Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.Introduction Results - Genetic substructure in the Iberian CA - Genetic turnover in the southern Iberian BA and the rise of El Argar - Mediterranean and central European ancestries shaped the genetic profile of southeastern BA groups in Iberia - A late Argar genetic outlier makes links to North Africa and the central Mediterranean - Insights into phenotypic variation, demography, and social correlates of CA and EBA El Argar societies Discussion Material and method

Genomic transformation and social organization during the Copper Age-Bronze Age transition in southern Iberia

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA

Ancient Plasmodium genomes shed light on the history of human malaria

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia bce, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.This project was funded by the National Science Foundation, grants BCS-2141896 and BCS-1528698; the European Research Council (ERC) under the European Union’s Horizon 2020 programme, grants 851511-MICROSCOPE (to S. Schiffels), 771234-PALEoRIDER (to W.H.) and starting grant 805268-CoDisEASe (to K.I.B.); and the ERC starting grant Waves ERC758967 (supporting K. Nägele and S.C.). We thank the Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean for supporting M. Michel, E. Skourtanioti, A.M., R.A.B., L.C.B., G.U.N., N.S., V.V.-M., M. McCormick, P.W.S., C.W. and J.K.; the Kone Foundation for supporting E.K.G. and A.S.; and the Faculty of Medicine and the Faculty of Biological and Environmental Sciences at the University of Helsinki for grants to E.K.G. A.S. thanks the Magnus Ehrnrooth Foundation, the Sigrid Jusélius Foundation, the Finnish Cultural Foundation, the Academy of Finland, the Life and Health Medical Foundation and the Finnish Society of Sciences and Letters. M.C.B. acknowledges funding from: research project PID2020-116196GB-I00 funded by MCIN/AEI/10.13039/501100011033; the Spanish Ministry of Culture; the Chiang Ching Kuo Foundation; Fundación Palarq; the EU FP7 Marie Curie Zukunftskolleg Incoming Fellowship Programme, University of Konstanz (grant 291784); STAR2-Santander Universidades and Ministry of Education, Culture and Sports; and CEI 2015 project Cantabria Campus Internacional. M.E. received support from the Czech Academy of Sciences award Praemium Academiae and project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague. This work has been funded within project PID2020-115956GB-I00 ‘Origen y conformación del Bronce Valenciano’, granted by the Ministry of Science and Innovation of the Government of Spain, and grants from the Canadian Institutes for Health Research (MZI187236), Research Nova Scotia (RNS 2023-2565) and The Center for Health Research in Developing Countries. D.K. is the Canada research chair in translational vaccinology and inflammation. R.L.K. acknowledges support from a 2019 University of Otago research grant (Human health and adaptation along Silk Roads, a bioarchaeological investigation of a medieval Uzbek cemetery). P.O. thanks the Jane and Aatos Erkko Foundation, the Finnish Cultural Foundation and the Academy of Finland. S. Peltola received support from the Emil Aaltonen Foundation and the Ella and Georg Ehrnrooth Foundation. D.C.S.-G. thanks the Generalitat Valenciana (CIDEGENT/2019/061). E.W.K. acknowledges support from the DEEPDEAD project, HERA-UP, CRP (15.055) and the Horizon 2020 programme (grant 649307). M. Spyrou thanks the Elite program for postdocs of the Baden-Württemberg Stiftung. Open access funding provided by Max Planck Society

Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between similar to 10,500 and similar to 400 years ago. We date the most recent common ancestor of all HBV lineages to between similar to 20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for similar to 4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.Molecular Technology and Informatics for Personalised Medicine and Healt

Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

Across and within-forest effects on breeding success in Mediterranean Great Tits Parus major

Forest type and habitat structure can have profound effects on different aspects of avian life histories. These effects may, however, strongly differ across and within forests that vary in vegetation composition and structure, especially when an ancient forest has been replaced by a new forest. To test for these differences in effect, we studied Great Tit Parus major life-history traits (280 first clutches) in two Mediterranean evergreen forests during 2005–07: an ancient Holm Oak Quercus ilex and a reforested pine forest. A comparison between forests revealed that females breeding in the Holm Oak forest started laying one week later, and produced larger clutches and broods both at hatching and at fledging. Chicks raised in the Holm Oak forest also fledged in better condition. Within forests, however, the reproductive success was not higher for pairs breeding in nestboxes surrounded by oaks within the pine forest, and also reproductive success was not lower in nestboxes surrounded by pines within oak forest. Instead, vegetation maturity around nestboxes, rather than tree species composition, affected hatching success. Surprisingly, hatching success was higher in nestboxes surrounded by immature vegetation. We suggest that this may be due to a lower nest predation rate in nestboxes surrounded by immature vegetation, compared to nestboxes surrounded by mature vegetation. We suggest that different factors appear to affect variation in breeding success in Mediterranean Great Tits comparing across forests (e.g. food availability) vs. within a forest (e.g. nest predation).

The design of artificial nestboxes for the study of secondary hole-nesting birds: A review of methodological inconsistencies and potential biases

The widespread use of artificial nestboxes has led to significant advances in our knowledge of the ecology, behaviour and physiology of cavity nesting birds, especially small passerines. Nestboxes have made it easier to perform routine monitoring and experimental manipulation of eggs or nestlings, and also repeatedly to capture, identify and manipulate the parents. However, when comparing results across study sites the use of nestboxes may also introduce a potentially significant confounding variable in the form of differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. However, the use of nestboxes may also introduce an unconsidered and potentially significant confounding variable due to differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. Here we review to what extent the characteristics of artificial nestboxes (e.g. size, shape, construction material, colour) are documented in the 'methods' sections of publications involving hole-nesting passerine birds using natural or excavated cavities or artificial nestboxes for reproduction and roosting. Despite explicit previous recommendations that authors describe in detail the characteristics of the nestboxes used, we found that the description of nestbox characteristics in most recent publications remains poor and insufficient. We therefore list the types of descriptive data that should be included in the methods sections of relevant manuscripts and justify this by discussing how variation in nestbox characteristics can affect or confound conclusions from nestbox studies. We also propose several recommendations to improve the reliability and usefulness of research based on long-term studies of any secondary hole-nesting species using artificial nestboxes for breeding or roosting.Peer Reviewe

Patterns of nest placement in a population of marsh tits Poecile palustris

The factors influencing nest placement by territorial birds are not fully understood, including the roles played by habitat, conspecific attraction and female experience of a previous nesting location. We used 7 years of Marsh Tit (Poecile palustris) nest-site and territory data, and high-resolution vegetation models derived from remote sensing, to investigate spatial patterns of nest placement with regard to previous female experience and age, conspecific attraction, and habitat in a woodland environment. We found no evidence for an effect of conspecific attraction or previous nest location on nest placement within the territory. However, first-year (FY) females placed nests in a random spatial pattern within their territories, and after first-year (AFY) females predominantly placed nests within the central parts of their territories, away from conspecifics. The core area of each breeding territory was centred on a region of comparatively taller overstorey and less understorey than other parts of the territory. Nest-sites were situated in localised areas of a similar structure, although absolute differences between selected and non-selected areas of the territory were not substantial. Both female age groups nested in areas of the territory where the overstorey contained relatively more Common Ash (Fraxinus excelsior) and Field Maple (Acer campestre), which may have been related to tree height, but there was no selection for English Oak (Quercus robur). We found no significant habitat differences between the territories of FY and AFY females that explained their differing patterns of nest placement

IAA : Información y actualidad astronómica (64) (2021)

SUMARIO : Encuentros temporales entre astronomía y prehistoria.-- Tercer año del proyecto Severo Ochoa del IAA.-- Deconstrucción. Visitantes interestelares.-- Historias...La máquina en el desierto.--El Moby Dick de...Antonio Claret (IAA-CSIC).-- Actualidad.-- Sala limpia.-- Pilares e incertidumbres.Este número ha contado con el apoyo económico de la Agencia Estatal de Investigación (Ministerio de Ciencia, Innovación y Universidades) a través de la acreditación de Centro de Excelencia Severo Ochoa para el Instituto de Astrofísica de Andalucía (SEV-2017-0709). La página web de esta revista ha sido financiada por la Sociedad Española de Astronomía (SEA).Peer reviewe