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Seongyeon Kang

@skang.bsky.social
1.2K followers 228 following 19 posts

PhD candidate in @uofa-eeb, Polyploidy and traits with phylo-comparative genomics🌼🧬 museum lover and dancer

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Reposted by Seongyeon Kang
Rosana Zenil-Ferguson @roszenil.bsky.social · 26/01/2026
New paper showing clustering of the many traits across reproductive strategies of angiosperms. Lots of interesting discussions that gave raise to this piece. But only possible thanks to the hard work of Andrew Helmstetter, Sylvain Glémin, and Jos Käfer. nph.onlinelibrary.wiley.com/doi/abs/10.1...
nph.onlinelibrary.wiley.com
An angiosperm‐wide perspective on reproductive strategies and floral traits
Flowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes ...
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Reposted by Seongyeon Kang
Natalie Cooper @nhcooper123.bsky.social · 25/03/2026
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
nhcooper123.github.io
Phylogenetic Comparative Methods
Phylogenetic Comparative Methods
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 21/04/2026
MutaPhy: A clade-based framework to detect genotype-phenotype associations on phylogenetic trees www.biorxiv.org/content/10.64898/20…
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Evolution Letters @evolletters.bsky.social · 27/04/2026
Choosing the right tree matters. Phylograms outperform chronograms for neutral traits but not for detecting selection. By @phylogenetrips.bsky.social et al. doi.org/10.1093/evle...
doi.org
Phylograms better fit neutrally evolving traits than chronograms
Many species are characterized by trait differences between each other. For example, the brain size of different primate and human lineages varies. The que
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Alessio Capobianco @acapomorphic.bsky.social · 04/03/2026
New paper out from @hoehna.bsky.social Lab, led by the brilliant @bjorntko.bsky.social! We applied the Pesto software (Kopperud & Höhna, 2025) to look at lineage-specific shifts in diversification rate on large, densely-sampled phylogenies across the Tree of Life doi.org/10.1093/evle...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 29/01/2026
GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomics www.biorxiv.org/content/10.64898/20…
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Nature @nature.com · 05/12/2025
Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes go.nature.com/4azJDF8
go.nature.com
Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.
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Pascal Title @ptitle.bsky.social · 05/12/2025
Check out our review/perspective piece on phylogenetic diversification analysis, intended for the 75th anniversary of @systbiol.bsky.social. I had the privilege of working with great coauthors, @fhenaodiaz.bsky.social, @tvasconcelos.bsky.social and @roszenil.bsky.social! doi.org/10.1093/sysb...
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Rowan J. Schley @rschley.bsky.social · 25/11/2025
🌿Excited to share our new study in New Phytologist! 🌿 Polyploidy is a major force in plant evolution, but is understudied in the tropics. We find that polyploidy evolved multiple times in Inga, a characteristic Neotropical tree radiation (1/n) 🧵. Full paper🔗: tinyurl.com/msnffhs8
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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 04/11/2025
Symbiotic diversification relies on an ancestral gene network in plants doi.org/10.1101/2025...
doi.org
Symbiotic diversification relies on an ancestral gene network in plants
Symbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification o...
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Avery Russell @draverbee.bsky.social · 23/10/2025
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!
Circular phylogeny showing the branching pattern of 30k plant species with lineages with poricidal and non poricidal taxa indicated. A small subset of poricidal taxa are illustrated around the phylogeny.
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)
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Journal of Experimental Botany @jxbotany.bsky.social · 23/09/2025
🌸 FLOWERING NEWSLETTER REVIEW 🌸 🧬 Since the discovery of the first plant sex-determining gene, more than 20 other genes have been identified. Here Marais et al. review what this tells us about the evolution of separate sexes (dioecy) in angiosperms 🌸 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪
Fig. 1 (shortened, full legend in paper): Advances in characterizing plant sex chromosomes using genomics in the last 15 years. Most of the systems have been characterized using non-standard methods (see text). References to this work are: Silene latifolia (Bergero and Charlesworth, 2011; Chibalina and Filatov, 2011; Muyle et al., 2012), Carica papaya (Wang et al., 2012), Diospyros lotus (Akagi et al., 2014), Rumex hastatulus (Hough et al., 2014), Asparagus officinalis (Harkess et al., 2017), Rumex rothschildianus (Crowson et al., 2017), Actinidia chinensis (Akagi et al., 2018), Fragaria species (Tennessen et al., 2018), Phoenix dactylifera (Torres et al., 2018), Mercurialis annua (Veltsos et al., 2019), Silene otites and Silene colpophylla (Balounova et al., 2019; Martin et al., 2019), Cannabis sativa (Prentout et al., 2020), Coccinia grandis (Fruchard et al., 2020), Populus and Salix species (Müller et al., 2020; Zhou et al., 2020a, b)...
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Ana Ignatieva @anaignatieva.bsky.social · 03/10/2025
Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)
academic.oup.com
The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies
Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla
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Matthew Hahn @3rdreviewer.bsky.social · 07/10/2025
New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance 1/ www.biorxiv.org/content/10.1...
biorxiv.org
Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees
Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 01/10/2025
Evolutionary and functional dynamics of chimeric pseudogenes ({varphi}genes) www.biorxiv.org/content/10.1101/202…
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 02/10/2025
Life-history evolution under artificial selection in a clonal plant www.biorxiv.org/content/10.1101/202…
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 07/10/2025
Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees www.biorxiv.org/content/10.1101/202…
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Hervé Sauquet @hsauquet.bsky.social · 30/11/2023
Excited to share the latest from the #eFLOWERproject: a morphospace study of angiosperm flowers led by Andrea López-Martínez and Marion Chartier! Angiosperm flowers reached their highest morphological diversity early in their evolutionary history nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
Angiosperm flowers reached their highest morphological diversity early in their evolutionary history
Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation a.....
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Josef Uyeda @pseudacris.bsky.social · 21/05/2025
Unsolicited listicle: My list of the most criminally underused/underappreciated phylogenetic comparative methods. Note, I am not involved in ANY of these methods; but I see them as things people are often asking of comparative data but have been surprised at how infrequently they have been cited.
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Hannah E. Marx, PhD @hannahmarx.bsky.social · 20/02/2025
"To plan for the future, it’s sometimes necessary to look to the past." Nice highlight of our work synthesizing temporal, taxonomic, and spatial trends in botanical collections to facilitate new research avenues @emlombardi.bsky.social @softcorebotany.bsky.social
news.unm.edu
New research prepares way for future botanical research
To plan for the future, it’s sometimes necessary to look to the past. To improve natural history collection and analysis in the future, a team of researchers is looking at collections of plants from a...
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Joseph W. Brown @josephwb.bsky.social · 11/12/2024
From Liam Revell et al. Testing for heterogeneous rates of discrete character evolution on phylogenies 🧪 academic.oup.com/jeb/article-...
academic.oup.com
Testing for heterogeneous rates of discrete character evolution on phylogenies
Abstract. Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is part
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Science News @scinews.bsky.social · 17/12/2024
13. How to prepare a high-quality manuscript PDF Download www.cell.com/action/showP...
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Science News @scinews.bsky.social · 21/12/2024
15. Tips on How to Write ‘Good’ "Develop your own voice and writing habits." bsky.app/profile/scin...
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Botanical Society of America @botsocamerica.bsky.social · 26/06/2025
A new interpretable #MachineLearning approach to identify plant traits associated with #PlantAdaptation to divergent ecoregions New in #AppsPlantSci by Sambadi Majumder & Chase Mason (@plantevoecophys.bsky.social) bsapubs.onlinelibrary.wiley.com/doi/full/10.... #ecophysiology #Helianthus #botany
Six maps of the two Level I ecoregions used in this study (the Great Plains, in pink, and the North American Deserts, in blue), showing visualizations of the predictions made using the gradient boosting machine (GBM) classifier, where points represent populations of Helianthus annuus. Each facet represents populations where a given proportion of genotypes was correctly predicted, arranged in descending order—all genotypes correctly predicted, four out of five, three out of four, two out of three, one out of two, and one out of four.
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Rob Waterhouse @rmwaterhouse.bsky.social · 27/08/2025
Genetic diversity matters because it determines species' capacity to adapt, persist, & recover onlinelibrary.wiley.com/doi/10.1111/... #biodiversity #genomics
onlinelibrary.wiley.com
Future Projections of Biodiversity Under Global Change Need to Include Genetic Diversity
This perspective argues that current methods for predicting biodiversity loss from future land use and climate change models are incomplete without incorporating projections of genetic diversity. Wit...
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plantgenomics.bsky.social @plantgenomics.bsky.social · 23/08/2025
Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution doi.org/10.1101/2025... Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions doi.org/10.1017/qpb....
doi.org
Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution
Dodders (Cuscuta spp.) is an obligated parasitic plant, which lost a large part of photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer (HGT). Their migrator...
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Joshua Weitz @joshuasweitz.bsky.social · 02/06/2025
Important modification... from the FAQ, it seems that students who are beginning their PhDs in Fall 2025 can apply (as long as matriculation date is August 1, 2025 or after). Awards start in Fall 2026. www.simonsfoundation.org/grant/simons...
simonsfoundation.org
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 24/08/2025
Partial retention of ancient function increases genetic pleiotropy in grass evolution www.biorxiv.org/content/10.1101/202…
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闵娅(Min Ya; Minya) PhD @minyaaa.bsky.social · 07/08/2025
I’m proud to present the main work from my postdoc, 3+ years in making from scratch, my ultimate #MimulusPropaganda up till now: The Moment That Symmetry Breaks. #plantscience #development #imaging #microscopy 🧪🌸🔬 w. Captain Yaowu & @biancatash.bsky.social www.biorxiv.org/content/10.1...
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Botanical Society of America @botsocamerica.bsky.social · 04/08/2025
The unique morphological basis & repeated evolutionary origins of personate flowers in #Penstemon New #AJB research by @trinitydepatie.bsky.social & @carriewessi.bsky.social doi.org/10.1002/ajb2... #botany #plantscience #phylogenomics #evolution #snapdragon
Personate flowered Penstemon hirsutus (top) and a closely related species with open flowers, P. smallii (bottom).
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Laurie Belcher @lauriebelch.bsky.social · 16/07/2025
OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...
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Pavel Kratina @kratina.bsky.social · 03/08/2025
Plasticity in climate change responses - just published in Biological Reviews What in the role of phenotypic plasticity as an adaptive response to climate change? Looking at mechanisms from the subcellular to the community and ecosystem levels. With Stollewerk, @davidboukal.bsky.social, et al.
onlinelibrary.wiley.com
Plasticity in climate change responses
Recent research has shown that climate change can both induce and modulate the expression of plastic traits but our understanding of the role of phenotypic plasticity as an adaptive response to clima...
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Kez Cleal @kezc.bsky.social · 26/06/2025
🚨 Our GW paper is out in Nature Methods!🥲 GW is a fast genomics browser (up to 100x faster!) github.com/kcleal/gw Also, just released a Python interface for GW github.com/kcleal/gwplot 📝 nature.com/articles/s4159… #Genomics #Bioinformatics
github.com
GitHub - kcleal/gw: Genome browser and variant annotation
Genome browser and variant annotation. Contribute to kcleal/gw development by creating an account on GitHub.
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Christian Landry @christianlandry.bsky.social · 17/06/2025
Loss-of-function mutations cannot simply eliminate some paralogous genes. Duplicated genes encoding homomeric proteins interfere with each other, leading to negative selection on the paralogs, even if they are fully redundant. See our new findings here: www.biorxiv.org/content/10.1...
biorxiv.org
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Sergi Valverde @svalver.bsky.social · 18/06/2025
A new paper in Nature Ecol & Evol by @rosafernandez.bsky.social et al. shows a #punctuated burst of genome evolution in #annelids as they transitioned from marine to land and freshwater habitats.
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Wayne Maddison @waynemaddison.bsky.social · 23/05/2025
Mesquite 4 beta released! Many new features, esp. phylogenomic. Check out the trailer and longer video on the home page: www.mesquiteproject.org, and use the download link there to get a copy. Feedback welcome! Ask and discuss on our new Google Group (groups.google.com/g/mesquite-p...).
The Mesquite icon shown, as a Mesquite leaf against a black background, and as a leave against the sun and a blue sky.
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Olivier Gimenez 🦦 @oaggimenez.bsky.social · 11/04/2025
🚨🎉 New paper "Ten quick tips to get you started with Bayesian statistics", hope you'll like it 😇🤗 ✍🏽 w/ Andy Royle, Marc Kéry and Chloé Nater 🔗 dx.plos.org/10.1371/jour... @plos.org @cnrsecologie.bsky.social @cnrsoccitanieest.bsky.social @umontpellier.bsky.social
Graphical summary of 10 quick tips to get started with Bayesian statistics and how they fit into a larger view of an analytical workflow with Bayesian models.
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Orlando Schwery @oschwery.bsky.social · 05/01/2025
🚨New #phylo paper alert!🚨 🌲+🔥= speciation? This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer evolution! (reading-access link on my website)
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Mike Barker @barkerms.bsky.social · 08/04/2025
The recording of last week's #PolyploidyWebinar featuring @raymondcast.bsky.social and @erichagen.bsky.social is now up! youtu.be/zmUyTO3jN6s
youtu.be
Polyploidy Webinar 2 April 2025
YouTube video by Mike Barker
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benkuhnhaeuser.bsky.social @benkuhnhaeuser.bsky.social · 13/03/2025
1️⃣ 🌍 Fresh out in #Science! The Asian tropics are among the most biodiverse places on Earth, but where does all that diversity come from? 🤔🔍 We used 🌴 phylogenomics and 🦴 new fossils to unravel the roles of different regions in generating and distributing species! 🌱 #Evolution
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Daohan "Rex" Jiang @rexjiang.bsky.social · 30/03/2025
My new preprint (with Matt Pennell & Lauren Sallan), which is my first at OIST, is now online! Finally, something cheerful in this depressing period... Thread 🧵 ahead:
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Pablo Garcia-Diaz @pablo-ecology.bsky.social · 14/03/2025
Shifting, expanding, or contracting? Range movement consequences for biodiversity 🌎🌐🧪 www.cell.com/trends/ecolo...
cell.com
Shifting, expanding, or contracting? Range movement consequences for biodiversity
Climate change is causing species ranges to shift, expand, and contract, with divergent and underappreciated consequences for local and global biodiversity. Widespread range shifts should increase loc...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 15/02/2025
Expanding plant trait databases using large language model: A case study on flower color extraction www.biorxiv.org/content/10.1101/202…
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Stacey D. Smith @iochromaland.bsky.social · 30/01/2025
1st paper from my lab this year. Chelsea & Erica showed that self-incompatible plants of this little groundcherry change to self-compatible as they get old, but they are only passable selfers, making less than half the number of seeds as plants are fixed for self-compatibility rdcu.be/d7ZM8
rdcu.be
Decay of self-incompatibility within a lifespan in Physalis acutifolia (Solanaceae)
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 28/01/2025
My favourite papers yield more questions than answers. This one is like that. Fascinating! www.biorxiv.org/content/10.1...
biorxiv.org
Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy
Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fit...
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André Marques @amarques.bsky.social · 13/11/2024
🧵𝐀 𝐭𝐡𝐫𝐞𝐚𝐝 𝐰𝐢𝐭𝐡 𝐟𝐞𝐚𝐭𝐮𝐫𝐞𝐝 𝐥𝐚𝐛 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬: 🧵 #1️⃣ Hofstatter, Thangavel, Lux et al. 2022 𝘊𝘦𝘭𝘭: 𝗥𝗲𝗽𝗲𝗮𝘁-𝗯𝗮𝘀𝗲𝗱 𝗵𝗼𝗹𝗼𝗰𝗲𝗻𝘁𝗿𝗼𝗺𝗲𝗿𝗲𝘀 𝗶𝗻𝗳𝗹𝘂𝗲𝗻𝗰𝗲 𝗴𝗲𝗻𝗼𝗺𝗲 𝗮𝗿𝗰𝗵𝗶𝘁𝗲𝗰𝘁𝘂𝗿𝗲 𝗮𝗻𝗱 𝗸𝗮𝗿𝘆𝗼𝘁𝘆𝗽𝗲 𝗲𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻 www.cell.com/cell/fulltex... @gokilavani.bsky.social #PlantSciences #Chromosome #Genomics #Meiosis4eva #Centromere 🌱🧬🔬
cell.com
Repeat-based holocentromeres influence genome architecture and karyotype evolution
While most eukaryotes contain single regional centromeres, several plant and animal lineages assemble holocentromeres along the entire chromosome length. The assembly of chromosome-scale holocentric g...
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André Marques @amarques.bsky.social · 07/01/2025
Happy to share our Tansley insight published in @newphyt.bsky.social nph.onlinelibrary.wiley.com/doi/epdf/10.... #plantscience #chromosome #centromere #meiosis
nph.onlinelibrary.wiley.com
Centromere diversity and its evolutionary impacts on plant karyotypes and plant reproduction
You have to enable JavaScript in your browser's settings in order to use the eReader.
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Jorge Navarro @jorgenavarro.bsky.social · 13/12/2024
Happy to announce the beta release of #BiGSCAPE2! This is the result of a great effort by Arjan Draisma, Catarina Loureiro and Nico Louwen, who worked tirelessly to improve the code from the ground up! Also major kudos to @marnixmedema.bsky.social for his leadership 💪 github.com/medema-group...
github.com
GitHub - medema-group/BiG-SCAPE: Similarity networks of biosynthetic gene clusters
Similarity networks of biosynthetic gene clusters. Contribute to medema-group/BiG-SCAPE development by creating an account on GitHub.
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