#phylogenetic — Public Fediverse posts

RE: https://mastodon.green/@plazi_species/116103658450230777

An interesting scientific paper on #Gilliesieae (#Amaryllidaceae), which have a limited distribution in #Chile, Argentina, Bolivia, and Peru. The authors N. García and Miersia (2026) describe four #newspecies of genera #Gilliesia and #Miersia. All species are found only in specific regions of Chile and are therefore #endemic. The authors also amplified and sequenced #DNA sequences to reconstruct the #phylogenetic positions of the new species. #Biodiversityresearch
© this text #StefanFWirth 2026

Preplanned Studies: #Phylogenetic and #Molecular Characteristics of An #H3N8 Avian #Influenza Virus Detected in Wild #Birds — #Beijing, #China, September 2024, https://etidiohnew.blogspot.com/2025/11/preplanned-studies-phylogenetic-and.html

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

Took a while, but finally out:

Pruning the Tree: Comparing #OTUs and #ASVs in High-Throughput Sequencing of 5S-IGS Nuclear Ribosomal DNA in #Phylogenetic Studies

How to reduced 100ks of reads down to the 100 really needed, a comparison between #Mothur and #dada2 pipelines using our nigh-#reticulate #beech dataset as test subject

https://doi.org/10.1002/ece3.72242

That would have been enough for a #phylogenetic #ResearchPaper. But one problem with classic German coauthors is that we don't scratch surfaces.

A new animal was found. A British researcher writes a half-page abstract a month later: The elephant, a new animal from Africa.
One year later, a French writes a 5 pp. long paper, content: The elephant, a new animal from Africa.
Five years later a 500 pp. German book is published: The Elephant. Part 1: Its trunk.

(5/)

Indo-European Phylogenetic And Linguistic Trees Concur
--
https://www.razibkhan.com/p/we-are-what-we-speak-indo-european <-- shared technical article
--
https://doi.org/10.1038/nature14317 <-- shared paper
--
#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

🚨New #phylogenetic paper alert!🚨
🌲+🔥= speciation?
This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer #Evolution !

https://doi.org/10.1002/ajb2.16454
(reading-access link on my website)
#AJB #macroevolution #botany

🚨New #phylogenetic paper alert!🚨
🌲+🔥= speciation?
This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer #Evolution !

https://doi.org/10.1002/ajb2.16454
(reading-access link on my website)
#AJB #macroevolution #botany

🚨New #phylogenetic paper alert!🚨
🌲+🔥= speciation?
This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer #Evolution !

https://doi.org/10.1002/ajb2.16454
(reading-access link on my website)
#AJB #macroevolution #botany

#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

#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

#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

#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

#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

#Phylogenetic Insights into #H7Nx #Influenza Viruses: Uncovering #Reassortment #Patterns and Geographic Variability

Source: Viruses, AbstractInfluenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6,…

https://etidioh.wordpress.com/2024/10/23/phylogenetic-insights-into-h7nx-influenza-viruses-uncovering-reassortment-patterns-and-geographic-variability/

#Phylogenetic & #mutational #analysis of #H10N3 avian #influenza A virus in #China: potential #threats to #human #health, Front Cell Infect Microbiol.: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2024.1433661/full

Analysis of aa mutation sites identified 4 mutations potentially hazardous to human health. Consequently, this underscores importance of continuous & vigilant monitoring of dynamics surrounding H10N3 subtype of avian influenza virus, utilizing advanced #genomic surveillance techniques.

'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

#Pathological and #phylogenetic characteristics of #fowl #AOAV-1 and #H5 isolated from naturally infected Meleagris Gallopavo https://pubmed.ncbi.nlm.nih.gov/38773480/?utm_source=Feedly&utm_medium=rss&utm_campaign=None&utm_content=1LGAx__djGAJ9poBzWGqPtjEbBDtz4ipSRRPUplmgHEyyF_Ihj&fc=None&ff=20240522050644&v=2.18.0.post9+e462414

To our knowledge, this is the first study that reports the isolation of AOAV-1 and H5Nx viruses from Hybrid Converter Turkeys in #Egypt.

📢 Postdoc job!

Knowledgeable in #phylogenetic comparative analyses and #macroevolution?

Join us to study the #evolution of biotic dispersal across seed #plants!

Details: https://computationalecology.github.io/posts/2024-postdoc-plant-macroevolution/

#postdoc

📢 Postdoc job!

Knowledgeable in #phylogenetic comparative analyses and #macroevolution?

Join us to study the #evolution of biotic dispersal across seed #plants!

Details: https://computationalecology.github.io/posts/2024-postdoc-plant-macroevolution/

#postdoc

📢 Postdoc job!

Knowledgeable in #phylogenetic comparative analyses and #macroevolution?

Join us to study the #evolution of biotic dispersal across seed #plants!

Details: https://computationalecology.github.io/posts/2024-postdoc-plant-macroevolution/

#postdoc

📢 Postdoc job!

Knowledgeable in #phylogenetic comparative analyses and #macroevolution?

Join us to study the #evolution of biotic dispersal across seed #plants!

Details: https://computationalecology.github.io/posts/2024-postdoc-plant-macroevolution/

#postdoc

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

"Minimal syntax for phylogenetic trees"

https://xtao.org/blog/phylo.html

An example of a specialized Jevko format that nicely encodes phylogenetic trees.

#jevko #minimal #format #syntax #phylogenetic #tree #dsl #newick #biology #biotechnology #biocomputing #programming

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

#Genome analysis of 46,000-year-old #roundworm from Siberian #permafrost reveals novel species.

#cryptobiosis #phylogenetic #nematode

https://phys.org/news/2023-07-genome-analysis-year-old-roundworm-siberian.html

The 31 new deorphanized #neuropeptide #GPCRs from #Nematostella and the #phylogenetic trees also allowed us to predict the ligand for many receptors across #cnidarians. We hope that cnidarian researchers will functionally characterising these e.g. by #CRISPR, as the Houliston lab has done for the MIH receptor.
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000614
#evolution #neuroscience

I'm curious, would anybody else find a Wikipedia-style cladogram system useful for their Wordpress site?

#cladograms #cladogram #evolution #phylogeny #phylogenetic #tree #Wikipedia #wordpress #cladistics #taxonomy #biology #zoology

An important breakthrough in understanding the origin and geographic distribution of #cycads. By combining genetic data with leaf morphological data from both #fossil and living species for the first time, the researchers created a #phylogenetic tree of these fascinating and #endangered #plants.
#Biology #Paleontology #sflorg
https://www.sflorg.com/2023/06/pal06132301.html

Complete #chloroplast #genomes clarify #phylogenetic placement of six #polygonatum species.

#genomics

https://phys.org/news/2023-06-chloroplast-genomes-phylogenetic-placement-polygonatum.html

#Hydrogen #isotope #fractionation in #carbohydrates of #leaves and #xylem tissues follows distinct #phylogenetic patterns: a common garden experiment with 73 #tree and #shrub species: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18976

@aetiology

does anyone know of a good #phylogenetic paper that shows 2009, 1977, and 1918 flu?

i found one that shows #1977flu looking sus … but i want the full picture of #H1N1

#1918flu #2009flu

cc other mes @[email protected] @[email protected] @[email protected] @[email protected]

@aetiology

does anyone know of a good #phylogenetic paper that shows 2009, 1977, and 1918 flu?

i found one that shows #1977flu looking sus … but i want the full picture of #H1N1

#1918flu #2009flu

cc other mes @[email protected] @[email protected] @[email protected] @[email protected]

@aetiology

does anyone know of a good #phylogenetic paper that shows 2009, 1977, and 1918 flu?

i found one that shows #1977flu looking sus … but i want the full picture of #H1N1

#1918flu #2009flu

cc other mes @[email protected] @[email protected] @[email protected] @[email protected]

@aetiology

does anyone know of a good #phylogenetic paper that shows 2009, 1977, and 1918 flu?

i found one that shows #1977flu looking sus … but i want the full picture of #H1N1

#1918flu #2009flu

cc other mes @[email protected] @[email protected] @[email protected] @[email protected]

@aetiology

does anyone know of a good #phylogenetic paper that shows 2009, 1977, and 1918 flu?

i found one that shows #1977flu looking sus … but i want the full picture of #H1N1

#1918flu #2009flu

cc other mes @[email protected] @[email protected] @[email protected] @[email protected]

Primer on #microbiome analysis (with #amplicon #sequencing of #phylogenetic marker #genes

https://intomed.bio.uth.gr/primer-on-microbiome-analysis/

@jobRxiv @academicchatter @academicsunite
#academicchatter @openscience @phdlife @PhD_Genie @phdstudents
#phdlife #highereducation #postdoclife #research #studyabroad #hostmicrobiota #hostmicrobe #microbialecology #microbeinteractions #symbiosis
@MicrobioJC @IMPACTT @openscience

*New #preprint alert* Patramanis et al. PaleoProPhyler: a #reproducible #pipeline for #phylogenetic inference using #ancient #proteins. 🦴

We developed a pipeline for aligning ancient #peptide data and performing #evolutionary analyses w/it. The pipeline can not only process #proteomic data, but also harness #genetic data in different formats (#CRAM, #BAM, #VCF) and translate it, so as to create reference panels for #phyloproteomics.

https://www.biorxiv.org/content/10.1101/2022.12.12.519721v1?med=mas

#ScienceMastodon #Evolution #EcoEvo

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

#introduction

#introduction I am a quantitative #biologist, striving to understand how changes in #temperature (and other factors) influence biological systems over various timescales. To this end, I employ a diverse set of approaches, such as #phylogenetic comparative methods, #ecoinformatics, #machinelearning, & comparative #genomics.

My research to date has primarily focused on the #physiological and #molecular levels, but I am planning to soon expand to higher levels (species interactions, #ecosystems).

#introduction I am a quantitative #biologist, striving to understand how changes in #temperature (and other factors) influence biological systems over various timescales. To this end, I employ a diverse set of approaches, such as #phylogenetic comparative methods, #ecoinformatics, #machinelearning, & comparative #genomics.

My research to date has primarily focused on the #physiological and #molecular levels, but I am planning to soon expand to higher levels (species interactions, #ecosystems).