Publications by authors named "Alfredo Coppa"

38 Publications

Multipronged dental analyses reveal dietary differences in last foragers and first farmers at Grotta Continenza, central Italy (15,500-7000 BP).

Sci Rep 2021 Feb 19;11(1):4261. Epub 2021 Feb 19.

Department of Maxillo-Facial Sciences, DANTE - Diet and Ancient Technology Laboratory, Sapienza University of Rome, Rome, Italy.

This paper provides results from a suite of analyses made on human dental material from the Late Palaeolithic to Neolithic strata of the cave site of Grotta Continenza situated in the Fucino Basin of the Abruzzo region of central Italy. The available human remains from this site provide a unique possibility to study ways in which forager versus farmer lifeways affected human odonto-skeletal remains. The main aim of our study is to understand palaeodietary patterns and their changes over time as reflected in teeth. These analyses involve a review of metrics and oral pathologies, micro-fossils preserved in the mineralized dental plaque, macrowear, and buccal microwear. Our results suggest that these complementary approaches support the assumption about a critical change in dental conditions and status with the introduction of Neolithic foodstuff and habits. However, we warn that different methodologies applied here provide data at different scales of resolution for detecting such changes and a multipronged approach to the study of dental collections is needed for a more comprehensive and nuanced understanding of diachronic changes.
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http://dx.doi.org/10.1038/s41598-021-82401-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895915PMC
February 2021

A minimally destructive protocol for DNA extraction from ancient teeth.

Genome Res 2021 Mar 12;31(3):472-483. Epub 2021 Feb 12.

Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary.

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
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http://dx.doi.org/10.1101/gr.267534.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919446PMC
March 2021

A genetic history of the pre-contact Caribbean.

Nature 2021 02 23;590(7844):103-110. Epub 2020 Dec 23.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large. Confirming a small and interconnected Ceramic Age population, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world.
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http://dx.doi.org/10.1038/s41586-020-03053-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864882PMC
February 2021

Population dynamics in pre-Inca human groups from the Osmore Valley, the Azapa Valley and the coast of the South Central Andes.

PLoS One 2020 16;15(12):e0229370. Epub 2020 Dec 16.

Facultad de Ciencias Antropológicas, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico.

The present study applies a dental morphological perspective to the understanding of the complex pre-contact population history of the South Central Andes, through the detection of the underlying dynamics, and the assessment of the biological ties among groups. It presents an analysis of 1591 individuals from 66 sites that date from the Archaic to the Late Intermediate phases from Bolivia, Chile and Peru. The results suggest this area is characterized by significant movement of people and cultures and, at the same time, by long standing population continuity, and highlight the need for wider perspectives capable of taking into account both the different micro-regional realities and the region in its entirety.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229370PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7743979PMC
January 2021

Economic access influences degenerative spine disease outcomes at rural Late Medieval Villamagna (Lazio, IT).

Am J Phys Anthropol 2021 03 28;174(3):500-518. Epub 2020 Nov 28.

Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.

Objectives: Degenerative joint disease in the spine is heavily influenced by genetic, environmental, and epigenetic factors, as well as exacerbated by physical activity and injury. The objective of this study was to investigate the multivariate relationship between known predictors of degenerative joint disease in the spine, such as age and sex, with mortuary indicators of economic access such as grave inclusions, burial location, and burial type.

Materials And Methods: The presence and severity of vertebral osteophytosis (VO) and vertebral osteoarthritis (VOA) was recorded for the vertebral columns of N = 106 adult individuals from the Late Medieval period at the rural monastery of San Pietro at Villamagna in Lazio, Italy (1300-1450 AD). Multiple skeletal indicators of degenerative joint disease, morphological sex, and age were compared with differences in mortuary treatment across four regions of the spine.

Results: There are marked differences in severe joint disease outcome between groups with more and less economic access. Relative risk ratios suggest that males and females with less economic access have elevated risk for VO and VOA in specific spine regions, although this effect is reduced among females.

Discussion: Current research on the consequences of economic and social inequality point to the important role of economic inequality in shaping disease outcomes. Our results suggest that biocultural effects of reduced economic access at the intraclass level may increase vulnerability to the downstream effects of risk exposure (e.g., biomechanical injure, physical activity, biochemical imbalance), and ultimately increase the risk and prevalence for severe degenerative disease outcomes in medieval Italy.
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http://dx.doi.org/10.1002/ajpa.24180DOI Listing
March 2021

Early life of Neanderthals.

Proc Natl Acad Sci U S A 2020 11 2;117(46):28719-28726. Epub 2020 Nov 2.

Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;

The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.
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http://dx.doi.org/10.1073/pnas.2011765117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682388PMC
November 2020

Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades.

Genome Biol Evol 2020 09;12(9):1579-1590

Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy.

The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.
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http://dx.doi.org/10.1093/gbe/evaa176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523727PMC
September 2020

Human auditory ossicles as an alternative optimal source of ancient DNA.

Genome Res 2020 03 25;30(3):427-436. Epub 2020 Feb 25.

Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
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http://dx.doi.org/10.1101/gr.260141.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111520PMC
March 2020

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.

Nat Ecol Evol 2020 03 24;4(3):334-345. Epub 2020 Feb 24.

Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain.

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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http://dx.doi.org/10.1038/s41559-020-1102-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080320PMC
March 2020

Ancient Rome: A genetic crossroads of Europe and the Mediterranean.

Science 2019 11;366(6466):708-714

Aix-Marseille University, Marseille, France.

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome's population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.
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http://dx.doi.org/10.1126/science.aay6826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093155PMC
November 2019

The formation of human populations in South and Central Asia.

Science 2019 09;365(6457)

Earth Institute, University College Dublin, Dublin 4, Ireland.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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http://dx.doi.org/10.1126/science.aat7487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619PMC
September 2019

Making sense of medieval mouths: Investigating sex differences of dental pathological lesions in a late medieval Italian community.

Am J Phys Anthropol 2019 06 28;169(2):253-269. Epub 2019 Mar 28.

Department of Archaeology, Foggia University, Foggia, Italy.

Objectives: Bioarchaeological investigations of sex-based differences in the prevalence of dental pathological lesions, particularly caries, have drawn considerable attention, and out of this work, two dominant models have emerged. Traditionally, the first model interprets sex-related patterns in caries as a product of gendered differences in diet. A more recent model interprets a generally higher propensity for caries prevalence in females in light of reproductive ecology. To test the hypothesis that females have higher risk of caries in accordance with reproductive ecology, we examined and analyzed caries prevalence and other potentially synergistic oral pathological lesions in a late medieval (A.D. 1300-1500) Italian archaeological sample.

Materials And Methods: We examined sex- and age-related prevalence in caries and other oral pathological lesions in a late medieval Italian skeletal assemblage excavated from Villamagna consisting of 38 females and 37 males (n = 1,534 teeth). We examined age- and sex-related patterns in six dental traits: antemortem tooth loss, caries, calculus, periapical inflammation, tooth wear, and periodontitis.

Results: Significant age-related increases in antemortem tooth loss, caries, calculus, and tooth wear were observed in both males and females. However, there was a lack of expected sex differences in oral pathological lesions, with instead older males exhibiting significantly more antemortem tooth loss and corrected caries than females.

Discussion: Results are discussed in relation to the ethnohistoric context of medieval rural dietary practices as well as biomedical salivary literature, which suggest that dietary changes throughout the life course may have facilitated trade-offs that buffered females from higher rates of dental pathological lesions.
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http://dx.doi.org/10.1002/ajpa.23821DOI Listing
June 2019

The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment.

PLoS One 2018 3;13(10):e0189773. Epub 2018 Oct 3.

Laboratoire HNHP, UMR 7194 CNRS, Muséum national d'Histoire naturelle (MNHN), Paris, France.

The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l'Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189773PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169847PMC
March 2019

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages.

Genome Biol 2018 02 12;19(1):20. Epub 2018 Feb 12.

Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy.

Background: Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

Results: In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase.

Conclusions: Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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http://dx.doi.org/10.1186/s13059-018-1393-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809971PMC
February 2018

Social reorganization and biological change: An examination of stature variation among Iron Age Samnites from Abruzzo, central Italy.

Int J Paleopathol 2017 09 31;18:9-20. Epub 2017 Jul 31.

Dipartimento di Biologia Ambientale, Università degli Studi di Roma 'La Sapienza', Italy.

Stature is a sensitive indicator of overall environmental quality experienced during growth and development, and can provide insights on a population's 'well-being'. This study investigated changes in estimated adult stature in a large (N=568) sample of Samnite Iron Age (800-27 BCE) people from central Italy, during a period of increasing sociopolitical complexity. Stature was analyzed diachronically, between sexes, and across social strata inferred using the 'Status Index' based on funerary treatment. It was expected: 1) a decrease in stature from the Orientalizing-Archaic period (O-A) to the fifth century BC (V SEC) and the following Hellenistic period (ELL), due to population increase and urbanization; 2) social status to positively influence the attainment of the full stature potential; 3) sexual dimorphism to be higher in more stratified groups. Results revealed no significant diachronic changes in stature (females: O-A: 154.2cm,V SEC: 154.2cm, and ELL: 153.6cm; males: O-A: 165.0cm,V SEC: 165.2cm, and ELL: 165.0cm) or sexual dimorphism. High-status males were taller than low-status (p=0.021), possibly due to a better diet, but only in the Orientalizing-Archaic period. Nonsignificant changes in females suggest either differential access to resources in women, or a better buffering from environmental optima or crises. The results of this study highlight the complex interrelation between social factors and human growth, and stress the importance of understanding the specific mechanisms leading to variation in adult stature.
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http://dx.doi.org/10.1016/j.ijpp.2017.07.003DOI Listing
September 2017

Virtual histological assessment of the prenatal life history and age at death of the Upper Paleolithic fetus from Ostuni (Italy).

Sci Rep 2017 08 25;7(1):9427. Epub 2017 Aug 25.

Servizio di Bioarcheologia, Museo delle Civiltà, Rome, Italy.

The fetal remains from the Ostuni 1 burial (Italy, ca 27 ka) represent a unique opportunity to explore the prenatal biological parameters, and to reconstruct the possible patho-biography, of a fetus (and its mother) in an Upper Paleolithic context. Phase-contrast synchrotron X-ray microtomography imaging of two deciduous tooth crowns and microfocus CT measurements of the right hemimandible of the Ostuni 1b fetus were performed at the SYRMEP beamline and at the TomoLab station of the Elettra - Sincrotrone laboratory (Trieste, Italy) in order to refine age at death and to report the enamel developmental history and dental tissue volumes for this fetal individual. The virtual histology allowed to estimate the age at death of the fetus at 31-33 gestational weeks. Three severe physiological stress episodes were also identified in the prenatal enamel. These stress episodes occurred during the last two months and half of pregnancy and may relate to the death of both individuals. Compared with modern prenatal standards, Os1b's skeletal development was advanced. This cautions against the use of modern skeletal and dental references for archaeological finds and emphasizes the need for more studies on prenatal archaeological skeletal samples.
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http://dx.doi.org/10.1038/s41598-017-09773-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572742PMC
August 2017

New regression formula to estimate the prenatal crown formation time of human deciduous central incisors derived from a Roman Imperial sample (Velia, Salerno, Italy, I-II cent. CE).

PLoS One 2017 12;12(7):e0180104. Epub 2017 Jul 12.

Laboratoire AMIS, UMR 5288, Université Toulouse III, Toulouse, France.

The characterization and quantification of human dental enamel microstructure, in both permanent and deciduous teeth, allows us to document crucial growth parameters and to identify stressful events, thus contributing to the reconstruction of the past life history of an individual. Most studies to date have focused on the more accessible post-natal portion of the deciduous dental enamel, even though the analysis of prenatal enamel is pivotal in understanding fetal growth, and reveals information about the mother's health status during pregnancy. This contribution reports new data describing the prenatal enamel development of 18 central deciduous incisors from the Imperial Roman necropolis of Velia (I-II century CE, Salerno, Italy). Histomorphometrical analysis was performed to collect data on prenatal crown formation times, daily secretion rates and enamel extension rates. Results for the Velia sample allowed us to derive a new regression formula, using a robust statistical approach, that describes the average rates of deciduous enamel formation. This can now be used as a reference for pre-industrial populations. The same regression formula, even when daily incremental markings are difficult to visualize, may provide a clue to predicting the proportion of infants born full term and pre-term in an archaeological series.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180104PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507505PMC
September 2017

Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.

Forensic Sci Int Genet 2017 03 29;27:123-131. Epub 2016 Dec 29.

Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy; Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy. Electronic address:

By using the recently introduced 6-dye Yfiler Plus multiplex, we analyzed 462 males belonging to 20 ethnic groups from four eastern African countries (Eritrea, Ethiopia, Djibouti and Kenya). Through a Y-STR sequence analysis, combined with 62 SNP-based haplogroup information, we were able to classify observed microvariant alleles at four Y-STR loci as either monophyletic (DYF387S1 and DYS458) or recurrent (DYS449 and DYS627). We found evidence of non-allelic gene conversion among paralogous STRs of the two-copy locus DYF387S1. Twenty-two diallelic and triallelic patterns observed at 13 different loci were found to be significantly over-represented (p<10) among profiles obtained from cell lines compared to those from blood and saliva. Most of the diallelic/triallelic patterns from cell lines involved recurrent mutations at rapidly mutating loci (RM Y-STRs) included in the multiplex (p<10). At haplotype level, intra-population diversity indices were found to be among the lowest so far reported for the Yfiler Plus, while statistically significant differences among countries and ethnic groups were detected when considering haplotype frequencies alone (F) or by using molecular distances among haplotypes (Φ). The strong population subdivision observed is probably the consequence of the patrilineal social organization of most eastern African ethnic groups, and suggests caution in the use of country-based haplotype frequency distributions for forensic inferences in this region.
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http://dx.doi.org/10.1016/j.fsigen.2016.12.015DOI Listing
March 2017

Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes.

Sci Rep 2016 05 5;6:25472. Epub 2016 May 5.

Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.

Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
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http://dx.doi.org/10.1038/srep25472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857117PMC
May 2016

The endocast of the one-million-year-old human cranium from Buia (UA 31), Danakil Eritrea.

Am J Phys Anthropol 2016 07 4;160(3):458-68. Epub 2016 Apr 4.

UMR 7194 CNRS-Muséum national d'Histoire naturelle, 75000, Paris, France.

Objectives: The Homo erectus-like cranium from Buia (UA 31) was found in the Eritrean Danakil depression and dated to 1 million years. Its outer morphology displays archaic traits, as well as distinctive and derived characters. The present study provides the description and metric comparison of its endocranial anatomy.

Materials And Methods: UA 31 was originally filled by a diffuse concretion. Following its removal and cleaning, the endocast (995 cc) was reconstructed after physical molding and digital scan. Its morphology is here compared with specimens belonging to different human taxa, taking into account endocranial metrics, cortical traits, and craniovascular features.

Results: The endocast is long and narrow when compared to the H. erectus/ergaster hypodigm, although its proportions are compatible with the morphology displayed by all archaic and medium-brained human species. The occipital areas display a pronounced bulging, the cerebellum is located in a posterior position, and the middle meningeal vessels are more developed in the posterior regions. These features are common among specimens attributed to H. erectus s.l., particularly the Middle Pleistocene endocasts from Zhoukoudian. The parietal lobes are markedly bossed. This lateral bulging is associated with the lower parietal circumvolutions, as in other archaic specimens. This pronounced parietal curvature is apparently due to a narrow cranial base, more than to wider parietal areas.

Conclusions: The endocast of UA 31 shows a general plesiomorphic phenotype, with some individual features (e.g., dolichocephaly and rounded lower parietal areas) which confirm a remarkable degree of morphological variability within the H. erectus/ergaster hypodigm. Am J Phys Anthropol 160:458-468, 2016. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajpa.22983DOI Listing
July 2016

Geographical and temporal changes of anthropometric traits in historical Yemen.

Homo 2016 Feb 28;67(1):11-22. Epub 2015 Sep 28.

Università di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente, Sezione di Antropologia, Monserrato 09042, Italy.

This study investigates secular changes of anthropometric variables among four geographic groups in historical Yemen, to evaluate possible regional differences in the evolution of living standards. Nineteen somatic and cephalic measures collected by Coon in 1939, and 8 anthropometric indices in 1244 Yemenite adult males were analyzed. The individuals were divided into 10-year age groups. Within-group variations were tested by One-way ANCOVA (age as covariate). ANCOVA (controlling for age), and Forward stepwise discriminant analysis were used to evaluate and represent regional differences. ANCOVA and discriminant analysis confirmed and enhanced previous findings. At the time, the Yemenite population presented high intergroup heterogeneity. The highest mean values of height at all ages were found in the "mountain" region, which is characterized by very fertile soils and where, nowadays, most of the cereals and pulses are grown and where most livestock is raised. Within-group variations were limited and generally inconsistent in all geographic regions and concern vertical dimensions, but mean values of height never differed. The prolonged internal isolation of these groups resulted in significant regional morphometric differentiation. The main evidence comes from height which suggests that socioeconomic factors have played a role. Nevertheless, the possible better living conditions experienced by the "mountain" group, with the highest mean values of stature in all periods, did not allow the secular trend to take place in that region, too.
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http://dx.doi.org/10.1016/j.jchb.2015.09.005DOI Listing
February 2016

Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent.

Genome Biol Evol 2015 Jun 24;7(7):1940-50. Epub 2015 Jun 24.

Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.
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http://dx.doi.org/10.1093/gbe/evv118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524485PMC
June 2015

A bioarchaeological approach to the reconstruction of changes in military organization among Iron Age Samnites (Vestini) From Abruzzo, Central Italy.

Am J Phys Anthropol 2015 Mar 31;156(3):305-16. Epub 2014 Oct 31.

Department of Archaeology, Durham University, Durham, DH1 3LE, UK; Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131.

The Samnites were an Iron Age population that shifted from warlike mountain dwellers to the largest sociopolitical unit of central Italy, able to dispute with Rome the domination over the peninsula. Archaeological and historical evidence suggests that this major shift in the scale of conflict may have involved a reorganization of the military system, which changed from an elite militia to a conscript or standing army from the Orientalizing-Archaic (800-500 BC) to Hellenistic times (400-27 BC). We propose a bioarchaeological framework jointly analyzing skeletal properties and funerary treatment in male Samnites to investigate on this shift in military organization. We anticipated that, when Samnites had an elite militia, the warring force was constituted by the wealthier segments of the society. Conversely, we expected the warring force of the standing/conscript army to be mainly drawn from the lower social strata. We considered high asymmetry in J, a measure of humeral torsional rigidity (calculated via cross-sectional geometry, CSG) as a proxy for pre- and peri-adolescent-onset weapon training. The social standing of the individual was approximated via funerary treatment analysis (Status Index). Results show that in the Orientalizing-Archaic period, humeral asymmetry and Status Index are positively correlated, and the high-status subsample shows significantly higher asymmetry than the low-status subsample. Among Hellenistic Samnites, no correlation between Status Index and humeral asymmetry is present, and the low-status subsample is the most lateralized. Results support the use of CSG in a strong theoretical framework to investigate past changes in military organization and their correlates in terms of sociopolitical development, alterations of power relationships, and warfare.
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http://dx.doi.org/10.1002/ajpa.22650DOI Listing
March 2015

The late Early Pleistocene human dental remains from Uadi Aalad and Mulhuli-Amo (Buia), Eritrean Danakil: macromorphology and microstructure.

J Hum Evol 2014 Sep 19;74:96-113. Epub 2014 May 19.

Département de Préhistoire, UMR 7194, MNHN, Paris, France; Département Géosciences, Université de Poitiers, France.

Fieldwork performed during the last 15 years in various Early Pleistocene East African sites has significantly enlarged the fossil record of Homo erectus sensu lato (s.l.). Additional evidence comes from the Danakil Depression of Eritrea, where over 200 late Early to early Middle Pleistocene sites have been identified within a ∼1000 m-thick sedimentary succession outcropping in the Dandiero Rift Basin, near Buia. Along with an adult cranium (UA 31), which displays a blend of H. erectus-like and derived morpho-architectural features and three pelvic remains, two isolated permanent incisors (UA 222 and UA 369) have also been recovered from the 1 Ma (millions of years ago) Homo-bearing outcrop of Uadi Aalad. Since 2010, our surveys have expanded to the nearby (4.7 km) site of Mulhuli-Amo (MA). This is a fossiliferous area that has been preliminarily surveyed because of its exceptional concentration of Acheulean stone tools. So far, the site has yielded 10 human remains, including the unworn crown of a lower permanent molar (MA 93). Using diverse analytical tools (including high resolution μCT and μMRI), we analysed the external and internal macromorphology and microstructure of the three specimens, and whenever possible compared the results with similar evidence from early Homo, H. erectus s.l., H. antecessor, H. heidelbergensis (from North Africa), Neanderthals and modern humans. We also assessed the UA 369 lower incisor from Uadi Aalad for root completion timing and showed that it compares well with data for root apex closure in modern human populations.
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http://dx.doi.org/10.1016/j.jhevol.2014.04.005DOI Listing
September 2014

Archaeometric classification of ancient human fossil bones, with particular attention to their carbonate content, using chemometrics, thermogravimetry and ICP emission.

Chem Cent J 2014 25;8:26. Epub 2014 Apr 25.

Department of Environmental Biology, University of Rome "La Sapienza", P.le Aldo Moro, 5-00185 Rome, Italy.

Background: The potential of coupling chemometric data processing techniques to thermal analysis for formulating an "archaeometric" classification of fossil bones was investigated. Moreover, the possibility of integrating the outcomes of this approach with the results of inductively coupled plasma (ICP) emission spectroscopy for an anthropological interpretation of the observed patterns was also examined.

Results: Several fossil bone samples coming from the necropolis of El Geili, in the middle Nile, an important archaeological site, were first of all subjected to thermogravimetric (TG) and derivative thermogravimetric (DTG) analysis and the main steps of the curves were analyzed. This allowed fossil bone samples to be differentiated, both by means of classical bidimensional and chemometric representations, namely Principal Component Analysis (PCA). In particular, two clusters were observed, attributable to samples of different antiquity. In addition, inductively coupled plasma (ICP) emission spectroscopy showed that the samples in the cluster corresponding to more recent burials are characterized by a higher Zn content, suggesting a more varied diet.

Conclusions: The experimental data obtained using thermogravimetry (TG-DTG) allows us to differentiate all the fossil bone samples analyzed into two separate clusters and to interpret this differentiation in terms of the observed transitions.
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http://dx.doi.org/10.1186/1752-153X-8-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008433PMC
May 2014

Beeswax as dental filling on a neolithic human tooth.

PLoS One 2012 19;7(9):e44904. Epub 2012 Sep 19.

Multidisciplinary Laboratory, "Abdus Salam" International Centre for Theoretical Physics, Trieste, Italy.

Evidence of prehistoric dentistry has been limited to a few cases, the most ancient dating back to the Neolithic. Here we report a 6500-year-old human mandible from Slovenia whose left canine crown bears the traces of a filling with beeswax. The use of different analytical techniques, including synchrotron radiation computed micro-tomography (micro-CT), Accelerator Mass Spectrometry (AMS) radiocarbon dating, Infrared (IR) Spectroscopy and Scanning Electron Microscopy (SEM), has shown that the exposed area of dentine resulting from occlusal wear and the upper part of a vertical crack affecting enamel and dentin tissues were filled with beeswax shortly before or after the individual's death. If the filling was done when the person was still alive, the intervention was likely aimed to relieve tooth sensitivity derived from either exposed dentine and/or the pain resulting from chewing on a cracked tooth: this would provide the earliest known direct evidence of therapeutic-palliative dental filling.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044904PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446997PMC
March 2013

Microgeographic differentiation in historical Yemen inferred by morphometric distances.

Hum Biol 2012 Apr;84(2):153-67

Università dell'Aquila, Dipartimento di Scienze Ambientali, 67100 L'Aquila, Italy.

This study analyzed the variations in space of 8 body dimensions and 11 measures of the head of 1,244 adult Yemenite males, collected in 1933/34 by Coon in Yemen and in Hadhramawt. The aim was to evaluate the presence of geographic microdifferentiation of the populations settled in the different regions of Yemen at the time. Coon sub-divided the sample into six geographical areas according to birthplace and ethnicity of the individuals: Tihamah, the Western Mountains, the Central Plateau, the South Coast, the Eastern Mountains, and Hadhramawt. The results of ANCOVA (age as covariate) show that the observed differences of all variables among the six groups were highly statistically significant. Tukey's post-hoc test reveals higher statistically significant differences among four main groups: (1) Tihamah; (2) the Western Mountains and Central Plateau; (3) the Eastern Mountains; and (4) the Southern Coast and Hadhramawt. Multiple discriminant analysis carried out using only the data of the 11 measures of the head, the more "genetically" determined variables, confirmed these differences. Indeed, the first canonical variate well separates the groups with the Tihamah, Southern Coast and Hadhramawt on the one side and the Eastern Mountains, Western Mountains and Central Plateau on the other. The second canonical variate separates the Tihamah, Western Mountains and Central Plateau from the Eastern Mountains, Southern Coast and Hadhramawt. In conclusion, the Yemenite population seems to be composed of three morphologically distinct groups and an Eastern Mountains group which is positioned between the group formed by the Southern Coast and Hadhramawt and the Western Mountains and Central Plateau group. The Tihamah is the most distant from all the other groups. These differences are probably due to the presence/absence of geographical and cultural barriers that have favored/blocked the gene flow over the years. Indeed, the entire coastal bell, through the centuries, has constituted one of the principal commercial routes between the East, Africa, and the eastern Mediterranean, while the high inland mountains have isolated the remaining communities. This data is also confirmed by genetic studies. Finally, the average height (162.6 cm) of the global Yemenite population, compared to data from the other six middle-eastern Arab countries and Egypt, was found to be 3-6 cm less. This characteristic will be further studied, analyzing variations in average height according to the different age classes in order to evaluate any possible secular changes.
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http://dx.doi.org/10.3378/027.084.0204DOI Listing
April 2012

Italian populations during the Copper Age: assessment of biological affinities through morphological dental traits.

Hum Biol 2009 Aug;81(4):479-93

Dipartimento di Biologia Animale e dell'Uomo, Universitá di Roma Sapienza, Ple. A. Moro 5, 00185 Rome, Italy.

The Copper Age (3rd millennium BC) was characterized by considerable socioeconomic transformations and coincided with the discovery of metallurgy. In this study we reconstruct the peopling of Italy during this period on the basis of dental morphology traits. Dental remains from 41 sites throughout Italy were analyzed; only three of the sites (Laterza and two from Sicily) span from the late Copper Age to the early Bronze Age. To work with adequate samples, we pooled the collections into nine geographically and culturally homogeneous groups. Dental morphological traits were scored on 8,891 teeth from 1,302 individuals using the ASUDAS scale. The correlation between the mean measure of divergence and geographic distances (calculated as air distances) was computed. Multidimensional scaling with the minimum spanning tree and maximum-likelihood methods was applied to assess the relationships between groups. The results revealed a substantial genetic homogeneity among the populations throughout the Italian peninsula during the Copper Age with the exception of Sardinia, which tends to diverge from the continental samples. Phenetic and geographic distances correlate highly significantly only when the southern samples from Sicily and Laterza are removed from the analysis, which indicates that these groups may have experienced genetic admixture with external populations.
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http://dx.doi.org/10.3378/027.081.0406DOI Listing
August 2009

A health assessment for imperial Roman burials recovered from the necropolis of San Donato and Bivio CH, Urbino, Italy.

J Anthropol Sci 2009 ;87:193-210

Department of Sociology, Anthropology & Social Work, MS 1012, Texas Tech University, Lubbock, TX 79409, USA.

Imperial Roman burials recovered from the sites of San Donato and Bivio CH, located in the city of Urbino, Italy were examined for skeletal lesions. Observed pathologies include arthritis, trauma, periostitis, cranial pitting and enamel hypoplasia. All of the adults exhibited at least one enamel hypoplasia. In general, the adult males exhibit greater rates of skeletal pathologies than the females. Clearly, chronic health problems appear to be common among all adults; nearly 89% of them exhibit at least one form of skeletal lesion. This is in stark contrast to what is seen for the sub-adults. Only one sub-adult showed skeletal lesions. Acute health problems may have been the primary contributing factors for the death of the children recovered from the site. Despite previous research and attention to malaria as a critical health problem of Roman sub-adults, it does not seem to be an issue for this burial sample. We compare the frequency of cranial pitting and periostitis for the Urbino burials to several other Imperial Roman skeletal samples as a means to assess the potential for malaria and other casual factors for the observed lesions. In conclusion, we see the extreme rate of skeletal lesions for this community as indication of an extremely poor quality of life for these Romans.
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September 2009