#phylogeny — Public Fediverse posts

I've written up some notes on the Open Tree of Life viewer iphylo.blogspot.com/2026/05/a-ne... which explain a little about how it works, and cites the papers that influenced the design. The browser itself is at iphylo.org/ott-viewer #treeoflife #blogpost #phylogeny

A new way to view the Tree of ...

I've written up some notes on the Open Tree of Life viewer iphylo.blogspot.com/2026/05/a-ne... which explain a little about how it works, and cites the papers that influenced the design. The browser itself is at iphylo.org/ott-viewer #treeoflife #blogpost #phylogeny

A new way to view the Tree of ...

Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.

🔗 https://doi.org/10.1093/molbev/msag093

#evobio #molbio #compbio #phylogeny

Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.

🔗 https://doi.org/10.1093/molbev/msag093

#evobio #molbio #compbio #phylogeny

Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.

🔗 https://doi.org/10.1093/molbev/msag093

#evobio #molbio #compbio #phylogeny

Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.

🔗 https://doi.org/10.1093/molbev/msag093

#evobio #molbio #compbio #phylogeny

Didelot et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking and residual analysis.

🔗 https://doi.org/10.1093/molbev/msag093

#evobio #molbio #compbio #phylogeny

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

A major #update to my #collection of #morphological #matrices worthy to infer #networks:
a bunch of matrices we generated and reanalysed for a paper by S. Renner, D. Sokoloff, and me dealing with ancestors, hard polytomies and seed plant evolution; depicted not as the usual cladograms (where ancestor-descendant pairs must trigger unsolvable hard trichotomies) but as a "Romerogram" (or spindle graph) that shows #dichotomy as well as #buddingEvolution, i.e., #phylogeny

https://doi.org/10.6084/m9.figshare.7067369

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

Ok I'd actually love to hear people's take on this one. Vigorous skepticism about inferred trees (based on alignments) that eventually also require manual adjustment, and what that means for phylogeny is a curiously often encountered conversation for me these days.

https://arxiv.org/abs/1808.07717

#phylogeny #bioinformatics #evolution

Genetic landscape of Borrelia burgdorferi sensu stricto in Canada: a study of genetic diversity https://www.byteseu.com/1557505/ #AccessoryGenome #Canada #Clonality #ComputationalBiologyAndBioinformatics #CoreGenome #Diseases #evolution #Genetics #HumanitiesAndSocialSciences #microbiology #Modularity #multidisciplinary #Phylogeny #Science

Zhang et al. present NeuralNJ, an accurate and efficient approach to phylogenetic inference whose innovation lies in its learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores for tree reconstruction.

🔗 https://doi.org/10.1093/molbev/msaf260

#evobio #molbio #phylogeny

#Sponges are back at the root of the animal tree! I knew the cnidarians-as-root hypothesis was just too hard justify given the sum total of evidence.
https://www.science.org/doi/10.1126/science.adw9456

#evolution #phylogeny

#Sponges are back at the root of the animal tree! I knew the cnidarians-as-root hypothesis was just too hard justify given the sum total of evidence.
https://www.science.org/doi/10.1126/science.adw9456

#evolution #phylogeny

#Sponges are back at the root of the animal tree! I knew the cnidarians-as-root hypothesis was just too hard justify given the sum total of evidence.
https://www.science.org/doi/10.1126/science.adw9456

#evolution #phylogeny

#Sponges are back at the root of the animal tree! I knew the cnidarians-as-root hypothesis was just too hard justify given the sum total of evidence.
https://www.science.org/doi/10.1126/science.adw9456

#evolution #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

200 isn't really a #milestone (wouldn't that be 1000?), but not a bad number of reads for a #preprint of a paper deemed not fit for publication.

https://www.researchgate.net/profile/Guido-Grimm/achievement/691574d72d8b361441dbb9bb

Currently processing the data to please the editor (more P.R.Chinese samples), nothing unexpected came up but all analyses will have to be updated and streamlined.
So enjoy the original, the final product will have more tips but not more content 😅
#Fagus #beech #phylogeny

Isolation and genetic characterization of parvovirus from Bengal tiger in China | Virology Journal

Luo S, Liu Y, Xu X. Tigers of the world: genomics and conservation. Annu Rev Anim Biosci. 2019;7:521–48.…
#NewsBeep #News #Health #AU #Australia #BengalTiger #CPV #ISOLATION #Mutation #PCR #Phylogeny #Virology #VP2
https://www.newsbeep.com/au/202924/

Kilara Waris et al. estimated global spatiotemporal patterns of #WoodDensity and their relationships with #ModernClimate and #Paleoclimate.

#Angiosperms | #Cenozoic | #GlobalVariation | #Phylogeny | #TraitEvolution

https://doi.org/10.1093/jpe/rtaf003

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

Who Stays, Who Goes: Predicting Community Dynamics From Evolutionary History
Summary & analysis by Deepika Gunasekaran of “Effects of Phylogeny on Coexistence in Model Communities” by Serván et al.

Read here!
https://www.amnat.org/an/newpapers/Feb-2025-Servan.html

#CommunityDynamics #EvolutionaryHistory #EEB #Phylogeny

Sketch, capture and layout phylogenies

"We present new algorithms for visualizing rooted phylogenetic networks as either combining or transfer networks, in both cladogram and phylogram style. In addition, we introduce a layout algorithm that aims to improve clarity by minimizing the total stretch of reticulate edges."

https://github.com/husonlab/phylosketch2

#phylogeny

@cenobyte

Well, you're also h. sapiens, rather than myxogastria. Better looking goes with the territory 😉

#taxonomy #phylogeny #myxogastria #slime #mold #SlimeMold

Inferring the Phylogeny of Large Language Models

https://arxiv.org/abs/2404.04671

#HackerNews #Inferring #the #Phylogeny #of #Large #Language #Models #AI #Research #LanguageModels #Phylogenetics #MachineLearning #HackerNews

Inferring the Phylogeny of Large Language Models

https://arxiv.org/abs/2404.04671

#HackerNews #Inferring #the #Phylogeny #of #Large #Language #Models #AI #Research #LanguageModels #Phylogenetics #MachineLearning #HackerNews

Inferring the Phylogeny of Large Language Models

https://arxiv.org/abs/2404.04671

#HackerNews #Inferring #the #Phylogeny #of #Large #Language #Models #AI #Research #LanguageModels #Phylogenetics #MachineLearning #HackerNews

Inferring the Phylogeny of Large Language Models

https://arxiv.org/abs/2404.04671

#HackerNews #Inferring #the #Phylogeny #of #Large #Language #Models #AI #Research #LanguageModels #Phylogenetics #MachineLearning #HackerNews

Uhhhhh holy shit no one told me _Dolomedes_ & co. got moved from Pisauridae to their own family, Dolomedidae? https://wsc.nmbe.ch/family/158/Dolomedidae

Morris, Hazzi & Hormiga 2025: https://doi.org/10.1016/j.ympev.2024.108247 :ClosedAccess:

If you have a WSC account you can get the PDF here: https://wsc.nmbe.ch/reference/18059

#Arachnews #phylogeny #taxonomy #arachnology #arachnids #spiders

Uhhhhh holy shit no one told me _Dolomedes_ & co. got moved from Pisauridae to their own family, Dolomedidae? https://wsc.nmbe.ch/family/158/Dolomedidae

Morris, Hazzi & Hormiga 2025: https://doi.org/10.1016/j.ympev.2024.108247 :ClosedAccess:

If you have a WSC account you can get the PDF here: https://wsc.nmbe.ch/reference/18059

#Arachnews #phylogeny #taxonomy #arachnology #arachnids #spiders