#phylonetworks — Public Fediverse posts

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.

Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus

https://doi.org/10.1101/2025.06.03.653586

Being not limited, we moved a few more figures from the supplement to the main text 😎

https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480

#PhyloNetworks #reticulate #evolution

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

PS If they only had a slightly invested #phylogeneticist at hand; they easily could have learned a lot about the strengths and weaknesses of their data and preferred tree (a Bayesian MRC, by the way, is a summary tree of various competing topologies sampled in the MCMC chain, not a phylogenetic tree)

Here's a quick #NeighbourNet based on their "toutes" matrix (inferred in less than a minute), annotated.
Overall #similarity makes #clades, surprise, surprise.

#PhyloNetworks #linguistics

This week 4 #OldPosts on what #PhyloNetworks have to offer for #Fossil #Phylogenetics in the context of exploratory data analysis (#EDA)

Summarizing non-trivial Bayesian tree samples for dating? Just use support consensus networks—https://phylonetworks.blogspot.com/2018/01/summarizing-non-trivial-bayesian-tree.html

Large morphomatrices – trivial signal—https://phylonetworks.blogspot.com/2020/02/large-morphomatrices-trivial-signal.html

Should we try to infer trees on tree-unlikely matrices?—https://phylonetworks.blogspot.com/2017/07/should-we-try-to-infer-trees-on.html

More non-treelike data forced into trees: a glimpse into the dinosaurs—https://phylonetworks.blogspot.com/2017/08/more-non-treelike-data-forced-into.html

@Thomashegna Given the problems with this group, jumping clades from analysis to analysis, hard to grasp taxonomically, deep rooting and unique, anyone ever thought of doing exploratory data analysis involving networks (data-display and phylogenetic)?

It may be one of the many groups where one simply faces "Hilgendorf's dilemma" #OldPosts on Geneal. World of Phylog. Networks by D. Morrison 2014

The dilemma of evolutionary networks and Darwinian trees—https://phylonetworks.blogspot.com/2014/01/the-dilemma-of-evolutionary-networks.html
#PhyloNetworks

#OldPosts trilogy time (still working on 3rd pt of my maple phylogenomics post). #Phylogenetics, or #Phylogenomics, is not just blackboxes, give your data a closer look using #Phylonetworks. Ex. in my 2019 "Why the emperor has no clothes on" miniseries
#1: The mighty matK—https://phylonetworks.blogspot.com/2019/10/why-emperor-has-no-clothes-on-mighty.html
#2: A thicket of trees—https://phylonetworks.blogspot.com/2019/11/why-emperor-has-no-clothes-on-thicket.html
#3: Conflict or not?—https://phylonetworks.blogspot.com/2019/11/why-emporer-has-no-clothes-on-conflict.html

@NaturalSelection

I agree.

The only thing I would have added is a summarising doodle, a cactus metaphor (#OldPost by D. Morrison: Tree metaphors and mathematical trees: https://phylonetworks.blogspot.com/2018/02/tree-metaphors-and-mathematical-trees.html)

Reds = maternal lineages (plastomes); blue = nucleomes, (speciation history), stippled arrows = "chloroplast captures" in #phylogenetics but is in fact hostile takeover via asymmetric #introgression or #hybridisation followed by backcrossing with one parent only.
#PhyloNetworks

I pondered organisation, so my followers can make the best of Mastodon's filter option (settings -> filters).

I'll hash my posts as follows
#NewPosts—for new #blogposts on Res.I.P. and others I follow.
#OldPosts—for historical ones
#PhyloNetworks—anything #phylogenetics-ish beyond mere tree-inference
#FightTheFog—anything shrouding science (like confidential #PeerReview)
#CommentTo—post-reviews
#NotScience—for the irrelevant rest