Tessera
Folgen

Silvia Prieto

@silviaprietob.bsky.social

🔎 Bioinformatics, Comparative/ Biodiversity/ Conservation Genomics & Marine Bio 👩‍💻 PhD student @DessimozLab @unil_qb 👩‍🎓 MSci @UoABioSci

10 Posts189 Follower293 Folgt
Dongwook Kim@dongwookkim.bsky.social · 8mo ago

Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n 📃 doi.org/10.64898/2026.01.26.701724

AmpliPhy improves gene trees by adding homologs without affecting alignments

In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical benchmark to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 216623, 10005715

doi.org

Silvia Prieto@silviaprietob.bsky.social · last yr.

You can find my poster "Microsynteny and functional relatedness in eukaryotes" at the slot 209 today and visit at around 5 if you want to know more or talk anything synteny, gene order, functional association or genome evolution related :) #ESEB2025

Bild
Silvia Prieto@silviaprietob.bsky.social · last yr.

It's been an exciting first day of #ESEB2025, with a great opening talk by Michael Lynch. Moreover, a very timely recap on lessons learnt in pines climate change adaptations by Santiago González, during a week marked by unprecedented wildfires in Spain. [Among many, many other interesting talks]

BildBild
Daniel Bruno@apetijo.bsky.social · last yr.

¿Has oído alguna vez hablar de los #incendios submarinos?🔥🌊 Hoy, @danigomezgras.bsky.social de @medrecover.bsky.social nos explica las consecuencias ecológicas y el impacto de este fenómeno, cada vez más intenso y frecuente, en los corales mediterráneos 🌡️ ecomandanga.wordpress.com/2025/07/23/i...

Incendios submarinos: las olas de calor son un infierno para los corales mediterráneos

Cantaba Mecano en los años 90 que «Hawaii y Bombay son dos paraísos». Lo que no podía imaginar Ana Torroja en aquel entonces es que, en el contexto actual de crisis climática, hasta el paraíso pued…

ecomandanga.wordpress.com

Silvia Prieto@silviaprietob.bsky.social · last yr.

Check out our recent paper “Tracing the evolution of key traits in dorid nudibranchs”! 🧬🐌 dx.plos.org/10.1371/jour... Nudibranchs are a fascinating and diverse group of molluscs, unique and interesting systems in ecology and evolutionary biology. @molluscular.bsky.social

Tracing the evolution of key traits in dorid nudibranchs

Reconstructing trait evolution is critically important for elucidating the processes generating biodiversity. However, this work is in its infancy in non-model clades for which we lack a basic underst...

dx.plos.org