Guido Barbujani | Università degli Studi di Ferrara (original) (raw)

Papers by Guido Barbujani

Supplementary Materials, 16 supplementary tables and appendix

Genes, 2020

There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (... more There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models a...

Science Advances, 2021

Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on ... more Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on their recent Anatolian origin.

Proceedings of the Royal Society B: Biological Sciences, 2019

Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of ... more Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but a...

European Journal of Human Genetics, 2019

From the first century AD, Europe has been interested by population movements, commonly known as ... more 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 earlymedieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC). Population genetics analysis and demographic modeling highlighted a similarity between LC individuals, as reflected by the sharing of quite rare haplogroups and by the degree of genetic resemblance between Hungarian and Italian LC necropoleis estimated via a Bayesian approach, ABC. The demographic model receiving the strongest statistical support also postulates a contact between LC and NLC communities, thus indicating a complex dynamics of admixture in medieval Europe.

Proceedings. Biological sciences, Jan 29, 2017

It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the lat... more It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.

Background. Anthropological and genetic data agree in indicating the African continent as the mai... more Background. Anthropological and genetic data agree in indicating the African continent as the main place of origin for modern human. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab peninsula into Southern Asia and Oceania, and later through a Northern route crossing the Levant. Results. Here we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa, and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of hybridization with archaic human forms in Australo-Melanesia. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions. We conclude tha...

Molecular Biology and Evolution, 2001

Ancient demographic events can be inferred from the distribution of pairwise sequence differences... more Ancient demographic events can be inferred from the distribution of pairwise sequence differences (or mismatches) among individuals. We analyzed a database of 3,677 Y chromosomes typed for 11 biallelic markers in 48 human populations from Europe and the Mediterranean area. Contrary to what is observed in the analysis of mitochondrial polymorphisms, Tajima's test was insignificant for most Y-chromosome samples, and in 47 populations the mismatch distributions had multiple peaks. Taken at face value, these results would suggest either (1) that the size of the male population stayed essentially constant over time, while the female population size increased, or (2) that different selective regimes have shaped mitochondrial and Y-chromosome diversity, leading to an excess of rare alleles only in the mitochondrial genome. An alternative explanation would be that the 11 variable sites of the Y chromosome do not provide sufficient statistical power, so a comparison with mitochondrial data (where more than 200 variable sites are studied in Europe) is impossible at present. To discriminate between these possibilities, we repeatedly analyzed a European mitochondrial database, each time considering only 11 variable sites, and we estimated mismatch distributions in stable and growing populations, generated by simulating coalescent processes. Along with theoretical considerations, these tests suggest that the difference between the mismatch distributions inferred from mitochondrial and Y-chromosome data are not a statistical artifact. Therefore, the observed mismatch distributions appear to reflect different underlying demographic histories and/or selective pressures for maternally and paternally transmitted loci.

Advances in the emergence of language, human cognition, and modern cultures, 2009

eLS, 2013

The origins of modern human diversity have long been debated within a framework set by two hypoth... more The origins of modern human diversity have long been debated within a framework set by two hypotheses: ‘Out-of-Africa’ versus multiregional evolution. Humans are genetically closer to each other than members of all other primate species, most of our genetic diversity is accounted for by individual differences within populations, and only a small fraction of the species' genetic variance represents differences among populations or geographic groups. All these findings are hard to reconcile with the notion of parallel evolution in different continents, implicit in the multiregional model; the alternative hypotheses are now better described as either complete replacement of archaic human populations, or as partial assimilation into anatomically modern populations. Critical information about human demographic history has emerged from analyses of genomic diversity, clearly supporting an African origin of our species, followed by dispersal of rather small groups of people in the other continents. However, ancient deoxyribonucleic acid from fossil specimens seems to suggest low, but significant, levels of hybridisation between anatomically archaic and modern humans in the course of the latter's expansion from Africa, although alternative explanations of the data cannot be ruled out. Key Concepts: Genetic differences between humans are smaller than in any other primate species. Genetic differences between human populations account for a minor fraction of the species' diversity. Most human polymorphic alleles are present in all continents. Each population contains an ample subset of human allelic variants. African populations show the highest genome diversity worldwide, and alleles in other continents can largely be regarded as subsets of African diversity. Differences between populations are structured in the geographical space, showing evidence of repeated founder effects as humans expanded to colonise the whole planet. Models of genetic replacement, partial or total, of archaic human forms by anatomically modern humans account for current diversity better than any alternative models. Non-African people consistently show an excess of DNA similarity with the Neandertal genome, which is often (but not necessarily) interpreted as a consequence of archaic hybridisation between Neandertals and anatomically modern people dispersing from Africa. Keywords: genomic diversity; DNA diversity; out-of-Africa; multiregional evolution; coalescence; neandertal; admixture

Trends in Genetics, 2010

This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright

Proceedings of the National Academy of Sciences, 2001

Historical sources indicate that the evangelist Luke was born in Syria, died in Greece, and then ... more Historical sources indicate that the evangelist Luke was born in Syria, died in Greece, and then his body was transferred to Constantinople, and from there to Padua, Italy. To understand whether there is any biological evidence supporting a Syrian origin of the Padua body traditionally attributed to Luke, or a replacement in Greece or Turkey, the mtDNA was extracted from two teeth and its control region was cloned and typed. The sequence determined in multiple clones is an uncommon variant of a set of alleles that are common in the Mediterranean region. We also collected and typed modern samples from Syria and Greece. By comparison with these population samples, and with samples from Anatolia that were already available in the literature, we could reject the hypothesis that the body belonged to a Greek, rather than a Syrian, individual. However, the probability of an origin in the area of modern Turkey was only insignificantly lower than the probability of a Syrian origin. The genet...

Molecular Biology and Evolution, 2009

The ancient inhabitants of a region are often regarded as ancestral, and hence genetically relate... more The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far, this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA (mtDNA) variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mtDNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations, we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by approximate Bayesian computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland.

PLoS biology, Jan 19, 2010

The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neo... more The relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Near East have been intensely debated. Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men. Previous studies suggested a Paleolithic origin, but here we show that the geographical distribution of its microsatellite diversity is best explained by spread from a single source in the Near East via Anatolia during the Neolithic. Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage, and the contrast of this pattern with that shown by maternally inherited mitochondrial DNA suggests a unique role for males in the transition.

American Journal of Physical Anthropology, 2001

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkme... more The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population‐genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51–200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic‐speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y‐chromosome loci. That (admitted...

The American Journal of Human Genetics, 2000

Nature, 2019

Anatomically modern humans originated in Africa around 200 thousand years ago (ka) 1-4. Although ... more Anatomically modern humans originated in Africa around 200 thousand years ago (ka) 1-4. Although some of the oldest skeletal remains suggest an eastern African origin 2 , southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny 5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa 7 , approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeoclimate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence 8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes. Southern Africa has long been considered to be one of the regions in which anatomically modern humans (AMHs) originated. Home to contemporary populations who represent the earliest human lineages, evolutionary time estimates have largely been based on mitochondrial DNA (mitogenomes) 1,6. The maternal human phylogenetic tree consists of two major branches, the extensive L1'6-which includes the out-of-Africa ancestral L3 sub-branch (or haplogroup)-and the rare deep-rooting L0. The L0 lineage is predominated by southern African haplogroups: L0d, L0k and the recently described L0g 6. By contrast, the rare L0f and common L0a lineages are dispersed throughout sub-Saharan Africa 1,3,6. Through L0 pre-screening, we identified 198 southern Africans with poorly represented haplogroups for whom the mitogenome was sequenced (Supplementary Table 1), allowing for a combined analysis of 1,217 mitogenomes (Fig. 1a and Extended Data Table 1). We ethno-linguistically classified study participants as KhoeSansouthern African populations who traditionally practiced foraging and spoke languages containing 'click' consonants-or non-KhoeSan individuals. Non-KhoeSan who have KhoeSan-derived L0 mitogenomes are referred to in this study as KhoeSan ancestral, with further geographical classification (Fig. 1b and Extended Data Table 2; terminology pertaining to southern African KhoeSan populations is complex and contentious, see Methods for further discussion). Contemporary KhoeSan include Kalahari KhoeSan (Kx'a, Tuu and central Khoe-Kwadi speakers) and west-coastal KhoeSan (Khoe-Kwadi Nama speakers) 11. Peoples who speak Southern Bantu languages, who migrated down the east coast of Africa around 1,500 years ago, may have acquired an east-coastal KhoeSan heritage 12. The arrival of European colonists to the Cape in mid-1600s gave rise to the South African Coloured and Namibian Baster populations (of Eurasian and indigenous descent), who acquired a Cape KhoeSan heritage 13. Excluding the east African Sandawe and Hadza (whose languages also contain click consonants), indigenous KhoeSan populations appear to be absent northeast of the Zambezi river, supported by the lack of skeletal remains representing the KhoeSan-like hunter-forager morphology 14. We classified the 198 new