#phylogenetic — Public Fediverse posts

When editors of Q1-Journals leave the editing business to AI.

#BMCGenomics sending out a paper for review based on three, one per species, complete plastomes "[revealing] #Phylogenetic conflict [and] #reticulate evolution in #Quercus section Cerris subsection Campylolepides: Evidence from chloroplast genomes and its biogeographic implications (researchers from Shanghai Institute of Technology)
Key pic attached
#FightTheFog
1/2

When editors of Q1-Journals leave the editing business to AI.

#BMCGenomics sending out a paper for review based on three, one per species, complete plastomes "[revealing] #Phylogenetic conflict [and] #reticulate evolution in #Quercus section Cerris subsection Campylolepides: Evidence from chloroplast genomes and its biogeographic implications (researchers from Shanghai Institute of Technology)
Key pic attached
#FightTheFog
1/2

Retrospective #Phylogenetic Analysis of #Mayaro Virus, French #Guiana, 1996–2024, https://etidiohnew.blogspot.com/2026/04/retrospective-phylogenetic-analysis-of.html

Retrospective #Phylogenetic Analysis of #Mayaro Virus, French #Guiana, 1996–2024, https://etidiohnew.blogspot.com/2026/04/retrospective-phylogenetic-analysis-of.html

this information is combined together into one #phylogenetic tree that shows which species are more closely related and which are less the overall shape of the tree and the timing of when species branched off from another one help tell the story of that group past

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

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

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

trying out #strudel integration as a sequencing unit in the #phylogenetic #tree viewer at phylogeny.synth.is :

https://video.synth.is/phylosequencing/2025-08-18-00-02-00/

#Phylogenetic analysis of #H5N1 #influenza viruses isolated from dairy #cattle in #Texas in December 2024, https://etidiohnew.blogspot.com/2025/07/phylogenetic-analysis-of-h5n1-influenza.html

#Phylogenetic analysis of #H5N1 #influenza viruses isolated from dairy #cattle in #Texas in December 2024, https://etidiohnew.blogspot.com/2025/07/phylogenetic-analysis-of-h5n1-influenza.html

#Phylogenetic Analysis and Spread of HPAI #H5N1 in Middle Eastern Countries Based on #Hemagglutinin and #Neuraminidase Gene Sequences, https://etidiohnew.blogspot.com/2025/05/phylogenetic-analysis-and-spread-of.html

#Phylogenetic Analysis and Spread of HPAI #H5N1 in Middle Eastern Countries Based on #Hemagglutinin and #Neuraminidase Gene Sequences, https://etidiohnew.blogspot.com/2025/05/phylogenetic-analysis-and-spread-of.html

🆕 “High #phylogenetic distance between non-native #species and the recipient community increases #invasion success.”

- the formal definition #invasion #scientists propose in structured format for #Darwin’s #naturalisation hypothesis.

🔗 Check out the Hypothesis Description openly published with us: https://doi.org/10.3897/rio.11.e140548

#invasivespecies #invsp

Cc: @tinaheger @EvoMRI @LeibnizIGB

🆕 “High #phylogenetic distance between non-native #species and the recipient community increases #invasion success.”

- the formal definition #invasion #scientists propose in structured format for #Darwin’s #naturalisation hypothesis.

🔗 Check out the Hypothesis Description openly published with us: https://doi.org/10.3897/rio.11.e140548

#invasivespecies #invsp

Cc: @tinaheger @EvoMRI @LeibnizIGB

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/)

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/)

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

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

Amazing things we can learn about #LUCA (last universal common ancestor) by #phylogenetic analysis, e.g. it already had a rudimentary immune system.
https://www.theguardian.com/science/2025/jan/19/luca-is-the-progenitor-of-all-life-on-earth-but-its-genesis-has-implications-far-beyond-our-planet

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

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

🚨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

#Detection and #Phylogenetic Characterization of #Influenza D in Swedish #Cattle, https://etidiohnew.blogspot.com/2024/12/detection-and-phylogenetic.html

#Detection and #Phylogenetic Characterization of #Influenza D in Swedish #Cattle, https://etidiohnew.blogspot.com/2024/12/detection-and-phylogenetic.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

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

An #epizootic of highly pathogenic avian #influenza virus #H7N3 in a #Mexican ecological #reserve, Arch Virol.: https://link.springer.com/article/10.1007/s00705-024-06200-6

#Phylogenetic #analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.

An #epizootic of highly pathogenic avian #influenza virus #H7N3 in a #Mexican ecological #reserve, Arch Virol.: https://link.springer.com/article/10.1007/s00705-024-06200-6

#Phylogenetic #analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.

PS The #research we started there never ended.This is how we picture that very reticulate evolution (now proven) and the #phylogenetic relationships of #beech species right now, half a dozen papers later.
I like to imagine what we could have done, if we would have gotten any #funding for this kind of research. But it never was "high-impact" enough 🤷‍♀️

#Phylogenetic Characterization of Novel #Reassortant 2.3.4.4b #H5N8 Highly Pathogenic Avian #Influenza Viruses Isolated from Domestic #Ducks in #Egypt During the Winter Season 2021–2022

Source: Viruses, AbstractAvian influenza (AI) is an extremely contagious viral disease of domestic and wild birds that can spread rapidly among bird populations, inducing serious economic losses in the poultry industry. During the winter season 2021–2022, we isolated seventeen highly…

https://etidioh.wordpress.com/2024/10/23/phylogenetic-characterization-of-novel-reassortant-2-3-4-4b-h5n8-highly-pathogenic-avian-influenza-viruses-isolated-from-domestic-ducks-in-egypt-during-the-winter-season-2021-2022/

#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 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/

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.

Descriptive #epidemiology & #phylogenetic analysis of #HPAI #H5N1 clade 2.3.4.4b in British Columbia (#BC) & #Yukon, #Canada, Sept 22 to Jun 23, Emerg Microbes Infect.: https://www.tandfonline.com/doi/full/10.1080/22221751.2024.2392667

Phylogenetic data suggests multiple #spillover events from wild #birds to #poultry and #mammals but could not rule out transmission among farms and among mammals.

#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.

Tetrapods are models for #biodiversity science. @mariormoura @walterjetz &co present #TetrapodTraits, a database of 33,281 #tetrapod species, integrating #taxonomic, spatial, #phylogenetic & attribute data through #phylogeny-based imputation #PLOSBiology https://plos.io/3WhkNm5

#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.

Scientists Map Biodiversity Changes In The World's Forests
--
https://phys.org/news/2024-05-scientists-biodiversity-world-forests.html <-- shared technical article
--
https://doi.org/10.1038/s41467-024-48276-3 <-- shared paper
--
#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

#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.

#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.

#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

Been working on this #rshiny visualization for my masters #research. Its more functional than it is pretty. Wish I could share a link, but it contains a bunch of use notes for my advisor at the top 😂

This visualization has been the single most useful tool for understanding my results. It connects various #phylogenetic, #conservation, #bioclimatic, and #geographic data for the worlds #turtles in a single interactive page.

Next step is to add @Wwf ecoregions as a comparison map.

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