Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[VladMC]

Kinship practices at the early bronze age site of Leubingen in Central Germany

Abstract
With the beginning of the Early Bronze Age in Central Europe ~ 2200 BC, a regional and supra-regional hierarchical social organization emerged with few individuals in positions of power (chiefs), set apart by rich graves with extensive burial constructions. However, the social organization and stratification within the majority of people, who represent the non-elite, remain unclear. Here, we present genome-wide data of 46 individuals from the Early Bronze Age burial ground of Leubingen in today’s Germany, integrating archaeological, genetic and strontium isotope data to gain new insights into Early Bronze Age societies. We were able to reconstruct five pedigrees which constitute the members of close biological kinship groups (parents and their offspring), and also identify individuals who are not related to individuals buried at the site. Based on combined lines of evidence, we observe that the kinship structure of the burial community was predominantly patrilineal/virilocal involving female exogamy. Further, we detect a difference in the amount of grave goods among the individuals buried at Leubingen based on genetic sex, age at death and locality but see no difference in the types of grave goods.

https://www.nature.com/articles/s41598-024-54462-6

[TanTin]

300 k years old  hominin fossil from China

https://www.sciencedirect.com/science/ar...8423000908

Morphological and morphometric analyses of a late Middle Pleistocene hominin mandible from Hualongdong, China

Abstract
Excavations in Hualongdong (HLD), East China, have yielded abundant hominin fossils dated to 300 ka. There is a nearly complete mandible that fits well with a partial cranium, and together they compose the skull labeled as HLD 6. Thus far, detailed morphological description and comparisons of the mandible have not been conducted. Here we present a comprehensive morphological, metric, and geometric morphometric assessment of this mandible and compare it with both adult and immature specimens of Pleistocene hominins and recent modern humans. Results indicate that the HLD 6 mandible exhibits a mosaic morphological pattern characterized by a robust corpus and relatively gracile symphysis and ramus. The moderately developed mental trigone and a clear anterior mandibular incurvation of the HLD 6 mandible are reminiscent of Late Pleistocene hominin and recent modern human morphology. However, the weak expression of all these features indicates that this mandible does not possess a true chin. Moreover, a suite of archaic features that resemble those of Middle Pleistocene hominins includes pronounced alveolar planum, superior transverse torus, thick corpus, a pronounced endocondyloid crest, and a well-developed medial pterygoid tubercle. The geometric morphometric analysis further confirms the mosaic pattern of the HLD 6 mandible. The combination of both archaic and modern human features identified in the HLD 6 mandible is unexpected, given its late Middle Pleistocene age and differs from approximately contemporaneous Homo members such as Xujiayao, Penghu, and Xiahe. This mosaic pattern has never been recorded in late Middle Pleistocene hominin fossil assemblages in East Asia. The HLD 6 mandible provides further support for the high morphological diversity during late Middle Pleistocene hominin evolution. With these findings, it is possible that modern human morphologies are present as early as 300 ka and earlier than the emergence of modern humans in East Asia.

[pelop]

"Until death do us part". A multidisciplinary study on human- Animal co- burials from the Late Iron Age necropolis of Seminario Vescovile in Verona (Northern Italy, 3rd-1st c. BCE)


Zita Laffranchi  ,Stefania Zingale ,Umberto Tecchiati ,Alfonsina Amato,Valentina Coia,Alice Paladin,Luciano Salzani,Simon R. Thompson,Marzia Bersani,Irene Dori,Sönke Szidat,Sandra Lösch,Jessica Ryan-Despraz,Gabriele Arenz,Albert Zink ,Marco Milella


Abstract
Animal remains are a common find in prehistoric and protohistoric funerary contexts. While taphonomic and osteological data provide insights about the proximate (depositional) factors responsible for these findings, the ultimate cultural causes leading to this observed mortuary behavior are obscured by the opacity of the archaeological record and the lack of written sources. Here, we apply an interdisciplinary suite of analytical approaches (zooarchaeological, anthropological, archaeological, paleogenetic, and isotopic) to explore the funerary deposition of animal remains and the nature of joint human-animal burials at Seminario Vescovile (Verona, Northern Italy 3rd-1st c. BCE). This context, culturally attributed to the Cenomane culture, features 161 inhumations, of which only 16 included animal remains in the form of full skeletons, isolated skeletal parts, or food offerings. Of these, four are of particular interest as they contain either horses (Equus caballus) or dogs (Canis lupus familiaris)–animals that did not play a dietary role. Analyses show no demographic, dietary, funerary similarities, or genetic relatedness between individuals buried with animals. Isotopic data from two analyzed dogs suggest differing management strategies for these animals, possibly linked to economic and/or ritual factors. Overall, our results point to the unsuitability of simple, straightforward explanations for the observed funerary variability. At the same time, they connect the evidence from Seminario Vescovile with documented Transalpine cultural traditions possibly influenced by local and Roman customs.

https://journals.plos.org/plosone/articl...ne.0293434

[J1_DYS388=13]

Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK

Open Access
G. Michael Taylor1ORCID icon, Katie White-Iribhogbe2ORCID icon, Garrard Cole3ORCID icon, David Ashby4ORCID icon, Graham R. Stewart1ORCID icon, Heidi Dawson-Hobbis4ORCID icon
View Affiliations
Published: 16 February 2024 https://doi.org/10.1099/jmm.0.001806

ABSTRACT

Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.

Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.

Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.

Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.

Keywords
aDNA, leprosy, mediaeval, PCR, tuberculosis

https://www.microbiologyresearch.org/con...m.0.001806

[pelop]

https://www.nature.com/articles/s41467-024-45438-1

Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA

Rohrlach et al

Abstract
Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice.

(doesn't include new samples)

[Shuzam87]

"Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium"

Description: This collection includes the EIGENSTRAT format genotype data of 9 ancient individuals, from two archaeological sites in eastern Mongolia (Gurvan Dov and Tavan Khailaast) for the 1240K SNP panel. These individuals were newly analyzed in the study "Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium".

Subject: Biology

Keyword: Xiongnu-Xianbei; Turk-Uygyur; Zubu; ancient genomes; genetic stability

https://edmond.mpg.de/dataset.xhtml?pers...7/3.DDZCWN

[VladMC]

Data for "Reconstructing the genetic relationship between ancient and present-day Siberian populations"

This collection includes the EIGENSTRAT format genotype data of 205 ancient individuals for the 1240K SNP panel. The individuals were previously published elsewhere but only FASTQ or BAMs were made publicly available by the original studies. We deposit the 1240K genotype call of these individuals which we used in our study titled "Reconstructing the genetic relationship between ancient and present-day Siberian populations".

https://edmond.mpg.de/dataset.xhtml?pers...7/3.QZBM1X

[teepean]

The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina

Abstract

The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly-generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies the Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

"No new samples were collected in this study. Whole genome data was generated from samples collected in 2005, initially studied using only mitochondrial DNA markers (D-loop)."

https://www.biorxiv.org/content/10.1101/...81063v1?ct=

[ilabv]

Data for "Reconstructing the genetic relationship between ancient and present-day Siberian populations"

This collection includes the EIGENSTRAT format genotype data of 205 ancient individuals for the 1240K SNP panel. The individuals were previously published elsewhere but only FASTQ or BAMs were made publicly available by the original studies. We deposit the 1240K genotype call of these individuals which we used in our study titled "Reconstructing the genetic relationship between ancient and present-day Siberian populations".

https://edmond.mpg.de/dataset.xhtml?pers...7/3.QZBM1X

Since these are 1240k I assume this means lower quality than the original FASTQ or BAM formats due to SNP reduction that 1240k format does?

[teepean]

Not sure if this has been discussed before.

Network of large pedigrees reveals social practices of Avar communities

From 567/68 CE, the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years. An extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological, and historical contextualization on four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present the largest set of pedigrees reconstructed so far through aDNA, spanning over 9 generations comprising ~300 individuals. We uncover a strict patrilineal kinship system, where patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were commonly practiced. The absence of consanguinity indicates this society maintained a detailed memory of ancestry over generations. These kinship practices correspond to the evidence of historical sources and anthropological research on Eurasian Steppe societies. Novel network analyses of identity-by-descent DNA connections suggest social cohesion between communities was maintained via females. Finally, despite the absence of major ancestry shifts, the level of resolution reached by our analyses allowed us to detect genetic discontinuity: the replacement of a community at one of the studied sites. This was paralleled with changes in the archaeological record and was likely due to local political realignment.

Looks like there's 440 samples!

The data is already available:

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

[JMcB]

Courtesy of lg16:


Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France

Luciana G. Simões, Rita Peyroteo-Stjerna, Grégor Marchand and Mattias Jakobsson



Significance:

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of hunter-gatherers. We generated different types of biomolecular data, including deep coverage complete genome sequencing, from human skeletal remains buried in the iconic sites of Téviec and Hoedic in Brittany, representing some of the last hunter-gatherers of western Europe. The data show that these last foragers were part of a network of people who maintained exogamic practices. These socio-cultural dynamics contributed to avoiding inbreeding. Some of the forager individuals overlapped in time with the arrival of Neolithic farmers to neighboring regions. However, we did not find any farmer-associated ancestry in the analyzed hunter-gatherers and the mate-exchanging networks appear to be exclusive for the foraging group.


Abstract:

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

https://www.pnas.org/doi/10.1073/pnas.2310545121

[TanTin]

Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France

https://doi.org/10.1073/pnas.2310545121

https://www.pnas.org/doi/10.1073/pnas.2310545121

Abstract
Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

FASTQ files available:
https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

[RCO]

Several good presentations
EAA European Association of Archaeologists
30th EAA Annual Meeting in Rome, Italy
28 - 31 August 2024

Search here:
https://submissions.e-a-a.org/eaa2024/re...chtimeslot=

A good one:

Title: The demographic impact of the Roman and Visigothic presence in the Iberian Peninsula
Content:The transformation of the political landscape in West Eurasia can be attributed to the Roman Empire, the decline of its Western segment, and the consequential Great Migration era. The influence of these events on the demographic composition of various regions, such as the Iberian Peninsula, remains not fully elucidated. We have collected genome-wide data from 255 newly reported ancient individuals from Iberia spanning from the Roman era to the Great Migration period. The Roman presence in the peninsula dates back to the 3rd century BCE and was fully annexed by the 1st century BCE. It remained intricately connected with the broader Mediterranean through Roman roads and sea routes until its collapse in the 5th century. Our findings reveal that the populations in Roman-period Iberia were as diverse as those in other central and western Mediterranean regions, like central Italy (Antonio et al. 2019) and the Danubian frontier (Olalde & Carrion et al. 2023). Historical records indicate the impact of various groups on Iberia in the 5th century, including Germanic tribes (Buri, Suevi, Vandals & Visigoths) and Sarmatian people (Alans). While some, like the Suevi, established kingdoms, the Visigoths formed the most significant Germanic kingdom in the late 5th century, persisting until the Umayyad conquest in the 8th century. Despite the identification of individuals with Germanic ancestry at specific sites, overall, we observe a remarkable degree of population continuity in Roman-period Iberian populations. Thus, indating limited demographic changes during this era. The close interconnections of these Germanic groups are evident in the discovery of close relatives at distant archaeological sites.
Keywords: Ancient DNA, Population Genomics, Human Genetics, Great Migrations, Mediterranean Sea, Roman Empire

Main authorsablo Carrion1
Co-author:Iñigo Olalde2
Juan Manuel Jiménez-Arenas3
Josep María Vergès4
Miguel Angel Cuadrado5
Javier Heras-Mora6
Virginia García-Entero7
Neus Coromina8
Carles Lalueza-Fox9
David Reich10

[Manofthehour]

They changed the title on the upcoming Picenes paper and the wording of the abstract.

EAA2024: Abstract
Abstract is part of session #848:The archaeogenetics of ancient Italy: socio-cultural changes, interaction and mobility from Prehistory to the Middle Ages
Title & Content
Title:New insights in the population dynamics of the Italic Iron Age: archaeogenetic analysis of the Middle-Adriatic cultures.

Content:The Italic Iron Age (approximately 10th-3rd century BCE) was characterized by a mosaic of different cultural groups, thoroughly characterized by an archaeological perspective. While some of these ethnicities have been partially investigated from a genomic point of view (providing new insights into population dynamics) a comprehensive genetic portrait remains elusive, particularly for those populations residing along the mid-Adriatic coast. To better understand the evolution and history of Iron Age Italic populations, we focused our attention on the Picenes, a civilization that flourished along the Adriatic coasts of Central Italy from the 9th to the 3rd century BCE, until Roman colonization. The Picenes were composed of many local groups not necessarily related from a genetic perspective. We analyzed the genome of 81 ancient individuals buried in three different Iron Age necropolises located in Central Italy, two associated to the Picene culture (Novilara and Sirolo-Numana, 8th-5th century BCE) and one Etruscan necropolis (Monteriggioni/Colle di Val D’Elsa, 8th-6th century BCE). Our investigation unveiled genetic homogeneity not only among the two Picene sites, indicating extensive gene flow, but also between the Picenes and other contemporary populations, pointing to a common genetic origin of the Italic Iron Age ethnic groups. Despite this homogeneity, relevant genetic distinctions emerged between coeval Adriatic and Tyrrhenian populations, pointing to genetic contacts between the Adriatic coast of Italy and the Balkans and/or Northern Europe. Furthermore, the identification of genetic outliers (indicating foreign ancestries) within the cultures here analyzed suggests that the Italic Iron Age was characterized by a multicultural society where individuals with diverse genetic origins from across Europe coexisted.

Keywords:Italic Iron Age, Middle-Adriatic cultures, Picenes

https://submissions.e-a-a.org/eaa2024/re...tract=3808

[Qrts]

Uncovering population change and regional diversity in the Central Levant from 2nd to 1st Millennium BCE through ancient DNA analysis

Abstract

The 2nd and 1st millennium BCE in the central Levant have been studied extensively, revealing how the region was greatly influenced by Hittite, New Kingdom Egypt, Neo-Assyrian, Babylonian, and Persian empire expansions, triggering significant human mobility. However, due to the dearth of genetic data available, particularly from inland sites in the 1st millennium BCE, it remains unclear if population genetic patterns reflect the cultural and demographic changes noted in historical and archaeological records. To address this, we have analyzed ancient human DNA from 28 individuals who were buried at the tell site of Kamid el-Loz in the Beqa'a plain of present-day Lebanon, dating to two distinct periods: the Middle Bronze Age (c. 2000-1500 BCE) and the Persian-Hellenistic period (c. 539-63 BCE). This site, identified as Kumidi in Late Bronze Age textual sources, and overlooking important trade routes, developed into a fortified city during the Middle Bronze period, and potentially acted as the Egyptian administrative seat in the 14th century BCE. The site shrank in importance during the Iron Age I and II and was extensively used as a cemetery during the Persian-Hellenistic Periods. Through this new genomic dataset, we report evidence of diverse ancestries and population structure between Kamid el-Loz and the nearby contemporaneous coastal site of Sidon in the Middle-Late Bronze Age, and detect gene flow at Kamid el-Loz after the Bronze Age, bringing Iranian- or Caucasus-like ancestry. These findings extend our genetic knowledge of the region to inland sites, and shed new light on regional patterns of demography, genetic structure and mobility in the 2nd to 1st millennium BCE central Levant.

https://submissions.e-a-a.org/eaa2024/re...tract=4300

Our first post-Bronze age samples from the inner Levant!