Seongyeon Kang

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...

GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomics https://www.biorxiv.org/content/10.64898/2026.01.27.702036v1

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.

Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes

go.nature.com/4azJDF8

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...

🌿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

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...

Symbiotic diversification relies on an ancestral gene network in plants
doi.org/10.1101/2025...

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!

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)

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)...

🌸 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 🧪

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

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)

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...

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...

Evolutionary and functional dynamics of chimeric pseudogenes ({varphi}genes) https://www.biorxiv.org/content/10.1101/2025.10.01.679709v1

Life-history evolution under artificial selection in a clonal plant https://www.biorxiv.org/content/10.1101/2025.10.01.679824v1

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees https://www.biorxiv.org/content/10.1101/2025.10.06.680724v1

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/...

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.

"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

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

From Liam Revell et al. Testing for heterogeneous rates of discrete character evolution on phylogenies 🧪 academic.oup.com/jeb/article-...

13. How to prepare a high-quality manuscript

PDF Download
www.cell.com/action/showP...

15. Tips on How to Write ‘Good’

"Develop your own voice and writing habits."

bsky.app/profile/scin...

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.

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

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...

Genetic diversity matters because it determines species' capacity to adapt, persist, & recover onlinelibrary.wiley.com/doi/10.1111/... #biodiversity #genomics

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...

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....

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...

Partial retention of ancient function increases genetic pleiotropy in grass evolution https://www.biorxiv.org/content/10.1101/2025.08.22.670905v1

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...

Personate flowered Penstemon hirsutus (top) and a closely related species with open flowers, P. smallii (bottom).

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

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...

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...

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.

GitHub - kcleal/gw: Genome browser and variant annotation Genome browser and variant annotation. Contribute to kcleal/gw development by creating an account on GitHub.

🚨 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