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PubMed2026

[Syphilis and human treponemes: a long evolutionary history revealed by paleogenomics].

Recent discoveries in paleogenomics have revolutionized our understanding of syphilis and other human treponematoses. Far from being a pathogen that suddenly appeared in Europe in the late Middle Ages, we now know that Treponema pallidum has been circulated among human populations for millennia. Ancient genomes recovered from pre-Columbian contexts in the Americas show that major treponemal lineages had already diversified well before the modern era, often in the absence of recognizable skeletal lesions. Genomic analyses further indicate that treponemal diversity is not the result of extensive genetic acquisition, but rather of small-scale modulation of a highly conserved genome, notably via antigenic variation involving the tpr gene family. Combined with data on endemic treponematoses, congenital syphilis, and historical pathology collections, these findings support a model in which syphilis, yaws, and bejel represent context-dependent expressions of an ancient treponemal continuum, with implications for diagnosis, epidemiology, and vaccine design.

Humans↗
PubMed2026

Paleogenomic sex inference of mammoth remains sheds light on the anthropogenic nature of bone accumulations.

Whether large accumulations of woolly mammoth (Mammuthus primigenius) bones reflect natural mortality or deliberate human resource exploitation has long been debated, with major implications for understanding Late Pleistocene human-megafaunal interactions.1,2,3,4,5 Here, we use ancient DNA to investigate site-formation hypotheses by comparing genetic sex ratios from mammoth remains recovered in putative anthropogenic bone accumulations and from geographically dispersed, non-anthropogenic contexts. We studied genome-wide data from 521 woolly mammoths-including 100 mammoths from bone accumulation sites and 421 mammoths from natural depositional settings across Eurasia and North America-of which 448 are newly generated. Genetic sex determination reveals a striking contrast between contexts: mammoths from dispersed sites show a male bias (∼66.5%), which is consistent with the heightened vulnerability of solitary males to hazards such as natural traps, where bones are more likely to be preserved, whereas mammoths from anthropogenic bone accumulations are predominantly female (∼70%). This female bias is pervasive across multiple sites, indicating an anthropogenic origin for these accumulations as a result of Upper Paleolithic hunters preferentially exploiting female mammoths, possibly derived from herd contexts. Together, these results provide population-scale genetic evidence that highlights the central role of mammoths in the subsistence and material economies of some Paleolithic communities.

Animals↗
PubMed2026

Paleogenomics and habitat modeling reveal temperate Eurasian origins of woolly rhinoceroses.

The woolly rhinoceros was a prominent Ice Age megafaunal species, and there is limited knowledge regarding its origin and responses to past glacial cycles. We sequenced 29 mitochondrial and 14 nuclear genomes from Pleistocene specimens across Eurasia and modeled the species' habitats over the past 500,000 years. Our results suggest that its maternal genetic diversity mainly evolved in temperate Eurasia around 460 thousand to 420 thousand years ago during a prolonged glacial-interglacial transition. We found that a ~170-thousand-year-old East Asian individual was ancestral to all later populations, indicating East Asia as one possible origin of Late Pleistocene ancestry. We also identified the Altai region as a major climatic refugium. These findings highlight the crucial role of temperate Eurasia in the evolution of woolly rhinoceroses and the diversification of cold-adapted megafauna.

Animals↗
PubMed2026

Reconstruction of ancestral plant genomes for inter-crop translational research.

We present Ancestral Genome Reconstruction (AGR), an exploratory framework for the automated inference of "paleogenomes" from large-scale comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral angiosperm genomes millions of years old. These reconstructed ancestors were instrumental in (1) estimating when angiosperms emerged, when major botanical families originated, and when shared ancestral whole-genome duplication events occurred; and (2) tracing the evolutionary trajectories of ancestral chromosomes and genes, especially those that may have driven the emergence of key life-history traits (e.g., woody vs. herbaceous, aquatic vs. terrestrial, C3 vs. C4, and symbiotic root-nodulating vs. non-nodulating species). We demonstrated that these paleogenomes serve as tractable backbones for inter-crop translational research. Through an open-access web tool, OrthoViewer, we identified orthologs that have retained the same ancestral genomic context, favoring the identification of genes associated with "phenologs"- orthologous genes across species driving analogous phenotypes, traits, or processes-exemplified by FUWA for yield components, FLC for flowering time, and DDM1 for DNA methylation. Taken together, this study provides a testable paleogenomic workflow, opening novel avenues for integrating evolutionary genomics data into modern climate-smart crop breeding and supporting the agroecological transition.

Genome, Plant↗
PubMed2026

Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.

Ancient DNA (aDNA) has transformed evolutionary biology and anthropology by providing direct, chronologically validated genetic evidence over millennia. This review synthesizes significant findings from the paleogenomic era (2010-2025), demonstrating how ancient DNA has resolved persistent debates across four interconnected themes: (i) human migration and admixture, revealing complex population transitions from archaic hominins to Holocene expansions; (ii) adaptation, tracking allele frequency changes during domestication and selection; (iii) pathogen history, clarifying the origins of pandemics and the evolution of microbiomes; and (iv) ecosystem dynamics, identifying extinction causes through sedimentary DNA and conservation genomics. We contend that scientific rigor and ethical stewardship are crucial for accurate conclusions, given ancient DNA study requires the destructive collection of culturally significant remains. This review argues that continued advancement will depend on the integration of genomic data with archaeological, isotopic, and proteomic evidence, and highlights the necessity for equitable involvement with descendant communities. By conceptualizing the past as a continuum of dynamic processes rather than static events, ancient DNA provides a revised historical narrative and insights relevant to contemporary concerns in conservation, health, and social justice.

Evolution↗
PubMed2026

FALCON2: compression-based metagenomic classification of ancient viruses.

MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples. RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC = 0.625), Kraken2 (AUPRC = 0.184), and CLARK-S (AUPRC = 0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40 bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses. AVAILABILITY AND IMPLEMENTATION: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.

Metagenomics↗
PubMed2026

Tracing the evolution and diversity of human parvovirus B19 across human history.

Human parvovirus B19 (B19V) is an ubiquitously spread, exclusively human pathogen, mainly posing risks to children, as well as pregnant and immunocompromised individuals. Despite evidence of B19V infection of human populations as far back as 7,000 years, the evolutionary history of B19V remains poorly understood. In this study, we present B19V genomic data from the remains of 53 globally distributed individuals spanning more than 8,000 years, including 7 children. Our findings suggest that the most recent common ancestor of all present B19V lineages existed around 12,000 years ago, at the end of the last Ice Age. Additionally, we identified an extinct Eurasian clade that participated in the recombination event that led to the emergence of B19V genotype 2 (GT-2). We date this event to ∼3,200-1,800 BP, potentially in the greater Mediterranean area. Our study shows aspects of how ancient parvovirus variants arose, disseminated, and impacted human health through time.

ancient DNA↗
PubMed2026

Eastern origin and three-millennia persistence of a founding grapevine lineage in Iberian viticulture.

Viticulture became central to most Mediterranean civilizations a few millennia after the grapevine (Vitis vinifera L.) was domesticated in the South Caucasus/Near East. To elucidate the origins of the grapevines that enabled this westward spread over the past 3,000 years, we analyzed 28 grapevine seeds from seven archaeological sites in the Iberian Peninsula and Sardinia. Ancient DNA recovered from the oldest seeds with domesticated-like morphology (from ∼1,000 BCE), found in southwestern Spain, revealed nuclear and chloroplast genome signatures of Eastern Mediterranean cultivars. Seeds from the same and later Iron Age Iberian sites, however, showed genomic signatures suggesting hybridization between local wild grapevines and eastern-origin cultivars. The genetic makeup of Sardinian and northeastern Spanish seeds supports that local diversification giving rise to the Central European and Iberian wine genetic lineages had already occurred in the early Iron Age. In Iberia, Roman-period seeds were first-degree related to both the earliest eastern-introduced domesticates and a Medieval seed whose genetic makeup matches the extant Iberian variety "Pasa Valenciana." Another Medieval seed was inferred as an offspring of the extant "Heben," indicating that this major founder of Iberian germplasm has been continuously propagated for over 1,100 years. Our results confirm previous evolutionary models indicating that Western Mediterranean viticulture began with introductions of eastern domesticated grapevines, followed by early hybridization with local Iberian wild grapevines that may have facilitated viticulture adaptation to the new environment. The aDNA unveils that these introductions gave rise to extant cultivars through only a few sexual generations and long-term reliance on clonal propagation.

Iberian Peninsula↗