Genome Biology and Evolution

GBE | SmithRNAs: A Common Feature among Metazoa

Marturano et al. surveyed the presence and biological features of smithRNAs - a novel class of small noncoding RNAs - across Metazoa, identifying their presence in all species studied, including vertebrates, cnidarians, and arthropods.

🔗 doi.org/10.1093/gbe/evaf208

#genome #evolution

Chromosome-scale Genomes Show Rapid Diversification and Ancient Gene Flow Among Bear Species Abstract. Reconstructions of evolutionary history can be restricted by a lack of high-quality reference genomes. To date, only four of the eight species of

@tywooldr.bsky.social et al. present assemblies for three bear species — the sun, sloth, and Andean bears — and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae.

🔗 doi.org/10.1093/gbe/evaf188

#genome #evolution

Great contribution to GBE, Alex and colleagues, congratulations!

Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years Abstract. Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistoce

Our manuscript on bovine deep-time paleogenomics at Denisova Cave and in the broader mid-latitude Asia is online! doi.org/10.1093/gbe/... 🦬🦴🧬

Main findings in the 🧵 below ⬇️

@cpgsthlm.bsky.social @genomebiolevol.bsky.social #aDNA

GBE | Large Inversion Polymorphisms are Widespread in North American Songbirds The Yellow-bellied Flycatcher (Empidonax flaviventris) is a North American migratory bird species whose nondescript exterior conceals dramatic genomic polymorphisms, including the putative inversion highlighted on the upper left in elevated orange points. Population genomic data from across the species’ breeding range revealed that this large 57-Mb region produces PCA plots with a distinctive 3-cluster pattern (upper right), not present in other parts of the chromosome (lower left). The middle cluster in the 3-cluster PCA corresponds to individuals heterozygous for the polymorphism, while the other two clusters represent the two classes of homozygotes. Pegan & Winger (2025) used whole genome data to find that evidence for large inversion polymorphisms is common even in species that lack known external phenotypic variation, which is frequently associated with inversions in studies on avian genomics. The depicted polymorphism is one of 170 identified across 28 species. Photo: Georg Langebrake.

Pegan & Winger tested whether inversions are common within populations without phenotypic polymorphisms in 28 N. American bird species, finding that many polymorphisms are present at balanced frequencies, but possibly segregating neutrally.

🔗 doi.org/10.1093/gbe/evaf205

#genome #evolution #birds

GBE | De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods

Grandchamp, @drdomain.bsky.social et al. publish a new Review on commonly used methods for de novo gene detection, address the limitations of nomenclature and detection methods, and establish a de novo gene annotation format to standardize reporting

🔗 doi.org/10.1093/gbe/evaf197

#genome #evolution

New genome assembly of a land snail🐌🎉

GBE | Nuclear and Mitochondrial Genome Assemblies of Indrella ampulla, a Terrestrial Gastropod Endemic to the Western Ghats A) A red morph individual of Indrella ampulla (PC:Dr. Kushankur Bhattacharyya) B) PSMC plot illustrating historical effective population size trends (black line) of Indrella ampulla over time. The X-axis represents time in years before the present, scaled by the generation time (g) and mutation rate (μ), and the Y-axis shows the effective population size (Ne). LGM represents Last Glacial Maximum and LIG represents Last Interglacial period.

Krishnan et al. present annotated nuclear and mitochondrial genome assemblies of Indrella ampulla, a color polymorphic land snail endemic to the Western Ghats of India. The assembly has N50 of 632 kb, and 93.5% BUSCO completeness.

🔗 doi.org/10.1093/gbe/evaf199

#genome #evolution #snail

GBE | Inferring Domestic Goat Demographic History Through Ancient Genome Imputation

@jolijnerven.bsky.social @gingerhowley.bsky.social et al. used genotype imputation on published goat palaeogenomes to study their domestication; their findings challenge long-standing assumptions about domestication bottlenecks.

🔗 doi.org/10.1093/gbe/evaf181

#genome #evolution #domestication

Congratulations on the great paper, Jolijn, Kevin and colleagues!

Check out our paper, we now included a comparison between glimse1 and glimpse2!

Inferring Domestic Goat Demographic History Through Ancient Genome Imputation Abstract. Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a chall

Our paper on imputation of ancient goat genomes is now available at GBE - congratulations to @jolijnerven.bsky.social #aDNA

Co-authors on Bluesky: @alexjprobst.bsky.social @emilruff.bsky.social l @geomicrosoares.bsky.social

Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

@katharinasures.bsky.social @probstlab.bsky.social et al. analysed CRISPR-Cas systems of metagenome-assembled genomes from two subsurface environments, shedding new light on the diversity of CRISPR spacers in natural microbial communities.

🔗 doi.org/10.1093/gbe/evaf201

#genome #evolution #CRISPR

Very proud to share our perspective on "The Genomic Kaleidoscope" doi.org/10.1093/gbe/... out @genomebiolevol.bsky.social

Precious collaboration w/ colleagues across the world, led alongside the amazing @mbrasovives.bsky.social and the one&only @jrotwitguez.bsky.social

Check out his great thread!

Congratulations on publishing this great article, Alexander and colleagues, and thank you for publishing with GBE!

Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬

Have a read!! ➡️ doi.org/10.1093/gbe/...

@emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!

🚨 New Paper Alert!

Our latest perspective piece is out, and it’s one you won’t want to miss- 'The Genomic Kaleidoscope'

academic.oup.com/gbe/article/...

Co-lead by @mbrasovives.bsky.social @jrotwitguez.bsky.social & @diegoharta.bsky.social

📌 Check the full post here👇

First publication during my PhD is now accepted! Thanks SMBE24 'Hidden Dimensions' team for making it happen.

Great to see this exciting perspective by young evolutionary biologists lead by the amazing @mbrasovives.bsky.social out!

Authors include @mbrasovives.bsky.social @diegoharta.bsky.social @jrotwitguez.bsky.social @luisapallares.bsky.social @jphippstan.bsky.social @aruizherrera.bsky.social @theafrogers.bsky.social @hhydrochaerus.bsky.social

GBE | The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity

Brasó-Vives et al. publish a new Perspective in GBE, highlighting underexplored dimensions of genomic variation that contribute to phenotypic diversity beyond the DNA sequence, contributing to our understanding of genome evolution.

🔗 doi.org/10.1093/gbe/evaf204

#genome #evolution

Are you looking for a brief and clear perspective on the factors associated with between-individual variation that go beyond SNPs? Check out the thread below 👇 It was a pleasure to particpate in this, and shout-out to James @jphippstan.bsky.social who led our contribution to this perspective🧬

GBE | An Ocean of Opsins

@xodroont.bsky.social et al. explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, identifying opsins across the different metazoan groups.

🔗 doi.org/10.1093/gbe/evaf189

#genome #evolution #opsins

Fantastic paper, fantastic thread - thank you, Juan and colleagues, for this great contribution to GBE!

🔊New perspective piece out @genomebiolevol.bsky.social.

"The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity" 💡🌀🌈
doi.org/10.1093/gbe/...

Co-led with @mbrasovives.bsky.social and @diegoharta.bsky.social

Check out our thread! 🧵👇 (1/n)

Great work Elias and colleagues - thank you for publishing your article with GBE!

🧩 Thrilled to share our new paper in @genomebiolevol.bsky.social !

We present a comprehensive review of de novo gene emergence — providing a classification of current detection methods and a roadmap for addressing major challenges in the field of gene birth from non-genic sequences.

Kyle McElroy is a postdoctoral researcher at Iowa State University, using comparative genomics and molecular genetics to investigate how light-sensing systems evolve. He is interested in connecting organismal and genomic evolution, including reproductive mode with genome architecture and sensory organs with gene recruitment.

@kylemcelroy.bsky.social is a postdoctoral researcher at Iowa State University, investigating how light-sensing systems evolve. He is interested in connecting organismal and genomic evolution, including reproductive mode with genome architecture and sensory organs with gene recruitment.

Joseph Jalinsky, visiting assistant professor at the U. Iowa investigates the genomics of asexual reproduction in lichenized fungi and snails, immune gene evolution in the snail hosts of schistosomiasis, and how R-loops drive DNA damage in C. elegans, using comparative genomics and bioinformatics.

Joseph Jalinsky, visiting assistant professor at the U. Iowa investigates the genomics of asexual reproduction in lichenized fungi and snails, immune gene evolution in the snail hosts of schistosomiasis, and how R-loops drive DNA damage in C. elegans, using comparative genomics and bioinformatics.