#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

Nice to (finally) see bootstrap consensus networks picked up, #Phylogenomics meeting #PhyloNetworks

Raiyemo & Tranel, 2023, BMC Ecol Evol, #OpenAccess

Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-023-02121-1

1st pic, semi-classic cladogram, but adding internode certainty values below the branches.
2nd pic, the maximum likelihood bootstrap consensus network visualising the competing alternatives.

@laufran

Very nice that finally somebody looked into this. Simply love it!
The suspicion(s) has (have) been out there for quite some time.

Remember discussing this as a potential issue on the #PhyloNetworks workshop in Leiden a few years ago

Distinguishability in Phylogenetic Networks
https://phylonetworks.blogspot.com/2018/08/distinguishability-in-phylogenetic_22.html

Nice, we now know, we worried not for vain ;)

@phylofred

With an interest in messy and recombinant trees, or as I'd call them #PhyloNetworks, you might want to browse through the now dormant but still worth a look
Genealogical World of Phylogenetic Networks by David Morrison
http://phylonetworks.blogspot.com/

Pic is from the last post by Leo van Irsel.

And don't miss Philippe Gambet's Who is Who in Phylogenetic Networks
http://phylnet.univ-mlv.fr/

@chasewnelson

A classic. I still use it for simple things, MP and LS/NJ bootstrapping and distance matrix calculations. But it's more <2000, the last version was 2002 I think.

In 2006, we had already #MrBayes and #GARLI

And I already had gone #PhyloNetworks with SplitsTree in conjunction with PAUP* (for distance matrix), #RAxML (-III just out) and MrBayes.

Pics from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674679/

@chasewnelson

A classic. I still use it for simple things, MP and LS/NJ bootstrapping and distance matrix calculations. But it's more <2000, the last version was 2002 I think.

In 2006, we had already #MrBayes and #GARLI

And I already had gone #PhyloNetworks with SplitsTree in conjunction with PAUP* (for distance matrix), #RAxML (-III just out) and MrBayes.

Pics from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674679/

@chasewnelson

A classic. I still use it for simple things, MP and LS/NJ bootstrapping and distance matrix calculations. But it's more <2000, the last version was 2002 I think.

In 2006, we had already #MrBayes and #GARLI

And I already had gone #PhyloNetworks with SplitsTree in conjunction with PAUP* (for distance matrix), #RAxML (-III just out) and MrBayes.

Pics from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674679/

@chasewnelson

A classic. I still use it for simple things, MP and LS/NJ bootstrapping and distance matrix calculations. But it's more <2000, the last version was 2002 I think.

In 2006, we had already #MrBayes and #GARLI

And I already had gone #PhyloNetworks with SplitsTree in conjunction with PAUP* (for distance matrix), #RAxML (-III just out) and MrBayes.

Pics from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674679/

@chasewnelson

A classic. I still use it for simple things, MP and LS/NJ bootstrapping and distance matrix calculations. But it's more <2000, the last version was 2002 I think.

In 2006, we had already #MrBayes and #GARLI

And I already had gone #PhyloNetworks with SplitsTree in conjunction with PAUP* (for distance matrix), #RAxML (-III just out) and MrBayes.

Pics from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674679/

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

@PlantEvoGenomics @PaleoGenomics

Well, bears never were really picky about species barriers, were they? Their genomes are a beautiful mess.

Why we used them as the real-world example when introducing the "networx" object in #R/#phangorn https://doi.org/10.1111/2041-210X.12760

#PhyloNetworks

@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

A #phylogenomics #paper very much of my liking.
https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18525
—Right spot to look at (to dig out interesting genotypes): Caucasia (indeed a "cradle of #biodiversity)
—Combining tree- and network-inferences
—*Not* mingling plastid with nuclear data
—concordance analyses
—D-statistics
—#openaccess

#PhyloNetworks #phylogenetics

@smollestbunny @simon
I'd call it fascinating, nice use of #tanglegrams
Also reminds me of one of our #OldPosts at the Geneal. World Phylog. Networks
A new playground for networks and exploratory data analysis
https://phylonetworks.blogspot.com/2019/11/a-new-playground-for-networks-and.html
Why adding #networks and #EDA? Humans are notorious in mixing their geno- and lingotypes as soon as we hit the road (which we always loved to do, too)

#PhyloNetworks

@smollestbunny @simon
I'd call it fascinating, nice use of #tanglegrams
Also reminds me of one of our #OldPosts at the Geneal. World Phylog. Networks
A new playground for networks and exploratory data analysis
https://phylonetworks.blogspot.com/2019/11/a-new-playground-for-networks-and.html
Why adding #networks and #EDA? Humans are notorious in mixing their geno- and lingotypes as soon as we hit the road (which we always loved to do, too)

#PhyloNetworks

@smollestbunny @simon
I'd call it fascinating, nice use of #tanglegrams
Also reminds me of one of our #OldPosts at the Geneal. World Phylog. Networks
A new playground for networks and exploratory data analysis
https://phylonetworks.blogspot.com/2019/11/a-new-playground-for-networks-and.html
Why adding #networks and #EDA? Humans are notorious in mixing their geno- and lingotypes as soon as we hit the road (which we always loved to do, too)

#PhyloNetworks

@smollestbunny @simon
I'd call it fascinating, nice use of #tanglegrams
Also reminds me of one of our #OldPosts at the Geneal. World Phylog. Networks
A new playground for networks and exploratory data analysis
https://phylonetworks.blogspot.com/2019/11/a-new-playground-for-networks-and.html
Why adding #networks and #EDA? Humans are notorious in mixing their geno- and lingotypes as soon as we hit the road (which we always loved to do, too)

#PhyloNetworks

@smollestbunny @simon
I'd call it fascinating, nice use of #tanglegrams
Also reminds me of one of our #OldPosts at the Geneal. World Phylog. Networks
A new playground for networks and exploratory data analysis
https://phylonetworks.blogspot.com/2019/11/a-new-playground-for-networks-and.html
Why adding #networks and #EDA? Humans are notorious in mixing their geno- and lingotypes as soon as we hit the road (which we always loved to do, too)

#PhyloNetworks

Mondays, don't like them (still a great song), after https://ecoevo.social/@grimmiges/109371372669322413 here's the next list.

#2: Leo van Irsel and David on (rooted) phylogenetic networks

An explanation of graph types—https://phylonetworks.blogspot.com/2012/04/explanation-of-graph-types.html

Different topological restrictions of rooted phylogenetic networks. Which make biological sense?— https://phylonetworks.blogspot.com/2013/03/different-topological-restrictions-of.html

Are phylogenetic networks as scientific as trees?—https://phylonetworks.blogspot.com/2012/11/are-phylogenetic-networks-as-scientific.html

#OldPosts #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

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

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

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

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