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#genomes
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Continued thread
The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.
Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus
https://doi.org/10.1101/2025.06.03.653586
Being not limited, we moved a few more figures from the supplement to the main text 
https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480
**Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa**
“_For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from North Africa._”
Oteo-Garcia, G., Silva, M., Foody, M.G.B. et al. Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa. Genome Biol 26, 108 (2025). https://doi.org/10.1186/s13059-025-03570-1.
#OpenAccess #OA #Research #Biology #Science #Archaeology #Archaeodons #Genetics #Genomes #History #Medieval #Iberia #Academia #Academics @science @archaeodons
BioMed CentralMedieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa - Genome BiologyBackground The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late medieval period through ancient DNA. Results Our comprehensive genomic analysis uncovers gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncover one of the earliest dated Islamic burials in Spain, which shows high levels of consanguinity. For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from North Africa. Conclusions This study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade, underscores the low impact of the Reconquista in the genetic landscape, and shows the lasting impact of post-medieval events, such as the Expulsion of the Moriscos in 1609 CE, on the region’s genetic and cultural landscape, through mass population displacement and replacement.
Do ancestral #genomes of today's #crops hold the keys to feeding the future?
Find out in this new #OpenAccess research paper from He et al.
Free to read in #JIPB! 
https://doi.org/10.1111/jipb.13902
@wileyplantsci
#PlantSci #CropSci #PlantBreeding #FoodSecurity #oats #Avena #botany
Our recent article on non-visual opsins in lizards - which made the May cover - is the focus of a new Highlight.
"Highlight: More Than Meets the Eye—Nonvisual Opsins Are Crucial for Light-Sensing in Vertebrates"
doi.org/10.1093/gbe/evaf075
The tuatara and many lizards possess a parietal eye, where non-visual opsins are expressed. Romero & @fsjsouza.bsky.social compared 60+ genomes to study the evolution of non-visual opsins, suggesting a functional role associated with the parietal eye.
doi.org/10.1093/gbe/evaf058
"After more than two decades of work, researchers have achieved a genetics milestone: they have successfully sequenced the complete genomes of six ape species, a feat that seemed impossible just a few years ago."
www.nature.comWhat makes us human? Milestone ape genomes promise cluesDNA sequences for the chimpanzee, orangutans and more will help scientists to determine what sets humans apart from other apes.
This is the best explanation I've ever seen for lungfish genome sizes
https://xkcd.com/3064/
#XKCD #Genomes #MolecularEvolution #lungfish
xkcdLungfish
Free to read!
From our special issue on the uplift history of the Himalayas, Gui et al. use #chloroplast #genomes and ribosomal #DNA to gain insights into divergence and morphological #evolution of alpine Tongoloa.
https://doi.org/10.1111/jse.13028
@WileyEcolEvol
#PlantSci #JSE #botany
#Bacterial ' #jumping_genes' can target and control #chromosome ends.
#transposons #telomeres #Streptomyces #genomes
https://phys.org/news/2025-03-bacterial-genes-chromosome.html
phys.orgBacterial 'jumping genes' can target and control chromosome endsTransposons, or "jumping genes"—DNA segments that can move from one part of the genome to another—are key to bacterial evolution and the development of antibiotic resistance.
Mollusks encompass species ranging from squid 
to sea snails 
- 13 new #genomes from across the phylum to assemble a new phylogeny for Mollusca https://www.science.org/doi/10.1126/science.ads0215 #biodiversity #genomics #evolution #phylogenomics
25 #genomes & 62 transcriptomes of ladybird beetles 
- evolution of chemosensory, digestive, detoxifying, & immune #genes associated with dietary shifts 
<=>
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-025-02174-2 #biodiversity #genomics #evolution
BioMed CentralMolecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory - BMC BiologyBackground Dietary shifts are major evolutionary steps that shape ecological niches and biodiversity. The beetle family Coccinellidae, commonly known as ladybirds, first transitioned from a fungivorous to an insectivorous and subsequently a plant diet. However, the molecular basis of this dietary diversification remained unexplored. Results We investigated the molecular evolution of dietary shifts in ladybirds, focusing on the transitions from fungivory to carnivory (Coccinellidae) and from carnivory to herbivory (Epilachnini), by comparing 25 genomes and 62 transcriptomes of beetles. Our analysis shows that chemosensory gene families have undergone significant expansions at both nodes of diet change and were differentially expressed in feeding experiments, suggesting that they may be related to foraging. We found expansions of digestive and detoxifying gene families and losses of chitin-related digestive genes in the herbivorous ladybirds, and absence of most plant cell wall-degrading enzymes in the ladybirds dating from the transition to carnivory, likely indicating the effect of different digestion requirements on the gene repertoire. Immunity effector genes tend to emerge or have specific amino acid sequence compositions in carnivorous ladybirds and are downregulated under suboptimal dietary treatments, suggesting a potential function of these genes related to microbial symbionts in the sternorrhynchan prey. Conclusions Our study provides a comprehensive comparative genomic analysis to address evolution of chemosensory, digestive, detoxifying, and immune genes associated with dietary shifts in ladybirds. Ladybirds can be considered a ubiquitous example of dietary shifts in insects, and thus a promising model system for evolutionary and applied biology.
**Ancient genomes reveal trans-Eurasian connections between the European Huns and the Xiongnu Empire**
_“We provide new compelling evidence on the origins of the Hun-period population, its considerable diversity and its ties to the steppe and the Xiongnu elites.”_
G.A. Gnecchi-Ruscone, Z. Rácz, S. Liccardo, J. Lee, Y. Huang, L. Traverso, R. Radzevičiūtė, Z. Hajnal, A. Szécsényi-Nagy, B. Gyuris, O. Mateovics-László, Z. Bernert, T. Szeniczey, T. Hajdu, B. Mészáros, M. Bálint, B.G. Mende, B. Miller, Z. Samashev, A. Childebayeva, L. Djansugurova, P. Geary, H. Ringbauer, T. Vida, C. Jeong, W. Pohl, J. Krause, & Z. Hofmanová, Ancient genomes reveal trans-Eurasian connections between the European Huns and the Xiongnu Empire, Proc. Natl. Acad. Sci. U.S.A. 122 (9) e2418485122, https://doi.org/10.1073/pnas.2418485122 (2025).
#OpenAccess #OA #Research #Article #DOI #Anthropology #Science #Biology #Ancient #Genomes #DNA #Eurasia #Huns #Xiongnu #MiddleAges #Academia #Academics @science @biology @anthropology
**Inference of human pigmentation from ancient DNA by genotype likelihood**
_“We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye and hair color evolved over the past 45,000 years. The shift towards lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Copper and Iron ages.”_
Perretti, S. et al. (2025) 'Inference of human pigmentation from ancient DNA by genotype likelihood,' bioRxiv (Cold Spring Harbor Laboratory) [Preprint]. https://doi.org/10.1101/2025.01.29.635495.
#Ancient #DNA #Genomes #Phenotype #Science #Eurasia #CopperAge #IronAge @science
bioRxiv · Inference of human pigmentation from ancient DNA by genotype likelihoodLight eyes, hair and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic, and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in two high-coverage ancient samples, the Paleolithic Ust’-Ishim from Russia and the Mesolithic SF12 from Sweden. We could thus compare three approaches to pigmentation inference, concluding that, for suboptimal levels of coverage (<8x), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye and hair color evolved over the past 45,000 years. The shift towards lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Copper and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.
### Competing Interest Statement
The authors have declared no competing interest.
Celebrating World #Pangolin Day with new #genomes to aid the world's most trafficked animal
#conservation #biodiversity #Manis #genomics #genetic_diversity
https://phys.org/news/2025-02-celebrating-world-pangolin-day-genomes.html
phys.orgCelebrating World Pangolin Day with new genomes to aid the world's most trafficked animalPangolins are unique as they are the only mammal to be covered in scales. Even though they are scaly, photos of them are typically met with "awwws" from the viewers, who find them adorable. Importantly, though, pangolins play an essential role in maintaining their ecosystem.