#phylogenetic

R package StratPal update
Full integration with the FossilSim package to study effects of #taphonomy and #ecology on #phylogenetic trees with sampled ancestors, and simplified handling of categorical niche models
#stratigraphy
https://mindthegap-erc.github.io/StratPal/index.html

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

https://www.biorxiv.org/content/10.1101/2025.02.11.637735v1

#MAGs #phylogenetic #chytrid #fungi

Indo-European Phylogenetic And Linguistic Trees Concur
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https://www.razibkhan.com/p/we-are-what-we-speak-indo-european <-- shared technical article
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https://doi.org/10.1038/nature14317 <-- shared paper
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#GIS #spatial #mapping #language #IndoEuropean #spatialanalysis #spatiotemporal #linguists #historians #archaeologists #phylogenetic #tree #HumanGenomeProject #genetics #cultures #migration #paleogenomics #genotypes #prehistory #ancient #ancienthumans #DNA #prehistoric #populations #genetictree

Meet PyNCBIminer!
This open-source, user-friendly software automates the assembly of large #DNA data sets from #GenBank for #phylogenetic reconstruction using the supermatrix method--and eliminates the need for large local #databases!
https://doi.org/10.1111/jse.13155
@WileyEcolEvol
#JSE #bioinformatics #BioinformaticsTools

To address 3 key questions regarding #torpor #evolution, we compiled a #dataset of a) torpor capabilities and b) 21 ecophysiological variables for 1,338 species of #mammals and #birds.

We then analysed this dataset using a series of #phylogenetic comparative methods.

5/12

#Phylogenetic and #Pathogenic #Analysis of #H5N1 and #H5N6 High Pathogenicity Avian #Influenza Virus Isolated from #Poultry Farms (Layer and Broiler Chickens) in #Japan in the 2023/2024 Season, https://etidiohnew.blogspot.com/2024/12/phylogenetic-and-pathogenic-analysis-of.html

Our new #preprint is out
Cardoni et al. Pruning the tree: Comparing OTUs and ASVs for processing HTS 5S-IGS data
https://doi.org/10.22541/au.173437938.80481043/v1

Organising 100k of reads per studied sample (5S #rDNA intergenic spacers) into a handier amount of tips (~100) for #phylogenetic inferences and assessing #biodiversity

#phylogenetics #taxonomy #genetics #NGS

The largest #cartilaginousfish is the #whaleshark, the largest/heaviest Actinopterygii is the sunfish. Due to the #phylogenetic situation in early #vertebrates, when using the general term "#fish", one should be aware that this is a #paraphyletic group.
© #StefanFWirth Berlin

My article on X
https://x.com/wirthstef/status/1843663461059813801?t=GxBElm6qp9nT93rN_E2_jQ&s=19

Photos
#sunfish, Denmark, by Per-Ola Norman, 2009, the © holder published into pub. domain

Whale Shark, by Sh.
ElkCloner, 2012, licensed  Cr. Commons Attr-ShareAlike 3.0 Unp.

#Molecular #epidemiology & #phylogenetic analysis of #influenza viruses #H3N2 & B/Victoria during #COVID19 #pandemic in #Guangdong, #China https://pubmed.ncbi.nlm.nih.gov/39090685/?utm_source=Feedly&utm_medium=rss&utm_campaign=None&utm_content=1fgJURi2yzLesFml6et0Bb6krzs_FrNIYgPYVFN50JPwVNFg9s&fc=None&ff=20240802015852&v=2.18.0.post9+e462414

Despite the extraordinarily low detection rate of influenza infection, concealed influenza #transmission may occur between individuals during strict COVID-19 control. This ultimately leads to the #accumulation of viral #mutations and accelerated #evolution of H3N2 and B/Victoria viruses.

PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data

https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-024-02256-9

#GBIF #phylogenetic #pipeline

Scientists Map Biodiversity Changes In The World's Forests
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https://phys.org/news/2024-05-scientists-biodiversity-world-forests.html <-- shared technical article
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https://doi.org/10.1038/s41467-024-48276-3 <-- shared paper
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#GIS #spatial #mapping #forest #forests #biodiversity #mapping #spatialanalysis #spatiotemporal #global #vegetation #climatechange #ecosystem #conservation #restoration #carbonsink #biodiversity #species #tropical #boreal #biomass #biome #forestmanagement #model #modeling #remotesensing #phylogenetic #earthobservation

'A Variational Approach to Bayesian Phylogenetic Inference', by Cheng Zhang, Frederick A. Matsen IV.

http://jmlr.org/papers/v25/22-0348.html

#phylogenetic #bayesian #variational

If you work on evolutionary networks (ancestral recombination graphs, #admixture graphs, #phylogenetic networks), please **submit an abstract to our symposium** on "Networks in population genetics and phylogenetics: Theory, methods, and applications". It will be part of #Evol2024 in Montreal, July 26-30: https://www.evolutionmeetings.org

#evolution #network #migration #introgression

Finding a home for the wandering mushrooms—#phylogenetic and taxonomic updates of #Agaricales.

#genomics

https://phys.org/news/2024-01-home-mushrooms-phylogenetic-taxonomic-agaricales.html

We revised the #fossil coleoid Syllipsimopodi bideni and suggest it to be identical to Gordoniconus beargulchensis of same locality due the great degree of similarity. Differences can be explained by incomplete preservation and misinterpretation of tentacles. Hence, the phylogeny by Whalen & Landman (2022) and the extension of the #phylogenetic split of the Decabrachia and Octobrachia (Vampyropoda) into the Carboniferous needs some fundamental revision:

https://doi.org/10.1038/s41467-023-42842-x #paleobiology

Researchers reinvestigate #phylogenetic and biogeographic history of trees in #Cryptocaryeae.

#Lauraceae #evolution #plastomes #trnK

https://phys.org/news/2023-11-reinvestigate-phylogenetic-biogeographic-history-trees.html

Researchers reinvestigate #phylogenetic and biogeographic history of trees in #Cryptocaryeae.

#Lauraceae #evolution #plastomes #trnK

https://phys.org/news/2023-11-reinvestigate-phylogenetic-biogeographic-history-trees.html

"#Phylogenetic analyses determined this species to be the sister taxon of the much larger Dynatoaetus gaffae recently described from several Australian sites, and so we name it as Dynatoaetus pachyosteus sp. nov. Further fragmentary remains attributable to either A. audax, C. lacertosus or D. pachyosteus are recorded from sites in the Wellington Caves complex, NSW. This study increases the known diversity of #raptors in #Pleistocene Australia"

https://www.tandfonline.com/doi/full/10.1080/03115518.2023.2268780

Sir David's long-beaked #echidna (#Zaglossus #attenboroughi):

Sequences in #genebank: 0

Eastern long-beaked echidna (Zaglossus #bartoni):

Sequences in genebank: 0

So, that's why you've never seen a molecular #phylogenetic tree representing all five living #monotreme species.

Researchers have reconstructed the in-depth evolutionary history of #Heliconius butterflies using a #phylogenetic approach that will help disentangle the history of other difficult lineages that have experienced gene flow. #ReviewedPreprint https://elifesciences.org/reviewed-preprints/90656?utm_source=mastodon&utm_medium=social&utm_campaign=organic