#phylogenomics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #phylogenomics, aggregated by home.social.
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Supplementary files from: The evolutionary history of praying mantises
DATASET 📊 https://datadryad.org/dataset/doi:10.5061/dryad.hqbzkh1zd
#biology #evolution #Phylogenomics #entomology #morphology #opendata #science #scholcomms #scholcomms
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Supplementary files from: The evolutionary history of praying mantises
DATASET 📊 https://datadryad.org/dataset/doi:10.5061/dryad.hqbzkh1zd
#biology #evolution #Phylogenomics #entomology #morphology #opendata #science #scholcomms #scholcomms
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Excited to share our new #preprint!
Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in #Cucurbitaceae
🔗 https://doi.org/10.1101/2025.10.06.680802We uncover family-level losses of anthocyanin and proanthocyanidin biosynthesis genes — shedding light on the evolution of pigment diversity in cucurbits.
#Phylogenomics #Evolution #PlantGenomics #Anthocyanins #OpenScience
@PuckerLab -
Excited to share our new #preprint!
Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in #Cucurbitaceae
🔗 https://doi.org/10.1101/2025.10.06.680802We uncover family-level losses of anthocyanin and proanthocyanidin biosynthesis genes — shedding light on the evolution of pigment diversity in cucurbits.
#Phylogenomics #Evolution #PlantGenomics #Anthocyanins #OpenScience
@PuckerLab -
Excited to share our new #preprint!
Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in #Cucurbitaceae
🔗 https://doi.org/10.1101/2025.10.06.680802We uncover family-level losses of anthocyanin and proanthocyanidin biosynthesis genes — shedding light on the evolution of pigment diversity in cucurbits.
#Phylogenomics #Evolution #PlantGenomics #Anthocyanins #OpenScience
@PuckerLab -
Researchers explore the #hagfish #genome, reconstruct the early genomic history of #vertebrates.
https://phys.org/news/2024-04-explore-hagfish-genome-reconstruct-early.html
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Researchers explore the #hagfish #genome, reconstruct the early genomic history of #vertebrates.
https://phys.org/news/2024-04-explore-hagfish-genome-reconstruct-early.html
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Researchers explore the #hagfish #genome, reconstruct the early genomic history of #vertebrates.
https://phys.org/news/2024-04-explore-hagfish-genome-reconstruct-early.html
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#Genetic analysis and #archaeological insight combine to reveal the ancient origins of the #fallow_deer.
#Dama #evolution #phylogenomics #conservation
https://phys.org/news/2024-02-genetic-analysis-archaeological-insight-combine.html
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#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training -
#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training -
#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training -
#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training -
#SIB course:
"#Biodiversity #bioinformatics: from large-scale #phylogenomics to gene families and functions"
30.08-1.09 Lausanne #UNIL.
- key evolutionary concepts
- methodological approaches
- hands-on in comparative genomic analyses, protein-coding gene evolution and function across animal genomes, from model and non model species; using e.g. #OrthoDB, #BUSCO, #OMA @bgeedb
Trainers: @rmwaterhouse, N Glover, C Dessimoz, & me https://www.sib.swiss/training/course/20230830_COMGE #MolecularEvolution #Genomics #training -
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. -
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. -
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. -
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. -
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. -
🥁Our #Phylogenomics course is back🔙with this amazing lineup of instructors.
We'll also have a guest lecture by Prof Ziheng Yang about #MSCi!
Check it out: https://www.physalia-courses.org/courses-workshops/phylogenomics/
#genomics #bioinformatics #evolution -
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
7 and end/thread -
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
7 and end/thread -
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
7 and end/thread -
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
7 and end/thread -
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
7 and end/thread -
New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread -
New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread -
New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread -
New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread -
New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
1/thread -
I learned recently that while the #EvoDevo and #phylogenomics literature overwhelmingly use the term #Metazoa, it is an obsolete junior synonym to #Animalia. #zoology
#NCBI taxonomy uses Metazoa, consistent with the use in molecular fields https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock
but @gbif uses Animalia https://www.gbif.org/species/1, as does @Wikipedia https://en.wikipedia.org/wiki/Animal
As for #ICZN, they don't seem to care for modern concerns about phylogeny and such http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html -
I learned recently that while the #EvoDevo and #phylogenomics literature overwhelmingly use the term #Metazoa, it is an obsolete junior synonym to #Animalia. #zoology
#NCBI taxonomy uses Metazoa, consistent with the use in molecular fields https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock
but @gbif uses Animalia https://www.gbif.org/species/1, as does @Wikipedia https://en.wikipedia.org/wiki/Animal
As for #ICZN, they don't seem to care for modern concerns about phylogeny and such http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html -
🎉What better way to start 2023 than with this #free access "big picture" invited review on #phylogenomics and the #FloweringPlant tree of life.🌸🌳🔓⬇️
https://doi.org/10.1111/jipb.13415
@wileyplantsci
#PlantScience #evolution #genomics #JIPB #PhylogeneticTree🎄 -
#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 -
#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 -
#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 -
#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 -
#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 -
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 -
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 -
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 -
Introduction: I am a Senior Research Leader at Royal Botanic Gardens Kew and study diversity, evolution and conservation of plants. Focus area: (sub)tropics with most experience in #Africa and #Madagascar. Focus plant group: #Cyperaceae. Focus topics: #taxonomy #phylogenomics and more recent interest in using #ai for species identification and delimitation of #herbarium specimens.
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Introduction: I am a Senior Research Leader at Royal Botanic Gardens Kew and study diversity, evolution and conservation of plants. Focus area: (sub)tropics with most experience in #Africa and #Madagascar. Focus plant group: #Cyperaceae. Focus topics: #taxonomy #phylogenomics and more recent interest in using #ai for species identification and delimitation of #herbarium specimens.
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Introduction: I am a Senior Research Leader at Royal Botanic Gardens Kew and study diversity, evolution and conservation of plants. Focus area: (sub)tropics with most experience in #Africa and #Madagascar. Focus plant group: #Cyperaceae. Focus topics: #taxonomy #phylogenomics and more recent interest in using #ai for species identification and delimitation of #herbarium specimens.
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Introduction: I am a Senior Research Leader at Royal Botanic Gardens Kew and study diversity, evolution and conservation of plants. Focus area: (sub)tropics with most experience in #Africa and #Madagascar. Focus plant group: #Cyperaceae. Focus topics: #taxonomy #phylogenomics and more recent interest in using #ai for species identification and delimitation of #herbarium specimens.
