PhyloSIB, our annual workshop about molecular evolution, phylogenetics, and comparative phylogenomics took place Wednesday in Lausanne as a satellite event preceding Biology25.

15 SIB Groups gave presentations on recent developments in the field. We had a full house with 80 participants. A lively and fruitful open discussion forum concluded the workshop.

@richardneher, @marcrr, @dessimoz, @mariedangles, @rmwaterhouse

Your morning #coffee may be more than a half million years old.

#genomics #agriculture #phylogenomics

https://phys.org/news/2024-04-morning-coffee-hundreds-thousands-years.html

Computational tools fuel reconstruction of new and improved #bird family tree.

#bioinformatics #phylogenomics #B10K #evolution #biodiversity

https://phys.org/news/2024-04-tools-fuel-reconstruction-bird-family.html

Unraveling the #evolutionary origins of #umami and sweet #taste preferences.

#sensing #TAS1R #phylogenomics

https://phys.org/news/2023-12-unraveling-evolutionary-umami-sweet.html

Single-celled #protists in the #guts of #animals thrive without #mitochondria, study finds.

#oxymonads #evolution #phylogenomics

https://phys.org/news/2023-12-single-celled-protists-guts-animals-mitochondria.html

In my reading list:

AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

https://www.biorxiv.org/content/10.1101/2023.10.06.561091v2

PhylteR, our new tool for filtering phylogenomics datasets, is now out!

https://doi.org/10.1093/molbev/msad234

PhylteR identifies with precision, from a collection of gene trees, the "outlier" sequences responsible for a lack of concordance among gene trees.

How it works? A small thread

Another phylogenetic controversy: are Arachnida actually monophyletic?

I am puzzled by this Ballesteros et al 2022 article:
https://academic.oup.com/mbe/article/39/2/msac021/6522129

Traditionally, horseshoe crabs (Xiphosura) are viewed as the closest parent of arachnids, but here they find that they are nested within, when coping for artefacts (saturation, taxon occupancy)...

I'm not expert of arachnids, but this does not seem in line with the fossil record, so what's wrong, #orthology again?

Dear All,

The Workshop on Genomics, and the Workshop on Phylogenomics are now open for applications for 2024!

Workshop on Genomics - 7th - 20th January 2024 - https://evomics.org/2024-workshop-on-genomics/

Workshop on Phylogenomics - 21st - 2nd February 2024 - https://evomics.org/2024-workshop-on-phylogenomics-cesky-krumlov/

There is also some limited Equal Opportunities funding available.

#bioinformatics #genomics #phylogenomics
#transcriptomics #evomics24 #evomics2024

#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training

New preprint about the evolution of #parasitism in early-branching #fungi: #Phylogenomics including new sequence data of phytoplankton-infecting #chytrids reveals multiple independent lifestyle transitions across the phylum!
https://doi.org/10.1101/2023.06.28.546836
with Jürgen F.H. Strassert et al.

What is the best way to visualize the results of gene Gain/Loss in #evolution and #genomics research nowadays? I do have a phylogenetic tree from complete genomes and an #orthology analysis but I don't see a nice way to make a figure...
#phylogenetics #phylogenomics and #Evolution researchers...

Looking for a new remote-work opportunity, please forward if you know anyone who may be hiring someone with my skillset. TIA!

Molecular ecologist. Full cycle experience: field, lab, analysis, publication. Complex multi-trophic community analyses from bulk soil, water, mixed macroinverts. Freshwater ecology. Mycology.
#metabarcoding #EnvironmentalGenomics #Phylogenetics #Phylogenomics

Bioinformatician. Strong data analysis skills. #Linux #pipelines #db #HPC #HTS #Python #R #Perl

https://scientificnetwork.de/@cellbionews/110282524428283560

#Phylogenomics can be so beautiful.

But, just thinking of a few tips of the #mammalian Tree of Life such as bears and cats, or lizards and birds...wouldn't it be time to look for the anastomoses? Using all those genomes to start defining the Coral of Life rather than redefining the classic 1-dimensional graph?

Or do only today's species hybridise and the last 100 million years, it was exclusively one splitting into two?

New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread

Brilliant work led by @paredesmig (wepa!) from @trvrb 's group. A very practical case study showing how genomic epidemiology can bring light to transmission and inform actionable local-level public health policy.

#epidemiology #covid #publichealth #genomicepidemiology #phylogenomics

Check out the preprint here:
https://www.medrxiv.org/content/10.1101/2022.12.15.22283536v1

Been here for a little bit but still haven’t done a #introduction — I’m a PhD candidate at Pitt working on #phylogenomics, specifically using #genomics #bigdata to predict gene function de novo by looking at how genetic regions have evolved together over time.
I write lots of code in #R and #C for #bioconductor, feel free to tag me on anything related to this post! I also write tutorials based on the work I do and have a blog (both linked on my profile page)
#rstats

Belatedly, I am a plant systematist at The Morton #Arboretum, with active projects in #oaks (#phylogenetics / #phylogenomics, #hybridization, #introgression, genetic and functional #diversity), #prairies (effects of #phylogenetic and functional diversity on #restoration outcomes), #sedges (#genome and #chromosome evolution), and other plant groups. I also tweet on #botany and #NaturalHistory of the #Chicago region and other areas. Meet my lab at: https://systematics.mortonarb.org