Gemma Martínez Redondo

nature.comConvergent genomic trajectories shape adaptation to life on land across animal lineages - Nature CommunicationsAnimals have moved from water to land many times, but whether they used the same genetic routes has remained unclear. This study shows that independent land transitions relied mostly on ancient, conse...

What a nice feeling to come back from holidays and see the last paper of my PhD finally published in its final form in @natcomms.nature.com !! www.nature.com/articles/s41... Want to learn a bit more about the genomic basis of animal terrestrialization? A thread 🧵1/14

Many questions about animal terrestrialization remain unanswered: how many times did it happen? How did each lineage reshape its molecular networks to survive on land? Our results provide a first glimpse into many understudied animals and, hopefully, a starting point for future research. 13/14

Finally, huge thanks to our supervisor, @rosafernandez.bsky.social, and our amazing co-authors! Judit, Nuria, @vargaschavezc.bsky.social, @cefafalopodo.bsky.social, Belén, Raquel, Javi, Libe, Iñaki, Cristina, Eduard, @bombarelya.bsky.social❤️ 14/14

So, did animals use the same genomic solution when moving to land? Not really. Instead, each terrestrial lineage independently recruited different sets of genes that converged functionally! 11/14

doi.orgConvergent genome evolution shaped the emergence of terrestrial animals - NatureComparisons of 154 genomes from 21 animal phyla and outgroups have been used to reconstruct ancestral adaptation to life on land across 11 distinct terrestrialization events, revealing strong evidence...

Interestingly, @jialinwei.bsky.social et al. independently reached a broadly similar conclusion, providing complementary evidence for the idea that different lineages can arrive at similar adaptive outcomes through different molecular routes. doi.org/10.1038/s415... 12/14

We identified 130 OGs that could distinguish aquatic from terrestrial species, of which 81 were also identified in our stress experiments. Most originated before terrestrialization, but their copy-number patterns were mainly lineage-specific. 9/14

Interesting examples include CYP450s, linked to plant terrestrialization, and FMOs, involved in fish odour! Or Selenoprotein L, lost in all terrestrial species. 10/14

However, even if not shared, genes had similar functions and were associated with the same biological pathways, suggesting convergence at the functional level rather than at the gene level. 7/14

But stress genes are only part of the picture. What about genes involved in development, anatomy or biochemistry? To look into this, we trained a machine learning model to distinguish between aquatic and terrestrial species based on the number of genes in each OG. 8/14

But genomes are not everything. Led by the brilliant @klarael.bsky.social (co-first author), we exposed aquatic and terrestrial animals from 7 phyla to environmental stressors associated with land (O2, desiccation…), and used gene co-expression networks to identify shared stress responses. 5/14

Surprisingly, only 42 orthogroups (OGs) out of the 50k were shared across all the species in our stress experiments. These OGs originated before terrestrialization, pointing to independent co-option of pre-existent genes instead of a “universal terrestrialization toolkit”. 6/14

Many naturalists and scientists have studied this transition from morphological and physiological perspectives, but its molecular basis has been much less explored. Did different animals use the same molecular solutions to adapt to life on land, or did each lineage find its own way? 3/14

To answer that question, we first surveyed the genomes of almost 1000 animals, with 15 terrestrialization events represented, and found that they were characterised by higher gene loss than gain. 4/14

science.orgA comprehensive and accessible database of jawed-vertebrate ohnologsA reliable ohnolog database yields insights into vertebrate evolution.

Animals transitioned from water to land in at least 9 animal phyla. Tetrapods and arthropods are the best-known examples, but other, much less studied animals, like flatworms or nemerteans changed their habitat too! 2/14

Gemma Martínez Redondo reposted

WGDip

@wgdip.bsky.social

10 Aug

Congratulations to Lukasz Niezabitowski, @roisinlong.bsky.social , @phylogenie.bsky.social & Aoife McLysaght on their paper “A comprehensive and accessible database of jawed-vertebrate ohnologs” 🐟🧪 Read here: www.science.org/doi/10.1126/... Access the database here: ohnologs.com

Gemma Martínez Redondo reposted

22 Apr

The SMBE Community Service Award for 2026 goes to Aoife McLysaght @ucddublin.bsky.social, who has served our society in many roles throughout the years. Visit our website to learn more about the SMBE Faculty Awards 🔗 smbe.org/faculty-awards #society

@rosafernandez.bsky.social

7 Nov 2025

Happy to see my illustration featured on the cover!

Trends in Genetics@cp-trendsgenetics.bsky.social

TiG’s November issue is live! Huge thanks to Rosa Fernández (@rosafernandez.bsky.social) and colleagues for the cool cover image! Check out their Review on massive genome rearrangements in clitellates. The entire contents list with links to articles is at www.cell.com/trends/genet...

Gemma Martínez Redondo reposted

Rosa Fernández

7 Oct 2025

How did animals repeatedly conquer land? 🌊➡️⛰️ We analysed ~1,000 gene repertoires (24M genes!) from all animal phyla to uncover how this happened. Work led by @gemmaeling.bsky.social & Klara Eleftheriadi, both first coauthors of this titanic effort! www.biorxiv.org/content/10.1...

biorxiv.orgIndependent genomic trajectories shape adaptation to life on land across animal lineagesHow animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared gen...

Gemma Martínez Redondo reposted

Instituto de Neurociencias CSIC-UMH

@neuroalc.bsky.social

26 Aug 2025

#SciencePhoto_IN “Stained glass axons” Author: Patricia Ordoño Lab: @eloisaherrera.bsky.social "Retinal ganglion cell axons from mouse optic nerve. In this image, myelinated axons appear as colourful flowers on a green field of unmyelinated axons. With a @zeiss-microscopy.bsky.social Sigma 300 VP."

Gemma Martínez Redondo reposted

Rosa Fernández

@rosafernandez.bsky.social

15 Aug 2025

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

nature.comFANTASIA leverages language models to decode the functional dark proteome across the animal tree of lifeCommunications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

Gemma Martínez Redondo reposted

Janina Rinke

@jannelrinke.bsky.social

23 July 2025

If you‘re at #SMBE2025 and you still have a tiny little bit of energy left for the last day tomorrow, I‘d be happy to see you joining my talk at 10:20 tomorrow morning in Room 2, where I‘ll be talking about how TEs can reshape entire genome structures in ants! 🐜🧬👩🏽‍🔬

Gemma Martínez Redondo reposted

Roli Roberts

@roliroberts.bsky.social

I can't post @gemmaeling.bsky.social's results, but she started her talk at #SMBE2025 with a great quote from Philippe Janvier about the ancient terrestrial environment being as alien to our marine ancestors as the surface of the moon is to us now.

Gemma Martínez Redondo reposted

Replying to @official-smbe.bsky.social

Gemma Martínez Redondo reposted

Replying to @official-smbe.bsky.social

Gemma Martínez Redondo reposted

Molecular Biology and Evolution

This morning ended with the Graduate Student Excellence Symposium, where our eight awardees presented their great work. 👏 Congratulations to all GSEA recipients! #SMBE2025

Gemma Martínez Redondo reposted

@molbioevol.bsky.social

30 June 2025

@svalver.bsky.social et al. analyzed 15 years of Gene Ontology evolution, finding that GO changes not just incrementally, but also via major, curator-driven restructurings. 🔗 doi.org/10.1093/molbev/msaf148 #evobio #geneontology

Gemma Martínez Redondo reposted

Sergi Valverde

@svalver.bsky.social

18 June 2025

A new paper in Nature Ecol & Evol by @rosafernandez.bsky.social et al. shows a #punctuated burst of genome evolution in #annelids as they transitioned from marine to land and freshwater habitats.

Gemma Martínez Redondo reposted

Institut de Biologia Evolutiva (IBE)

@ibe-barcelona.bsky.social

18 June 2025

Earthworms reveal an evolutionary mechanism which could defy Darwin🪱🧬 📕A new #IBE-led comparative genomics study of earthworms and their marine relatives shows that worms colonised land through evolutionary jumps.🧵 #UnravellingEvolution 👉https://shorturl.at/IyWqH

Gemma Martínez Redondo reposted

Sergi Valverde

@svalver.bsky.social

11 June 2025

Can the structure of knowledge evolve like life itself? In our new MBE paper, we show that the Gene Ontology evolves through mechanisms shared with cultural and technological systems—reuse, modularity, and curator-driven restructuring. Here’s what we found: 🧵

Gemma Martínez Redondo reposted

Society for the Study of Evolution

@sse-evolution.bsky.social

22 May 2025

Congratulations to this year's Hamilton Award finalists! 🎉 Join us Thursday, May 29 to hear these outstanding student talks. See the full schedule on the meeting website: www.evolutionmeetings.org/program-over... @evolmtg.bsky.social

Gemma Martínez Redondo reposted

Institut de Biologia Evolutiva (IBE)

@ibe-barcelona.bsky.social

8 May 2025

📣 Congratulations to Gemma Martínez, PhD student at @ibe-barcelona.bsky.social, on winning the @official-smbe.bsky.social Graduate Student Excellence Award! 🏆🎉 A fantastic recognition of her work in #UnravellingEvolution 🌍🧬

Society for Molecular Biology and Evolution@official-smbe.bsky.social

🐜 Today's GSEA focus is on Gemma Martínez Redondo, PhD candidate @ub.edu Gemma's research combines traditional phylogenetics, phylogenomics, and machine learning to understand the genomic basis of terrestrialization across animals More on Gemma ⬇️ and follow her: @gemmaeling.bsky.social

Gemma Martínez Redondo reposted

8 May 2025

Our latest GSEA winner is Alba Nieto Heredia, PhD student @psl-univ.bsky.social Alba's popgen and computational biology research focuses on population structure and its critical role in demographic inference. More on Alba ⬇️ and follow her: @albanietoh.bsky.social

Gemma Martínez Redondo reposted

25 Apr 2025

👋 For the next two weeks, we will highlight our GSEA recipients - we start with Hannah Verdonk, Bioinformatics PhD student at @temple.edu Hannah works on improving bioinformatic tools to account for weak selection on synonymous codon usage. 💻 More on Hannah ⬇️ and follow her: @hverdonk.bsky.social

Gemma Martínez Redondo reposted

27 Apr 2025

Meet Jacky Kaiyuan Li, Ph.D. student @ucberkeleyofficial.bsky.social, and winner of the Graduate Student Excellence Award. Jacky's research interests lie in statistical modeling for evolutionary biology and population genetics. 📊 Follow Jacky on LinkedIn: www.linkedin.com/in/jacky-kai...

Gemma Martínez Redondo reposted

29 Apr 2025

Huangyi He from Zhejiang University is on today! Huangyi's research focuses on the evolutionary and developmental mechanisms behind sperm heteromorphism and sex chromosome evolution in Drosophila. 🪰 More ⬇️ and follow Huangyi on social media X: @HuangyiH92641

Gemma Martínez Redondo reposted

30 Apr 2025

🪰 GSEA winner Philipp Hummer - PhD student @popgenviennaphd.bsky.social - is on today! Philipp is working at the intersection of genomics, museum collections, insect evolution, and transposable elements. More on Philipp ⬇️ and follow him: @philipphummer.bsky.social

Gemma Martínez Redondo reposted

2 May 2025

🧬 Today, we present GSEA winner Dylan Sosa, PhD candidate at the University of Chicago. Dylan investigates the rate, pattern, and mechanisms of transfer RNA gene duplication to understand its propagation and maintenance in D. melanogaster. More on Dylan ⬇️ and follow him: @dylansosa.bsky.social

Gemma Martínez Redondo reposted

6 May 2025

🌸 Today's Graduate Student Excellence Award highlight is Aidan Short, NSF Postdoctoral Fellow @sc.edu Aidan studies how divergent pollinator adaptation contributes to genome divergence and speciation. More on Aidan ⬇️ and follow him: @aidanwshort.bsky.social