The May issue of MBE is here, featuring the work of @topalwos.bsky.social et al., who evaluated genotype imputation accuracy in a large barn owl low-coverage WGS dataset. 🔗 academic.oup.com/mbe/issue/43/5 📷 Alex Labhardt #evobio #molbio

This is excellent! We find similar trends in teleosts. We believe pleiotropy and the polygenic nature of adaptations can explain this pattern. doi.org/10.1093/molbev/msag015

It happens. Having studied most of these clones for the best part of 20 years I am not convinced it is pervasive in the wild. It definitely happens though.

Di et al. investigate axis organization in Trichoplax adhaerens, uncovering a Wnt-dependent axial system and supporting the view that core components of metazoan body axis patterning were already established in early animal evolution. 🔗 doi.org/10.1093/molbev/msag089 #evobio #molbio

@topalwos.bsky.social et al. show that genotype imputation with a low-coverage WGS dataset showed very accurate results when over 500 samples were used and when accounting for missing data and low-frequency alleles. 🔗 doi.org/10.1093/molbev/msag094 #evobio #molbio #compbio

Berruga-Fernández et al. show that bacterial hybrid chromosome formation driven by conjugative mobile genetic elements may be an important and widespread mechanism in the emergence and evolution of high-risk bacterial pathogens. 🔗 doi.org/10.1093/molbev/msag085 #evobio #molbio #bacteria

Are you looking to sequence a bunch of samples from a wild population in low-coverage but don't have a reference panel? You might be surprised how well it can work. See for yourself in our new benchmark study: doi.org/10.1093/molb...

@lfceriotti.bsky.social et al. investigate the rewiring of organellar translation in the holoparasitic Balanophoraceae, revealing extreme changes in the anciently conserved machinery of plant organellar translation. 🔗 doi.org/10.1093/molbev/msag077 #evobio #molbio #PlantSky

@drpintothe2nd.bsky.social et al. present SCINKD as a framework to identify unannotated sex chromosomes and curate diploid genome assemblies from a single individual. 🔗 doi.org/10.1093/molbev/msag067 #evobio #molbio #compbio

Beautiful. Big news if you’re interested in identifying and compiling sex-determining mechanisms like me!

Happy to announce two-fold news! 1) The SCINKD paper is now published in @molbioevol.bsky.social - doi.org/10.1093/molb... 2) SCINKD [v2.2.4] release has reduced runtimes (about 2x) and the revitalized mode for genomes >5Gb is now live and tested on genomes up to 21Gb! 🐸 github.com/DrPintoThe2n...

#ERGAReads | Genomic comparisons and the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew 🧠 🧬 academic.oup.com/mbe/article/... #evolutionarybiology #genomes @ebpgenome.bsky.social #Eurasianshrew #biodiversitygenomics @molbioevol.bsky.social

De et al. studied CNVs in yeast, providing novel evidence that most segmental CNVs adapted to nitrogen limitation are stable upon removal of selection, but costly gene amplifications are readily reversible. 🔗 doi.org/10.1093/molb... #evobio #molbio #CNV

Mönttinen et al. suggest that conservation of protein structures over long periods of evolutionary time supports the use of protein structure comparisons to reconstruct deeper evolutionary histories of RNA viruses. 🔗 doi.org/10.1093/molb... #evobio #molbio #virus

My first paper w/ Matt, about how mRNA and protein levels of the same genes should be expected to coevolve. It was carried over from my PhD at Michigan w/ George Zhang, but started too late to be in my thesis. academic.oup.com/mbe/article/...

Cui et al. investigate the evolutionary trajectory leading to dim-light vision in vertebrates, concluding that it evolved via three main stages of molecular adaptation, at the origins of ancestral rhodopsin pigments. 🔗 doi.org/10.1093/molbev/msag096 #evobio #molbio #opsin

@ncochetel.bsky.social & @cantulab.bsky.social publish a new MBE Review on plant pangenomes, outlining major paradigms and showing how graph-based frameworks enable analyses that are difficult with single linear references. 🔗 doi.org/10.1093/molbev/msag087 #evobio #molbio #pangenome #PlantSky

A. Glaser-Schmitt & J. Parsch examined sex-biased gene expression within and among six Drosophila species, detecting contrasting patterns of sex-biased gene expression and turnover between the head and body. 🔗 doi.org/10.1093/molb... #evobio #molbio #drosophila

Bianchini, Zhu, @fcicconardi.bsky.social & @emoody.bsky.social present AliFilter, which uses machine learning to automate manual sequence alignment filtering. 🔗 doi.org/10.1093/molb... #evobio #molbio #compbio

Excited to announce a speedy new multiple-sequence alignment trimming software, led by Giorgio Bianchini: academic.oup.com/mbe/advance-... AliFilter aims to replicate manual trimming through learnt features, make your own model! Tutorial and docs here: github.com/arklumpus/Al... #phylogenetics

Thanks @molbioevol.bsky.social for highlighting the work of @ewanharney.bsky.social as a MSCA fellow @ec.europa.eu at @gonzalezlabbcn.bsky.social! @official-smbe.bsky.social @ibb-botanic.bsky.social

MBE's April Highlight by SMBE Fellow Shady Kuster features Harney and @gonzalezlabbcn.bsky.social transgenerational inheritance research in fruit flies. "A gift from a great-grand-fly—transgenerational epigenetic inheritance of heat shock response" 🔗 doi.org/10.1093/molbev/msag083 #evobio #molbio

Notarnicola, @jacek-radwan.bsky.social @mkonczal.bsky.social et al. investigated missing-self innate immunity in bank vole populations, an important reservoir for Borrelia, demonstrating diversifying selection, likely driven by pathogens. 🔗 doi.org/10.1093/molbev/msag082 #evobio #molbio #immunity

@xavierdidelot.bsky.social et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking, and residual analysis. 🔗 doi.org/10.1093/molbev/msag093 #evobio #molbio #compbio #phylogeny

Was fun to be a part of this study with Enrico Bazzicalupo, José Godoy, and colleagues. Lynx introgression. Check it out!

Our paper is out! We show that a 'missing-self' regulator (CFH) isn't as constrained as we thought, instead shows strong diversifying selection, likely driven by pathogen exploitation (e.g. Borrelia). Highlights how competing selective pressures shape innate immunity academic.oup.com/mbe/advance-...

Our new paper about polymorphism in a key regulator of missing-self innate immunity is now available in @molbioevol.bsky.social Congratulations @rocconotarnicola.bsky.social et al!

A milestone in C4 carbon concentration mechanism evolution: structural remodeling of NADP-malic enzyme in Poaceae academic.oup.com/mbe/article/... @molbioevol.bsky.social

Bazzicalupo et al analyzed introgression in Iberian and Eurasian lynx with the application of a deep convolutional neural network, detecting specific regions of the genome with signals of gene flow in three populations of these species. 🖌️Paula Martin Art 🔗 doi.org/10.1093/molb... #evobio #molbio

Böhm et al. resolve the structural basis of the NADP-malic enzyme divergence in C4 isoforms and propose that tetramerization mitigates aggregation at the high expression levels demanded by the C4 cycle. 🔗 doi.org/10.1093/molb... #evobio #molbio #PlantSky

Publishing Open Access maximizes the impact and visibility of your research. Through our publishing partner Oxford University Press, MBE and GBE offer Read & Publish agreements to many institutions. 🔗 academic.oup.com/pages/open-research/read-and-publish-agreements #societyjournal

@ewanharney.bsky.social & @gonzalezlabbcn.bsky.social show evidence of transgenerational developmental plasticity as a result of heat shock in fruit flies, documenting gene expression and phenotype changes 3+ generations following heat shock. 🔗 doi.org/10.1093/molbev/msag069 #evobio #molbio

Happy to see this one out! Not only for the science, but because it was the first project we led as a group. This paper helped us establish a collaborative culture and good relationships, shaping how we want to work together in the future. I feel lucky to work with this bunch! #popgen #consgen

Kuvassa mauritiuksenkyyhky, Nesoenas mayeri

@xuejingwang.bsky.social Wang et al. analyzed the genomes of three Mauritius bird species that experienced extreme population bottlenecks, showing that evolutionary context is essential for interpreting genomic risk. 📷 Gregory Guida 🔗 doi.org/10.1093/molbev/msag070 #evobio #molbio #congen

📢 New work with @gonzalezlabbcn.bsky.social out now in Molecular Biology and Evolution! Transgenerational effects of heat shock 🥵 on gene regulation 🧬 and fitness-related traits in natural Drosophila 🪰 populations: academic.oup.com/mbe/article/...

Tan et al. present panCG, an integrative pipeline for family-level super-pangenome analysis across coding and noncoding sequences, enabling the reference-free construction of pangene and pan-conserved noncoding sequences. 🔗 doi.org/10.1093/molbev/msag075 #evobio #molbio #pangenomes

First evidence of human adaptation to a toxic chemical Adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT in Argentinean Andes Human Adaptation to Arsenic-Rich Environments 🏺🧪 academic.oup.com/mbe/article/...

@suvamroy.bsky.social @elibbyscience.bsky.social & @peteralind.bsky.social modeled gene expression in P. aeruginosa efflux systems, analysing how the complex regulatory networks associated with efflux pumps might evolve under antibiotic treatments. 🔗 doi.org/10.1093/molbev/msag065 #evobio #molbio

Mulberry, Pilarski, Dinger, and @tanjastadler.bsky.social present a phylodynamic method that generalizes the traditional birth-death approach to model cellular dynamics to an age-dependent phylodynamic model. 🔗 doi.org/10.1093/molb... #evobio #molbio

Ketchum, Matute & Schrider investigated positive selection in Aedes aegypti populations from Africa and the Americas, revealing that soft sweeps are more common than hard sweeps, implying this species can respond quickly to environmental stressors. 🔗 doi.org/10.1093/molbev/msag068 #evobio #molbio

Nocchi et al. compared hybridization and local adaptation within Canada spruce hybrid zones, discovering a complex pattern of introgression, with strong differences in ancestry maintained even across small spatial scales. 🔗 doi.org/10.1093/molbev/msag074 📷️ Sam Yeaman #evobio #molbio #PlantSky

MBE is excited to launch our newest Call for Papers on the Major Transitions of Life, covering all aspects of phylogenomic research. 🔗 academic.oup.com/mbe/pages/call-for-papers-on-the-major-transitions-of-life Guest Editors: Davide Pisani Anja Spang #evobio #molbio #phylogenetics

Great to see Gabriele's paper out in MBE. I was really interested that we found large differences in ancestry maintained across opposite sides of a single valley (presumably with high gene flow). Strong divergent natural selection on cool/wet N-facing vs. hot/dry S-facing slopes.

Happy to share this paper with @samyeaman.bsky.social, now published in Molecular Biology and Evolution! Using replicated hybrid zones, we explored patterns of local adaptation and introgression in spruce and found strong signals even at very fine geographical scales! doi.org/10.1093/molb...

Next, we have the first publication from the amazing Gilmore/Davies lab postdoc, @ben-glass.bsky.social. He wrote this lovely invited review about our favorite transcription factor NFkB! NF-κB: A Diverse and Multifunctional Transcription Factor in Holozoans: academic.oup.com/mbe/article/...

@ben-glass.bsky.social @daviesswphd.bsky.social et al. review recent progress in understanding NF-κB transcription factors in unicellular holozoans, Porifera, Placozoa, and Cnidaria, which are involved in multiple biological functions. 🔗 doi.org/10.1093/molbev/msag059 #evobio #molbio

The April issue of Molecular Biology and Evolution features the work of Gu et al., who performed large-scale phylogenomic analyses of the white-bellied pangolin. 🔗 academic.oup.com/mbe/issue/43/4 🖌️ Ting Bai #evobio #molbio

Our paper is out! We compared introgression maps, both across populations and at the individual level. Some consistencies were observed across maps: A core set of genomic regions, lower background selection in introgressed regions, and some phenotypes were enriched across multiple maps. (1/3)

Yang et al. sequenced ancient individuals from the Bronze Age to historical periods in Xinjiang, revealing divergent genetic profiles of the western and eastern Tianshan, underscoring a complex population-culture interplay. 🔗 doi.org/10.1093/molbev/msag057 #evobio #molbio #humanevolution