-coverage data. We then applied Low-ABC to shed light on the relationship between Mesolithic and Early Neolithic European populations.

genomics↗

bioRxiv2023

Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)

The Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution for this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs, and 5,196 nuclear SNPs) using the Approximate Bayesian Computation algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model amongst the simulated datasets (where the model was known), but different markers typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is present in the Brisbane and North Pine Rivers where past translocations are documented. These results will inform ongoing conservation efforts for this endangered and iconic species and warrant careful consideration of future genetic management of the Australian lungfish populations.

evolutionary biology↗

bioRxiv2019

Contrasting paternal and maternal genetic histories of Thai and Lao populations

The human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of [~]2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic ([~]10 kya), with two later major male-specific expansions during the Neolithic period ([~]4-5 kya) and the Bronze/Iron Age ([~]2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories.

genetics↗

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↗

bioRxiv2017

New insights from Thailand into the maternal genetic history of Mainland Southeast Asia

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1,234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA sequences from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the extension and expansion of TK people through MSEA, although there is also some support for an admixture model. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.

genetics↗