Great recommendation from Github's project-recommender: GToTree, an automatic workflow for large-scale #phylogenomics

https://github.com/AstrobioMike/GToTree

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

https://www.mdpi.com/2076-2607/11/7/1830

#fungi #EarlyDivergingFungi #phylogenetics #phylogenomics #mycology

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...

**Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits**

https://www.nature.com/articles/s41559-023-02095-9

#mycology #fungi #phylogenomics #FungalEvolution #dikarya #FungalTreeOfLife

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

"**Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes"**
https://www.nature.com/articles/s41586-023-06186-2
#phylogenomics #Asgard #Archaea

With the progress in high quality genome assemblies and in bioinformatics of comparative genomics, it seems that we're going to see increasing resolution of tough points of animal phylogeny: "Ancient gene linkages support ctenophores as sister to other animals" https://www.nature.com/articles/s41586-023-05936-6 #phylogeny #phylogenomics #Metazoa

@dezene

You're welcome.

Admittedly, it's a general problem in #Phylogenomics, blind reliance on data and models, the dei-ex-machina.

Few ponder the results out of the black-boxes.

In this case it would have been easy, definining bioregions that are coherent over time (India for instance) and then use the constraint options of the DEC model to eliminate impossible dispersal routes at a given time such as "Neotropics"-"Indomalaya"

But there seem to be too few researchers left in science.

Was delighted to see the figures in the other paper, they have in the pipes.

Really fascinating to put two #preprints next to each other going online shortly after each other, one (on Fagales in total) by the same batch of authors sitting as coauthors on the other (on Fagaceae), that disagree in nearly every aspect where they thematically overlap.

Will make perfect material for #NewPosts. On coauthorships and #Phylogenomics

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 modern species hybridise but 100 million years ago, it was exclusively one splitting into two?

@andrewlhipp

Sigh, my first love. The maples.

Still largely unworked although there's now #Phylogenomics data out there from both the nucleus and chloroplast.

#Phylogeny #FunFact: The red and silver maples (sect. Rubra) are a deep diverging bunch, with a sister they forgot in Japan and a cousin that is the only maple ever to penetrate the tropics.

Morphologically, a type that once was pretty much everywhere maples ever have been. A very old and outdated pic.

#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB

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

I learned recently that while the #EvoDevo and #phylogenomics literature overwhelmingly use the term #Metazoa, it is an obsolete junior synonym to #Animalia. #zoology
#NCBI taxonomy uses Metazoa, consistent with the use in molecular fields https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock
but @gbif uses Animalia https://www.gbif.org/species/1, as does @Wikipedia https://en.wikipedia.org/wiki/Animal
As for #ICZN, they don't seem to care for modern concerns about phylogeny and such http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html

RT @darencard
Hot off the press! I am thrilled to highlight a recent review with @wb_jenning and @ScottVEdwards1 on #genome #evolution and #phylogenomics in #reptiles, which is now available in @Animals_MDPI. https://doi.org/10.3390/ani13030471 1/

Infectious disease forecasting is vital for epidemic and pandemic preparedness – but current models leave something to be desired. Could incorporating genetics, genomics, and phylodynamics close the accuracy gap?

https://thepathologist.com/outside-the-lab/a-weather-forecast-for-disease

#genetics #genomics #phylogenetics #phylogenomics #phylodynamics #epidemiology #IDMastodon #Infectious Disease #AntimicrobialResistance #AntimicrobialStewardship

#Phylogenomics and Population #Genomics: Inference and Applications #course #training https://www.ub.edu/certfem/ppgcourse/

@DrAnneCarpenter @vsbuffalo @academicchatter

The answer is like (often) "more/fewer". In my areas (crossings of #Phylogenetics; #EvolutionaryBiology, #Palaeontology) many meta-analyses testing some general hypothesis crumble in the light of in-depth studies but most MPU papers (standard in plant #Phylogenomics: publishing black-box trees with a few new plastomes added) are for the bin as they lack much-needed consilience.

One has to love #Phylogenomics and its fully resolved trees (first pic, based on a "supermatrix" combining complete plastomes, nrDNA and up to 500 nuclear loci)

But it can be a quick spoiler to look at the data behind them
(second pic; the authors and whoever is responsible for #PeerReview didn't bother to take the old "fragment" papers for serious)

#Tanglegrams #Maples