MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes

Summary Ancient DNA studies are increasingly targeting samples that are beyond the limit of radiocarbon dating (>50 thousand years old) and are often difficult or impossible to date using other geochr...

biorxiv.org

Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers - Genome Biology

Background Eastern hunter-gatherers (EHG) contributed varying proportions of genetic ancestry to many modern Europeans. However, how this contribution shaped the human leukocyte antigen (HLA) gene diversity remains unexplored. Sakhtysh in western Russia comprises one of the largest EHG-affiliated burial complexes. The site's continuous use offers a rare opportunity to investigate the genetic history, immune-gene diversity, and pathogen exposure within a hunter-gatherer population. Results Genome-wide data from 36 individuals (spanning Lyalovo–Volosovo traditions, 6800–4800 cal BP) place the Sakhtysh population within the EHG cluster, with high genetic affinity to contemporaneous groups across northwestern Russia and the eastern Baltic. This genetic composition remained stable for over two millennia and there is no evidence of admixture with neighboring western hunter-gatherer or farmer groups. We report HLA genotypes for 27 Sakhtysh individuals, representing the first true HLA calls from ancient hunter-gatherers. HLA diversity is low in the Sakhtysh population, likely due to their small population size. Specific alleles like B*27:05 are observed at high frequencies (~ 50%), despite being relatively rare in modern populations, suggesting shifts in selective pressures. Pathogen screening identified a restricted spectrum of causal agents including possible zoonoses with Erysipelothrix rhusiopathiae and chronic infections with hepatitis B virus and parvovirus B19. Conclusions The Sakhtysh community shows genetic continuity across cultural transitions. This population exhibits limited HLA diversity and unexpectedly high frequency of certain alleles. These patterns were likely influenced by low pathogen diversity and possible adaptation to specific environmental factors.

doi.org

Zaskakujące wyniki DNA. Nasi przodkowie wybierali samice mamutów

Jak polowali ludzie w epoce lodowcowej? Najnowsze badania genetyczne setek mamutów przynoszą zaskakującą odpowiedź. W miejscach obozowisk ludzkich przeważają szczątki samic. Ważną rolę w tych wnioskac...

national-geographic.pl

Beyond the scales: Marine archaeogenomics for the conservation and restoration of fisheries

Protection and restoration of marine environments are essential for food security and climate change mitigation. Yet historical and archaeological research have shown that conservation and management ...

science.org

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian ...

tandfonline.com

Recovering signatures of archaic hominin introgression using ancestral recombination graphs

Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unad...

science.org

Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes

Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id

academic.oup.com

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

Dental Calculus Formation Is Linked to Diet and Phylogeny in Mammals

In a survey of > 1600 specimens across all mammalian orders, we found that most species present dental calculus. We found calculus production to be strongly associated with herbivory, and we provide ...

doi.org

Mediterranean dispersal imposed bottlenecks in Neolithic sheep and goats

The Neolithic period in western Eurasia involved major dispersal events, including the translocation of livestock into Europe. These domestic animal translocations likely featured founder effects, fun...

biorxiv.org

Palaeogenetics with Hannah Moots

YouTube video by Archaeodeath

youtube.com

sciencedirect.com

Equal in death: Ancient genomic analysis of children’s early Christian burials

Ancient genomes challenge views of close kinship in multiple Christian burials, revealing flexible traditions around children.

science.org

Research Assistant/Research Associate in Statistical Modelling in Archaeology (Fixed Term) - Job Opportunities - University of Cambridge

Research Assistant/Research Associate in Statistical Modelling in Archaeology (Fixed Term) in the McDonald Institute for Archaeological Research at the University of Cambridge.

tinyurl.com

nature.com

Joint dog and wolf genealogies reveal the evolution of the canine genome

Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close ...

biorxiv.org

Ancient DNA analyses of remains of the Medici family (16th century) provide insights into the genetic variation of Plasmodium falciparum

Microbial genomics; Omics; Genomics; Archeology; History

cell.com

The agropastoral debate in context: the relationship between the consumption and management of animals at Azoria on Crete - Archaeological and Anthropological Sciences

Historians and archaeologists of the ancient Greek economy have argued for decades over the form (transhumance vs. mixed farming) and scale (largescale specialist herds vs. small herds) of ancient Gre...

link.springer.com

Call for New Task Force Members

CALL FOR NEW TASK FORCE MEMBERS Dear SMBE members, Are you passionate about inclusion, diversity, equity and/or access in science and academia and would like to be a part of the task force to improve ...

smbe.org

Sex and Gender in Human Skeletal Biology: Slow Movement Beyond the Binary

Despite advancing discussions to move beyond sex and gender binaries in human skeletal biology, including in forensic anthropology and bioarchaeology, such binaries largely persist in praxis and pedag...

annualreviews.org