Lisa Pokorny
@calyptrochaeta.bsky.social
Ramón y Cajal Researcher @ Real Jardín Botánico (RJB-CSIC) | Earlier @ IBB (CSIC-CMCNB), CBGP (UPM-INIA/CSIC) & Royal Botanic Gardens, Kew | Duke University & UAM alumna | #Biogeography #Evolution #Phylogenomics #Plants #Systematics
Reposted by Lisa Pokorny
If you're interested in understanding discordance in phylogenomic analyses, the @evojlinnsoc.bsky.social's special issue 'Phylogenomic Discordance: Patterns, Processes, and Solutions' is for you!
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
Phylogenomic Discordance: Patterns, Processes, and Solutions
Phylogenomics, the study of evolutionary relationships using genomic data, has revolutionized our understanding of the Tree of Life. As a field, phylogenomics h
academic.oup.com
September 29, 2025 at 4:00 PM
If you're interested in understanding discordance in phylogenomic analyses, the @evojlinnsoc.bsky.social's special issue 'Phylogenomic Discordance: Patterns, Processes, and Solutions' is for you!
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
Reposted by Lisa Pokorny
"This increases the known large-scale fungal phylogenetic diversity by roughly one-third." 🧪💻🧬
Thirty novel fungal lineages: formal description based on environmental samples and DNA mycokeys.pensoft.net/articles.php...
#fungi #sequencing
Thirty novel fungal lineages: formal description based on environmental samples and DNA mycokeys.pensoft.net/articles.php...
#fungi #sequencing
Thirty novel fungal lineages: formal description based on environmental samples and DNA
Molecular analyses of soil and water commonly reveal large proportions of fungal taxa that cannot be assigned to any taxonomic or functional groups. Some of these so-called dark taxa have been encoded...
mycokeys.pensoft.net
October 22, 2025 at 2:06 PM
"This increases the known large-scale fungal phylogenetic diversity by roughly one-third." 🧪💻🧬
Thirty novel fungal lineages: formal description based on environmental samples and DNA mycokeys.pensoft.net/articles.php...
#fungi #sequencing
Thirty novel fungal lineages: formal description based on environmental samples and DNA mycokeys.pensoft.net/articles.php...
#fungi #sequencing
Reposted by Lisa Pokorny
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
November 2, 2025 at 5:52 PM
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
Reposted by Lisa Pokorny
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
November 12, 2025 at 9:50 AM
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
Reposted by Lisa Pokorny
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
hoehnalab.github.io
November 11, 2025 at 9:00 AM
PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social
Reposted by Lisa Pokorny
New Nature paper!
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
A global coral phylogeny reveals resilience and vulnerability through deep time - Nature
The most recent common ancestor of the stony coral Scleractinia dates to about 460 million years ago and was probably a solitary, heterotrophic and free-living organism.
doi.org
October 23, 2025 at 4:46 PM
New Nature paper!
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Vaga et al. (2025) reconstruct a time-calibrated phylogeny of stony (scleractinian) corals, which suggests that some could be resilient to climate change.
Congrats @claudiavaga.bsky.social
Link to paper: doi.org/10.1038/s415...
Reposted by Lisa Pokorny
I cannot believe our work is finally out there and in @journal-evo.bsky.social ! This was an enormous group effort!
We provide an updated estimate of the number of buzz pollinated angiosperm species, genera, and families, look at consequences for diversification, number of transitions, and more!
We provide an updated estimate of the number of buzz pollinated angiosperm species, genera, and families, look at consequences for diversification, number of transitions, and more!
October 23, 2025 at 5:34 AM
I cannot believe our work is finally out there and in @journal-evo.bsky.social ! This was an enormous group effort!
We provide an updated estimate of the number of buzz pollinated angiosperm species, genera, and families, look at consequences for diversification, number of transitions, and more!
We provide an updated estimate of the number of buzz pollinated angiosperm species, genera, and families, look at consequences for diversification, number of transitions, and more!
Reposted by Lisa Pokorny
🌿 ¡Ya está abierta la inscripción al VI Simposio de Botánica Española!
📅 Hasta el 1 de noviembre de 2025
🎓 Gratuito para afiliados SEBOT y de sociedades botánicas afiliadas a SEBOT.
📍 Plazas limitadas
👉 Inscríbete aquí: www.simsebot.org/inscripcioac...
📅 Hasta el 1 de noviembre de 2025
🎓 Gratuito para afiliados SEBOT y de sociedades botánicas afiliadas a SEBOT.
📍 Plazas limitadas
👉 Inscríbete aquí: www.simsebot.org/inscripcioac...
October 2, 2025 at 11:45 AM
🌿 ¡Ya está abierta la inscripción al VI Simposio de Botánica Española!
📅 Hasta el 1 de noviembre de 2025
🎓 Gratuito para afiliados SEBOT y de sociedades botánicas afiliadas a SEBOT.
📍 Plazas limitadas
👉 Inscríbete aquí: www.simsebot.org/inscripcioac...
📅 Hasta el 1 de noviembre de 2025
🎓 Gratuito para afiliados SEBOT y de sociedades botánicas afiliadas a SEBOT.
📍 Plazas limitadas
👉 Inscríbete aquí: www.simsebot.org/inscripcioac...
Reposted by Lisa Pokorny
¡Hemos subido a YouTube las seis últimas charlas del ciclo de Cafés Sistemáticos ☕️🍀!
Las temáticas van de la genómica a la taxonomía, pasando por la etnobotánica, la paleobotánica y la biogeografía. ¡Qué las disfrutéis! 🧵
📺 youtube.com/playlist?lis...
Las temáticas van de la genómica a la taxonomía, pasando por la etnobotánica, la paleobotánica y la biogeografía. ¡Qué las disfrutéis! 🧵
📺 youtube.com/playlist?lis...
October 13, 2025 at 12:33 PM
¡Hemos subido a YouTube las seis últimas charlas del ciclo de Cafés Sistemáticos ☕️🍀!
Las temáticas van de la genómica a la taxonomía, pasando por la etnobotánica, la paleobotánica y la biogeografía. ¡Qué las disfrutéis! 🧵
📺 youtube.com/playlist?lis...
Las temáticas van de la genómica a la taxonomía, pasando por la etnobotánica, la paleobotánica y la biogeografía. ¡Qué las disfrutéis! 🧵
📺 youtube.com/playlist?lis...
Reposted by Lisa Pokorny
Free-to-read link @natgenet.nature.com: rdcu.be/eHzSP
News & Views: "The dawn of bryophyte genomics is here" rdcu.be/eHzS2
News & Views: "The dawn of bryophyte genomics is here" rdcu.be/eHzS2
September 22, 2025 at 2:31 PM
Free-to-read link @natgenet.nature.com: rdcu.be/eHzSP
News & Views: "The dawn of bryophyte genomics is here" rdcu.be/eHzS2
News & Views: "The dawn of bryophyte genomics is here" rdcu.be/eHzS2
Reposted by Lisa Pokorny
We’re excited to announce the Call for Symposia, Colloquia, & Workshop Proposals for #Botany2026, Aug. 1–5, 2026 in Tucson, AZ.
Help us explore this year’s theme: Biodiversity at the Boundaries.
There is a hard deadline of October 16 for Symposia and Colloquia proposals.
www.botanyconference.org
Help us explore this year’s theme: Biodiversity at the Boundaries.
There is a hard deadline of October 16 for Symposia and Colloquia proposals.
www.botanyconference.org
September 12, 2025 at 5:30 PM
We’re excited to announce the Call for Symposia, Colloquia, & Workshop Proposals for #Botany2026, Aug. 1–5, 2026 in Tucson, AZ.
Help us explore this year’s theme: Biodiversity at the Boundaries.
There is a hard deadline of October 16 for Symposia and Colloquia proposals.
www.botanyconference.org
Help us explore this year’s theme: Biodiversity at the Boundaries.
There is a hard deadline of October 16 for Symposia and Colloquia proposals.
www.botanyconference.org
Reposted by Lisa Pokorny
SPECIAL ISSUE CALL FOR PAPERS
#AppsPlantSci invites proposals for “Beyond #phylogenomics: Innovative applications of target capture data,” led by @emcassey.bsky.social, @erikarmoore11.bsky.social, Mafe Torres Jimenez & @yannickwoudstra.bsky.social
Deadline 30 Nov 2025
botany.org/home/publica...
#AppsPlantSci invites proposals for “Beyond #phylogenomics: Innovative applications of target capture data,” led by @emcassey.bsky.social, @erikarmoore11.bsky.social, Mafe Torres Jimenez & @yannickwoudstra.bsky.social
Deadline 30 Nov 2025
botany.org/home/publica...
September 2, 2025 at 5:14 PM
SPECIAL ISSUE CALL FOR PAPERS
#AppsPlantSci invites proposals for “Beyond #phylogenomics: Innovative applications of target capture data,” led by @emcassey.bsky.social, @erikarmoore11.bsky.social, Mafe Torres Jimenez & @yannickwoudstra.bsky.social
Deadline 30 Nov 2025
botany.org/home/publica...
#AppsPlantSci invites proposals for “Beyond #phylogenomics: Innovative applications of target capture data,” led by @emcassey.bsky.social, @erikarmoore11.bsky.social, Mafe Torres Jimenez & @yannickwoudstra.bsky.social
Deadline 30 Nov 2025
botany.org/home/publica...
Reposted by Lisa Pokorny
An evolving view of character macroevolution doi.org/10.32942/X28...
August 31, 2025 at 9:30 PM
An evolving view of character macroevolution doi.org/10.32942/X28...
Reposted by Lisa Pokorny
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
Abstract. The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic d
doi.org
August 19, 2025 at 7:35 PM
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
Reposted by Lisa Pokorny
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression
A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...
www.biorxiv.org
August 23, 2025 at 11:52 PM
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
Reposted by Lisa Pokorny
So excited that my Tansley Insight "On the role of mutualisms in plant biogeography: consequences for ecology, evolution, and invasion" is out today!! @newphyt.bsky.social
On the role of mutualisms in plant biogeography: consequences for ecology, evolution, and invasion
Most plant species world-wide depend on one or more mutualisms – beneficial associations with other species. Evidence is emerging that these biotic mutualisms shape plant biogeography (i.e. distribut....
doi.org
August 9, 2025 at 9:07 AM
So excited that my Tansley Insight "On the role of mutualisms in plant biogeography: consequences for ecology, evolution, and invasion" is out today!! @newphyt.bsky.social
Reposted by Lisa Pokorny
ASTER: A Package for Large-scale Phylogenomic Reconstructions. #Phylogenomics #SpeciesTreeInference @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
July 27, 2025 at 6:05 PM
ASTER: A Package for Large-scale Phylogenomic Reconstructions. #Phylogenomics #SpeciesTreeInference @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
Reposted by Lisa Pokorny
Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
July 23, 2025 at 8:43 AM
Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
Reposted by Lisa Pokorny
Suturing fragmented landscapes: Mosaic hybrid zones in plants may facilitate ecosystem resiliency
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
July 30, 2025 at 10:16 AM
Suturing fragmented landscapes: Mosaic hybrid zones in plants may facilitate ecosystem resiliency
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Lisa Pokorny
Now online! Ancient hybridization underlies tuberization and radiation of the potato lineage
Ancient hybridization underlies tuberization and radiation of the potato lineage
Genomic and functional analyses reveal that the potato lineage originated from a homoploid interspecific hybridization event between the Tomato and Etuberosum lineages 8–9 million years ago. The alternate inheritance of highly divergent parental alleles drove the origin of tubers and explosive species diversification and niche expansion into the high Andes.
dlvr.it
July 31, 2025 at 2:59 PM
Now online! Ancient hybridization underlies tuberization and radiation of the potato lineage
Reposted by Lisa Pokorny
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
www.nature.com
June 17, 2025 at 2:25 PM
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Reposted by Lisa Pokorny
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
May 25, 2025 at 10:27 AM
Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-inherent GC bias (likely viruses, too), but Nanopore long reads can address this. A results thread on our recent preprint 🧵.
Reposted by Lisa Pokorny
Very excited to share the first paper out of my Postdoc @CMR:
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio
doi.org
July 8, 2025 at 2:30 AM
Very excited to share the first paper out of my Postdoc @CMR:
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social
doi.org/10.1093/isme...
🧵1/7
Reposted by Lisa Pokorny
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
June 25, 2025 at 7:25 PM
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Reposted by Lisa Pokorny
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
July 2, 2025 at 8:32 PM
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community