Lightnews — Scholar-powered news

Rosa Fernández @rosafernandez.bsky.social · 1d

Big shout out to all the collaborators, particularly @cefafalopodo.bsky.social @aubombarely.bsky.social @vargaschavezc.bsky.social Judit Salces-Ortiz & Nuria Escudero, for endless adventures together while working on this project! 🙏

1 1 1

Rosa Fernández @rosafernandez.bsky.social · 1d

This study is a core outcome of our @erc.europa.eu
project SEA2LAND, revealing how life’s move from sea to land was driven not by gene invention, but by genomic flexibility uncovered through a multi-omics, systems biology lens. 🌊➡️🌍 @ibe-barcelona.bsky.social @csic.es

1

Rosa Fernández @rosafernandez.bsky.social · 1d

To truly understand life’s major evolutionary transitions, counting genes isn’t enough. We need multi-omics, systems-level approaches that reveal how genomes are rewired to meet new ecological challenges. Only then can we see how evolution turns old parts into new solutions.

1 1

Rosa Fernández @rosafernandez.bsky.social · 1d

The transition to land was powered by flexibility, not innovation, with animals reshaping old genomic parts to solve new problems.

1

Rosa Fernández @rosafernandez.bsky.social · 1d

Machine learning identified a small set of ancient gene families whose copy-number shifts correlate with habitat, not via shared expansions, but through independent, lineage-specific trajectories across Metazoa. No common gene families between terrestrial lineages identified!

1

Rosa Fernández @rosafernandez.bsky.social · 1d

Adaptation to land thus emerged through functional convergence and genomic network reorganization, not through repeated invention of new genes.

1 2

Rosa Fernández @rosafernandez.bsky.social · 1d

Stress-response multiomics experiments in 17 species from 7 animal phyla revealed that different lineages recruit distinct genes to face similar challenges, yet converge in function, not gene identity.

1 1

Rosa Fernández @rosafernandez.bsky.social · 1d

Across 15 independent terrestrialization events, most adaptive genes (at least related to response to the environment) were ancient, predating land life.

1 1

Rosa Fernández @rosafernandez.bsky.social · 1d

Using comparative genomics, transcriptomics, proteomics & machine learning, we found that gene loss, not gain, dominates at the evolutionary nodes where animals transitioned to land.

1 3

Rosa Fernández @rosafernandez.bsky.social · 1d

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...

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...

www.biorxiv.org

1 12 31

Reposted by Rosa Fernández

ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 28d

#ERGAReads | Clitellates - terrestrial & freshwater annelids - underwent dramatic #genome reshuffling, losing synteny with their marine relatives. This rare burst of genomic change reshaped chromosome structure in the group
🔗 rdcu.be/euNbT
#genomics #evolution #Annelida @rosafernandez.bsky.social

3 8

Rosa Fernández @rosafernandez.bsky.social · Aug 15

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...

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...

www.nature.com

2 30 57

Reposted by Rosa Fernández

Trends in Genetics @cp-trendsgenetics.bsky.social · Jul 7

"Breaking bad: when clitellate genomes go rogue"
by Rosa Fernández (@rosafernandez.bsky.social) & colleagues

"Clitellate genomes are the result of a profound genome reshaping...What triggered such extreme rearrangements...?"

FREE till Aug. 24th at this link:
authors.elsevier.com/a/1lNmQcQbJF...

Figure 1. From conserved macrosynteny to genome atomization in clitellates.

2 10

Rosa Fernández @rosafernandez.bsky.social · Jul 7

If you enjoyed our recent paper on massive genomic rearrangements in clitellates, don't miss our recent review on the topic, where we discuss some hypothesis and implications of our findings 👇🪱🧬💥👇 @cp-trendsgenetics.bsky.social @ibe-barcelona.bsky.social authors.elsevier.com/a/1lNmQcQbJF...

authors.elsevier.com

2 5 17

Reposted by Rosa Fernández

Academia Joven de España @academiajoven.bsky.social · Jul 3

Hoy es la entrega de los #PNI y desde la
@academiajoven.bsky.social
queremos felicitar a toda la gente premiada, en especial a las #AcadémicasJóvenes:

Cristina Blanco
Víctor Vilarrasa
@veronicabolon.bsky.social
@mariaescesc.bsky.social
@bpelaz1.bsky.social
@rosafernandez.bsky.social

2 3 8

Rosa Fernández @rosafernandez.bsky.social · Jun 18

Glad to see this paper finally out! An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
@natecoevo.nature.com @ibe-barcelona.bsky.social @csic.es @erc.europa.eu www.nature.com/articles/s41...

An episodic burst of massive genomic rearrangements and the origin of non-marine annelids - Nature Ecology & Evolution

An analysis of annelid genomes reveals massive reshuffling of chromosomes in the ancestral lineage leading to clitellates, a clade composed of non-marine annelids, with potential implications for the ...

www.nature.com

3 39 79

Reposted by Rosa Fernández

CSIC @csic.es · Jun 18

🐛Las lombrices de tierra revelan un mecanismo evolutivo que desafiaría a #Darwin

🧬El @ibe-barcelona.bsky.social muestra cómo los gusanos de mar rompieron su genoma para reconstruirlo de forma radicalmente distinta cuando pisaron la tierra hace 200 millones de años

👉 https://shorturl.at/Q0nTc

5 27

Reposted by Rosa Fernández

Andrej Spiridonov @andrejpaleo.bsky.social · Jun 18

Punctuated Equilibria gain the momentum!
🧪 ⚒️ #Paleobio #Geology #EvoBio

Sergi Valverde @svalver.bsky.social · Jun 18

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.

3 28

Reposted by Rosa Fernández

Sergi Valverde @svalver.bsky.social · Jun 18

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.

5 60 190

Reposted by Rosa Fernández

Sergi Valverde @svalver.bsky.social · Jun 11

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: 🧵

2 15 41

Rosa Fernández @rosafernandez.bsky.social · May 22

Happy #BiodiversityDay! What a pleasure to enjoy a symposium in Mallorca on this topic jointly organised by the Balear Center of Biodiversity and @ibe-barcelona.bsky.social. Cheers to all living forms!! 🧬🪱🐙🌽☘️🌵🐦🦠

4 13

Rosa Fernández @rosafernandez.bsky.social · May 8

The afternoon session of today is dedicated to TE annotation & deep learning-based genome annotation, again with the amazing
@bombarelya.bsky.social

7

Rosa Fernández @rosafernandez.bsky.social · May 8

The 4th day of our workshop starts with a super interesting session on OMAnnotator with
@whynevers.bsky.social
on how to use orthologous groups to make better gene sets for genome annotation 🧬🧩🕵️ @ibe-barcelona.bsky.social

6

Rosa Fernández @rosafernandez.bsky.social · May 7

The afternoon session of our workshop is dedicated to functional annotation & language models, with the great @amrojasm.bsky.social. She will guide us through the theory behind them and we'll talk about our recently-developed tool to explore the dark proteome: FANTASIA! ✨ @ibe-barcelona.bsky.social

1 1 7

Rosa Fernández @rosafernandez.bsky.social · May 7

The morning session of our workshop on genome annotation is dedicated to long reads, and we couldn't have better faculty! Many thanks
@anaconesa.bsky.social
and Pablo Atienza for guiding us through it! @ibe-barcelona.bsky.social

1 1 7