Francesca Brisighelli

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

Mitochondrial Haplogroup U5b3: A Distant Echo of the Epipaleolithic in Italy and the Legacy of the Early Sardinians

There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.

Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages

The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture, and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high-resolution single nucleotide polymorphism analysis with short tandem repeats variation of their subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.

Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage.

Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

Reconstructing ancient mitochondrial DNA links between Africa and Europe

Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ~65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.

Allele frequencies of the new European Standard Set (ESS) loci in the Italian population

Allele frequencies of five new STR loci (D22S1045, D10S1248, D1S1656, D12S391, D2S441) included in the new European Standard Set (ESS) were calculated in a sample of 209 unrelated Italians with the Powerplex ESI 17 system (Promega Corporation, Madison, WI). Forensic and population indices were estimated. Samples were collected from unrelated individuals in 19 different Italian regions following informed consent. DNA was extracted from saliva by Chelex method [1]. A prototype version of the PowerPlex ESI 17 (Promega Corporation, Madison, WI) was used to amplify individuals’ DNA according to manufacturer’s recommendations. This multiplex contains 17 loci of which five are novel STR loci (D22S1045, D10S1248, D1S1656, D12S391, D2S441) included in the new European Standard Set (ESS) [2,3]. The other loci include the amelogenin, D3S1358, D19S433, D2S1338, D16S539, D18S51, TH01, vWA, D21S11, D8S1179, FGA and SE33. PCR products were analysed by capillary electrophoresis in an ABI 3130xl Genetic analyzer (Applied Biosystem, Foster City, CA). Allele assignment was carried out by comparison with reference sequenced ladders (Promega Corporation, Madison, WI). Arlequin software ver 3.0 [4] was used to calculate allele frequencies, population pairwise genetic distances (FST), expected heterozigosity (He), observed heterozigosity (Ho), and also to assess departures from Hardy–Weinberg equilibrium. Statistical parameters of forensic interest (Power of Discrimination, Power of Exclusion and Matching Probability) were calculated using PowerStats v1.2 (Promega Corporation, USA) software package [5]. The laboratory participates in the quality control initiatives of the GEDNAP (German DNA Profiling) group [6] and [7] (http:// www.gednap.org). The whole genotype data set, allele frequencies and forensic indices are available as an e-component. Deviation from Hardy–Weinberg equilibrium has been detected only for D18S51, even after a Bonferroni correction. The combined power of exclusion (PE) and power of discrimination (PD) for the sixteen studied loci were 0.999999935 and 0.999999999, respectively. Based on heterozygosity and polymorphic information content (PIC), SE33 may be considered as the most informative loci. The exclusion of this locus slightly reduced the PE estimate (0.999999555). The PD value is similar for those calculated on a different Italian population set using the PowerPlex16 multiplex system (Promega Corporation, Madison, WI), the Identifiler kit (Applied Biosystems) and for the markers included in the US Combined DNA Index System (CODIS) [8–10], while for the PE, the value obtained with the PowerPlex ESI 17 System (Promega Corporation, Madison, WI) is higher. No pair of loci

Allele frequencies of fifteen STRs in a representative sample of the Italian population.

Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, HUMvWA, D8S1179, HUMTPOX and FGA) were analyzed in more than 400 unrelated individuals from nine different areas of Italy. After Bonferroni correction, no evidence of population structure was identified, either by considering each population as independent or by combining populations according to their geographic origin (North, Central and South of Italy). Forensic indexes were estimated considering all samples together. Combined power of discrimination (PD) and combined power of exclusion (PE) for the 15 tested STR loci were 0.9999999997 and 0.964708775, respectively. Low genetic distances were found between our data and those previously published for other neighboring European populations.

Moors and Saracens in Europe : estimating the medieval North African male legacy in southern Europe

To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.

The Etruscan timeline: a recent Anatolian connection

The origin of the Etruscans (the present day Tuscany, Italy), one of the most enigmatic non-Indo-European civilizations, is under intense controversy. We found novel genetic evidences on the mitochondrial DNA (mtDNA) establishing a genetic link between Anatolia and the ancient Etruria. By way of complete mtDNA genome sequencing of a novel autochthonous Tuscan branch of haplogroup U7 (namely U7a2a), we have estimated an historical time frame for the arrival of Anatolian lineages to Tuscany ranging from 1.1±0.1 to 2.3±0.4 kya B.P.

The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape

Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1-7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8-11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.Summary Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1, 2, 3, 4, 5, 6, 7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8, 9, 10, 11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia.