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Thread: Sicilian Hunter-Gatherer GEDmatch

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    Sicilian Hunter-Gatherer GEDmatch

    Prehistoric Sicilian from this paper: https://www.biorxiv.org/content/bior...92871.full.pdf

    Sample I2158 (Late Upper Paleolithic Sicilian hunter-gatherer) - kit number EM6278906

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    Geez, they had to dump all this good stuff on July 4th week-end? :)

    "In the last few years, developments in sequencing techniques have enabled the generation of an44 unprecedented amount of genomic data from past populations. In particular, ancient genomes from45 Upper Palaeolithic and Mesolithic periods have made it possible to explore the early genetic46 makeup of hunter-gatherers of the (Jones et al., 2015; Fu et al., 2016; Hofmanová et al., 2016;47 Posth et al., 2016; Modi et al., 2017; Mathieson et al., 2018).

    Given its geographic location and the48 presence of Upper Palaeolithic and Mesolithic human remains belonging to at least 3 individuals49 (Oriente A, B and C: Mannino et al., 1972; Lo Vetro and Martini, 2006; Di Salvo et al., 2012;50 Mannino et al., 2012; Martini et al., 2012a), Grotta d’Oriente, on the island of Favignana (SW51 Sicily), is a key site for the study of the human colonization of Sicily during the Upper Palaeolithic52 (Lo Vetro and Martini, 2012). Paleogenetic and morphological studies on the Mesolithic individual53 Oriente B indicated a close proximity with Late Epigravettians of the Italian Peninsula (D’Amore et54 al., 2010; Mannino et al., 2012), while genome-wide single nucleotide polymorphism (SNP) data55 showed that the Upper Palaeolithic Oriente C clusters closely with other Western European Hunter56 Gatherer (WHG) populations from Mesolithic and Late Palaeolithic Western Europe (Mathieson et57 al., 2018), confirming previous morphological analysis (Henke, 1989; Brewster et al., 2014).58 Here we generated new genome-wide data in order to refine the genetic affinities of Oriente C to59 other European hunter-gatherer populations.

    "We conclude that the individual probably was a young adult,160 maybe 25-30 years old. Oriente C lacks the diagnostic parts of the hip bones, but the long bone161 midshaft and epiphysis measurements – commonly used in sex determination of fragmentary human162 remains –indicated that the individual was most likely female (see Table S1 and Figure S1 in163 Supplementary material). This determination was later confirmed genetically (Mathieson et al.,"

    "The anatomical features of Oriente C are close to those of Late Upper Palaeolithic populations of192 the Mediterranean and show strong affinity with other Palaeolithic individuals of Sicily. As193 suggested by Henke (1989) and Fabbri (1995) the hunter-gatherer populations weremorphologically rather uniform. This interpretation is further supported by the low or negligible D2 194195 distance demonstrated by D’Amore et al. (2009) in the comparison between San Teodoro196 (individuals1-2-3-5-7) craniofacial morphometrics and other Upper Palaeolithic individuals.197 Like other Late Epigravettian burials in Sicily and Italy (Palma di Cesnola, 2006), Oriente C is a198 simple burial with little or no grave goods and personal ornaments. The only items in the pit were a199 pierced shell of Cerithium sp. (perhaps a clothing ornament) and a few small lumps of red ochre,200 next to the skull and the femoral head. Stable isotope analysis suggested a largely terrestrial diet201 with low-level consumption of marine foods which is comparable to other Late Upper Palaeolithic202 individuals from Sicily and Italy."

    "The resulting dataset contained information on 288,223 SNPs covered at least once, compared to216 61,547 in a previous publication (Mathieson et al.,2018), allowing for higher resolution analysis."

    "We confirmed the originally reported mitochondrial haplogroup assignment of U2'3'4'7'8'9. This229 haplogroup is present in both pre- and post-LGM populations, but is rare by the Mesolithic, when230 U5 dominates (Posth et al.2016)"

    "We further confirmed that the new genome-wide data was231 consistent with the original data by computing D-statistics (Patterson et al.,2012) of the form D232 (Mbuti, X, Original Oriente data, Merged Oriente data). None of these statistics were significantly233 non-zero when X ranged over other European Mesolithic hunter-gatherers (maximum |Z| = 1.8 in 34234 tests), and present-day French (Z = -0.35) and Sardinian (Z = -0.13) populations."

    "Multidimensional scaling (MDS) of f3-statistics shows that these238 axes form a “V” shape (Fig. 3). At the point of the “V” lie the individuals that have been described as belonging to the “Western hunter-gatherer” (WHG) population, clustering closely with the 8,000 BP Loschbour individual (Lazaridis et al.2014). One arm represents a cline of ancestry that links WHG with “Eastern hunter-gatherer” (EHG) populations who carry ancestry related to the “Ancient242 North Eurasian” (ANE) population represented by the 24,000 BP Mal’ta individual (Raghavan et243 al., 2014). Along this cline lie Eastern European hunter-gatherer populations such as those from the Balkan Peninsula, present-day Ukraine (Mathieson et al., 2018), the Baltic (Jones et al., 2017;245 Mathieson et al., 2018) and Scandinavia (Haak et al., 2015, Gunther et al., 2018). The other arm of the “V” is a cline containing Late Upper Palaeolithic and Mesolithic individuals from Iberia (for example the individuals from El Mirón and La Braña), and Late Upper Palaeolithic individuals from Central Europe (Goyet and Hohle Fels). As shown by Fu et al. (2016), this cline reflects an ancestry contribution from a population related to the 35,000 BP Aurignacian Goyet Q116-1250 individual. In this analysis, Oriente C falls at the tip of the “V”, at the extreme end of the WHG grouping.252 Focusing further on Oriente C, we find that it shares most drift with individuals from Northern Italy, Switzerland and Luxembourg, and less with individuals from Iberia, Scandinavia, and East and Southeast Europe (Fig. 4A-B). Shared drift decreases significantly with distance (Fig. 4C) and with255 time (Fig. 4D) although in a linear model of drift with distance and time as a covariate, onlydistance (p=1.3×10-6 256 ) and not time (p=0.11) is significant. Consistent with the overall E-W cline in257 hunter-gatherer ancestry, genetic distance to Oriente C increases more rapidly with longitude than258 latitude, although this may also be affected by geographic features. For example, Oriente C shares259 significantly more drift with the 8,000 year-old 1,400 km distant individual from Loschbour in260 Luxembourg (Lazaridis et al.,2014), than with the 9,000 year old individual from Vela Spila in261 Croatia (Mathieson et al.,2018) only 700 km away as shown by the D-statistic (Patterson et262 al.,2012) D (Mbuti, Oriente C, Vela Spila, Villabruna); Z=3.42. Oriente C’s heterozygosity was263 slightly lower than Villabruna (14% lower at 1240k transversion sites), but this difference is not264 significant."

    "Sicily falls within the area of expansion of the Epigravettian model widespread after the LGM in268 Mediterranean Europe, from Provence to the eastern Balkan border up to the Black Sea and the SW269 Anatolia (Fontana et al. in press). This “cultural province” is characterized by peculiar features270 which concern not only lithotechnics but also artistic production and burial customs. The271 Epigravettian (about 21.0-11.5 cal. ka BP) is a homogeneous cultural phenomenon despite the272 paleo-environmental differences occurring in a wide territory and some differentiations in resources273 exploitation strategies and human-environment interactions which were, perhaps, responsible for274 the appearance of regional variants. This homogeneous structure is also recognizable in Sicily275 despite the fact that the Late Epigravettian culture in the island presents a very specific local aspect,276 especially in lithic productions. The occurrence of cosmopolitan expressions and behaviours277 (iconographic languages, funeral rite) make Sicily the most continental of the Mediterranean islands278 with respect to material culture at the end of the Upper Palaeolithic."

    "
    The robust record of282 radiocarbon dates proves that they reached Sicily not before 15-14 ka cal. BP, several millennia283 after the LGM peak. In our opinion, in fact, the hypothesis about an early colonization of Sicily by284 Aurignacians (Laplace, 1964; Chilardi et al., 1996) must be rejected, on the basis of a recent re285 interpretation of the techno-typological features of the lithic industries from Riparo di Fontana286 Nuova."

    "Epigravettian culture might have300 reached Sicily during the migration of Upper Palaeolithic groups from Southern Italy around the301 LGM (Palma di Cesnola, 2006; Lo Vetro and Martini, 2012; Mannino et al., 2012), which accords302 with the morphological similarity of Late Upper Palaeolithic and Early Mesolithic populations in303 the region (Henke, 1989; Brewster et al., 2014). The find of genetic similarity of Oriente C with304 Late Upper Palaeolithic and Mesolithic individuals from Northern Italy (i.e. Villabruna) and Central305 Europe (i.e. Bichon, Loschbour) (Fig. 3) is also in line with previous studies according to which306 Sicilian hunter-gatherers were found to be morphologically closely related to Late Epigravettians of307 the Italian Peninsula and continental Europe (Fabbri, 1995; D’Amore et al., 2010)"

    "Our findings indicate that312 Oriente C shows a strong genetic relationship with Western European Late Upper Palaeolithic and313 Mesolithic hunter-gatherers, suggesting that the “Western hunter-gatherers” was a homogeneous314 population widely distributed in the Central Mediterranean, presumably as a consequence of315 continuous gene flow among different groups, or a range expansion following the LGM."


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