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Gemma Martínez Redondo

@gemmaeling.bsky.social
220 followers 264 following 21 posts

Postdoc at Trinity College Dublin on whole-genome duplications 🧬🧬 Previously: PhD on the genomic🧬 basis of animal terrestrialization 🦀🐙🐟🌊⏭🕷🐌🦇 at IBE, CSIC-UPF She/her

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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
comic from @beetlemoses.bsky.social showing tetrapod leaving water to avoid paying a debt
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
doi.org
Convergent genome evolution shaped the emergence of terrestrial animals - Nature
Comparisons 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...
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
Illustration of the 15 terrestrialization events in the study. Phylogenetic tree showing their relationships and background as blue (sea/freshwater) and green (land)
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
Interesting examples include CYP450s, linked to plant terrestrialization, and FMOs, involved in fish odour! Or Selenoprotein L, lost in all terrestrial species. 10/14
d, Functions from the top ten OGs as ranked by the machine learning model. OG name was obtained with BLASTp. GO terms on the right were predicted using FANTASIA.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
a, Simplified workflow of machine learning analysis (full workflow in Supplementary Fig. S272d). The pie chart shows the number of OGs from the top 130 that contain hubs from stress-related modules in GCN. b, Balanced accuracy for each model trained across all iterations of the dRFE workflow for training and testing datasets of all folds. The dashed dark green line shows the iteration where we select the top OGs. c, Logloss values for each model trained across all iterations of the dRFE workflow for training and testing datasets of all folds. The dashed dark green line shows the iteration where we select the top OGs.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
Simplified workflow of machine learning analysis. Input OGs are fed into XGBoost classifier with Kfold stratified cross validation and dRFE. Output is separation between aquatic and terrestrial, and top OGs
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
a, Graphical illustration of constellation plots of gene functions across species. Each dot represents a species and each polygon a distinct functional cluster. On the left side, each species belongs to a different cluster, showing the lack of functional convergence, and on the right side, all species cluster together, representing functional convergence. b, Constellation plots of functions of hub genes across 17 aquatic and terrestrial species for each experimental condition. Each polygon represents a distinct functional cluster formed by species with similar GO annotations, despite no orthogroup-level overlap across species. Cluster exemplars indicate the species that act as centroid in each cluster. The presence of hub genes from multiple species within the same functional cluster demonstrates convergence in stress-response roles across independent lineages. Only six experiments are shown for demonstration purposes, given that all experiments showed the same pattern (see also Supplementary Fig. S141). Functional convergence measured as GO-annotation similarity was inferred by calculating Wang semantic similarity between species’ GO term sets using the Best-Match Average method, followed by clustering with Affinity Propagation.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
d UpSet plot showing overlap of module-associated orthogroups resulted from species-specific co-expression networks. Dots connect species that have a number of module-associated orthogroups in common, the number indicated in each bar from the barplot on top.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
a Overview of abiotic stress experiments, gene co-expression network construction and proteomic detection of stress-related genes across 17 species from seven animal phyla, exposed to standardised stressors mimicking terrestrial abiotic factors.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
a Mirror phylogeny of 960 animal species plus outgroups. Circles at each internal branch represent the square-root-scaled number of orthogroups gained (left, blue) and lost (right, brown). Terrestrial lineages are highlighted in yellow; the right phylogeny labels individual terrestrial lineages, while the left phylogeny indicates the phyla containing those lineages. Exact numbers of OGs gained and lost can be found in Supplementary Fig. S1. b Phylostratigraphic origin of all genes in all nodes in a representative species (the earthworm Norana najaformis, Annelida), highlighting the gene gain burst in Protostomia (in yellow). c Comparison of gene gain and loss across the 15 terrestrial clades with independent terrestrialisation events.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
First tetrapod leaving water saying "C'mon out, folks! It looks like we're the first ones here." On the right, two myriapods say "First ones here? Please! We've been here for 60 million years!" and "I...I...I wonder what they eat?"
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
a Animal tree of life highlighting the phyla where there has been at least one terrestrialisation event. b Main animal terrestrialisation events within animal phyla discussed in this work (in bold), with the species used in the stress experiments below. c Simplified view of paths towards terrestrial life in animals, and the differences in some abiotic factors between habitats.
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Gemma Martínez Redondo @gemmaeling.bsky.social · 03/09/2026
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
nature.com
Convergent genomic trajectories shape adaptation to life on land across animal lineages - Nature Communications
Animals 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...
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WGDip @wgdip.bsky.social · 10/08/2026
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
science.org
A comprehensive and accessible database of jawed-vertebrate ohnologs
A reliable ohnolog database yields insights into vertebrate evolution.
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 22/04/2026
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
SMBE Community Service Award - Aoife McLysaght
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Gemma Martínez Redondo @gemmaeling.bsky.social · 07/04/2026
Congratulations, Jialin!
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Gemma Martínez Redondo @gemmaeling.bsky.social · 15/11/2025
Congrats, Jacob! It's an amazing pice of work
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Gemma Martínez Redondo @gemmaeling.bsky.social · 15/11/2025
Congratulations!
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Gemma Martínez Redondo @gemmaeling.bsky.social · 07/11/2025
Happy to see my illustration featured on the cover!
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Rosa Fernández @rosafernandez.bsky.social · 07/10/2025
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.org
Independent genomic trajectories shape adaptation to life on land across animal lineages
How 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...
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Instituto de Neurociencias CSIC-UMH @neuroalc.bsky.social · 26/08/2025
#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."
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Gemma Martínez Redondo @gemmaeling.bsky.social · 22/08/2025
Thanks, Rob!❤️
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Rosa Fernández @rosafernandez.bsky.social · 15/08/2025
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.com
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
Communications 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...
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Janina Rinke @jannelrinke.bsky.social · 23/07/2025
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! 🐜🧬👩🏽‍🔬
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Gemma Martínez Redondo @gemmaeling.bsky.social · 23/07/2025
This is great, Jacob! I'm sure you will do an amazing work❤️
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Roli Roberts @roliroberts.bsky.social · 21/07/2025
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.
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 21/07/2025
Jacky Kaiyuan Li - Graduate Student Excellence SymposiumPhilipp Hummer - Graduate Student Excellence SymposiumHuangyi He - Graduate Student Excellence SymposiumAlba Nieto Heredia - Graduate Student Excellence Symposium
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 21/07/2025
Dylan Sosa - Graduate Student Excellence SymposiumAidan Short - Graduate Student Excellence SymposiumGemma Martínez-Redondo - Graduate Student Excellence SymposiumHannah Verdonk - Graduate Student Excellence Symposium
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 21/07/2025
This morning ended with the Graduate Student Excellence Symposium, where our eight awardees presented their great work. 👏 Congratulations to all GSEA recipients! #SMBE2025
Graduate Student Excellence Symposium recipients at SMBE2025
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Molecular Biology and Evolution @molbioevol.bsky.social · 30/06/2025
@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
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Sergi Valverde @svalver.bsky.social · 18/06/2025
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.
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Institut de Biologia Evolutiva (IBE) @ibe-barcelona.bsky.social · 18/06/2025
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
Picture of the giant earthworm Norana najaformis, whose genome was newly sequenced for this study. Credit to Pau Balart-García.
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Sergi Valverde @svalver.bsky.social · 11/06/2025
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: 🧵
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Society for the Study of Evolution @sse-evolution.bsky.social · 22/05/2025
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
Text: Virtual Evolution 2025. Society for the Study of Evolution Hamilton Award Symposium. Thursday, May 29, 1:30 PM - 7:30 PM Eastern (GMT-4). 2025 Finalists: Meaghan Clark, Dylan DeBaun, Devon DeRaad, Simon Innes, Josh Knecht, Kip Lacy, Gina Lamka, Prothama Manna, Gemma Martinez-Redondo, David Peede, Gabriel Preising, Jeremy Summers, David Tian, Matthew Treaster, and Amanda Vieira da Silva.
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Institut de Biologia Evolutiva (IBE) @ibe-barcelona.bsky.social · 08/05/2025
📣 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 🌍🧬
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 08/05/2025
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
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 25/04/2025
👋 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
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 27/04/2025
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...
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 29/04/2025
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
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 30/04/2025
🪰 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
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 02/05/2025
🧬 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
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 06/05/2025
🌸 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
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Gemma Martínez Redondo @gemmaeling.bsky.social · 05/05/2025
Honored to receive this award — thank you! Excited to present my research at #SMBE2025 in Beijing!
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