#Phylogenomics-based
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respublications.bsky.social
New #OpenAccess research in #RESSystematicEnt

#Phylogenomics-based #ClickBeetle classification tackles multiple origins of phenotypic modifications
doi.org/10.1111/syen.70017

#Elateridae #Evolution #Classification
@gkergoat.bsky.social @wileyeco.bsky.social
November 18, 2025 at 11:05 AM
francoissabot.bsky.social
Surprise ! Using phylogenomics we identified/confirmed the presence of a third species, Bathycoccus catiminus! It was previously supposed to be a subgroup in the prasinos species (B3 type), but is in fact a single species!
Phylogenomic of the Bathycoccus genus and B. catiminus characterization. (A) Maximum-likelihood phylogenetic tree of Bathycoccus strains based on 1,200 shared genes. Species separation is derived from the branch length and marked by colors. The tree includes strain UST710 isolated and sequenced by Xu et al. (2024) for reference. O. tauri and M. pusilla are used as outgroups. Only branches with bootstrap values higher than 90% are displayed. Gene concordance factors are displayed for all visible branches. Transmission electron microscopy images of (B) B. prasinos, (C) B. catiminus strain isolated from the Banyuls bay, and (D) a close up of detached spider web scales from B. catiminus. N: nucleus, Cp: chloroplast, St: starch granule, Sc: scales. Bar = 100 nm. (E) Presence of B. catiminus in Banyuls bay seawater samples from 2019-2020 and 2020-2021 phytoplanktons blooms, identified using specific primers designed from non-conserved sequences of TOC1 ORF specific to B. catiminus. Fig S1: (A) Maximum-likelihood phylogeny and (B) 2D centroid structure of available Bathycoccus 18S rRNA ITS2 region. Only bootstrap values higher than 90% are displayed. Notable structural variations compared to B. prasinos 18S ITS2 region are marked by arrow and circles. 18S sequences were obtained from B. prasinos RCC1105 reference strain, B. calidus RCC716 strain and Bathycoccus sp. G8 strain respectively. Bathycoccus Kara environmental sequence was obtained from Belevich et al. (2021).
October 30, 2025 at 3:39 PM
10klepgenomes.bsky.social
🚀 Second STSM of 10kLepGenomes!
Jakub Tetla (Jagiellonian Univ., Poland) visited @jadrankarota.bsky.social (Lund, Sweden) from 24–26 Sept 2025.
The goal was to integrate museum collections with phylogenomics to study West Palearctic tiger moths.

#10kLepGenomes #Lepidoptera #Museomics
Jakub Tetla preparing a database of butterflies that will be used in the study, based on museum collections.
October 15, 2025 at 4:34 PM
laurentjacob.bsky.social
The decisions for LEGEND are out: legend2025.sciencesconf.org/data/book_le...

I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.

If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
Exploring the space of self-reproducing RNA using generative models, Martin Weigt Exploring the archaic introgression landscape of admixed populations through joint ancestry inference, Jazeps Medina Tretmanis [et al.] Predicting natural variation in the yeast phenotypic landscape with machine learning, Sakshi Khaiwal [et al.] Phylodynamic modeling with unsupervised Bayesian neural networks, Marino Gabriele [et al.] Likelihood-free inference of phylogenetic tree posterior distributions, Luc Blas- sel [et al.] Generative continuous time model reveals epistatic signatures in protein evolu- tion, Barrat-Charlaix Pierre Neural posterior estimation for high-dimensional genomic data from complex pop- ulation genetic models, Jiseon Min [et al.] A differentiable model for detecting diversifying selection directly from alignments in large-scale bacterial datasets, Leonie Lorenz [et al.] Detecting interspecific positive selection using transformers, Charlotte West [et al.] Predicting Multiple Sequence Alignment Uncertainty via Machine Learning, Lucia Martin-Fernandez [et al.] Graph Neural Networks for Likelihood-Free Inference in Diversification Mod- els, Amélie Leroy [et al.] Popformer: learning general signatures of genetic variation and natural selection with a self-supervised transformer, Leon Zong [et al.] PRIVET: PRIVacy metric based on Extreme value Theory, Antoine Szatkownik [et al.] Generative models for inferring the evolutionary history of the malaria vector Anopheles gambiae, Amelia Eneli [et al.] Language Models Outperform Supervised-Only Approaches for Conserved Ele- ment Comprehension, Eyes Robson [et al.] Identification and Classification of Orphan Genes, Spurious Orphan Genes, and Conserved Genes from the human microbiome, Chen Chen Neural Simulation-based inference of demography and selection, Francisco De Borja Campuzano Jiménez [et al.] Species Identification and aDNA Read Mapping Using k-mer Embeddings, Filip Thor [et al.] Contrastive Learning for Population Structure and Trait Prediction, Filip Thor [et al.] Protein and genomic language models chart a vast landscape of antiphage de- fenses, Mordret Ernest The Phylogenomics and Sparse Learning of Trait Innovations, Gaurav Diwan [et al.]
October 8, 2025 at 11:04 AM
journalsysevo.bsky.social
Family #tree level: Expert!

Wu et al. use #phylogenomics to shed light on the complex #evolutionary history of the #gymnosperm genus Cupressus, revealing East Asian–Tethyan disjunction.

Free to read version here:
doi.org/10.1111/jse....

#plant #systematics #JSE #cypress
This annotated world map, featuring clade diagrams and in situ morphological images, illustrates evolutionary history reconstructions of Cupressus L., based on 1991 single-copy nuclear genes and plastid genomes.
September 26, 2025 at 12:59 PM
microseqasm.bsky.social
✨ #MicroSeq2025 Plenary Highlight! ✨
Dr Jackie Mahar is an evolutionary virologist & bioinformatician based at CSIRO, managing projects on NGS-based phylogenomics of zoonotic & animal viruses for pathogen discovery, surveillance & viral ecology.
Register👇
trybooking.com/events/landing/1424679
Photograph of Dr Jackie Mahar, a researcher based at Agriculture Victoria Research. Her portrait is decorated with cartoons of microbes. Dr Jackie Mahar is an invited plenary speaker for MicroSeq2025.
September 1, 2025 at 4:42 AM
marcrr.ecoevo.social.ap.brid.gy
Jordi Paps: acoel flatworms to help distinguish the hypotheses of complex vs simple Urbilaterian. Problem: most deep animal “phylogenomics” is based on transcriptomics, which is biased. Instead, use only complete genomes (91 species) and incorporate genome-level processes into analysis.
Presence […]
Original post on ecoevo.social
ecoevo.social
August 21, 2025 at 12:42 PM
sinamajidian.bsky.social
Newly developed structure-based methods do not outperform standard sequence-based methods for large-scale phylogenomics
academic.oup.com/mbe/article/...
Fig. 1. Schematic representation of the pipeline. a) Primary amino acid sequences and 3Di-recoded structures from Homo sapiens’ proteins (seeds) are aligned against a dataset of 18 eukaryotic species with BlastP (Bp) and Foldseek (Fs), respectively. b) Before entering into the phylogenetic pipeline, Bp and Fs results are divided into four target sets per seed as shown in the Venn diagram. The number of query-target pairs in each target set before and after filtering is shown below. c) The four target sets of each seed are submitted to eight tree reconstruction methods. (For computational reasons, we restricted step C to 1,000 randomly selected seeds). *Among the randomly selected seeds, only those with at least four common hits entered into step C. Structure-based methods (3DI, GTR, FT, AF, and LLM) did not outperform sequence methods (LG, FM) in any of these metrics (Fig. 3). All the ML structure-based methods (3DI, GTR, AF, and LLM) clearly underperformed the ML sequence-based method (LG). Fig. 3.Boxplot distribution grouped by target set and tree reconstruction method of a) normalised Robinson–Foulds (RF) distance of decomposed single copy gene trees to the species tree, b) First Quartet Frequency support values (this measure indicates how many times the nodes in the species trees are observed in the gene trees), and c) number of gene duplications and losses inferred by gene tree-species tree reconciliation normalised by number of tips. Significant differences to LG are annotated as asterisks over each respective boxplot
August 20, 2025 at 1:45 AM
phypapers.bsky.social
Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes https://pubmed.ncbi.nlm.nih.gov/40809096/
August 15, 2025 at 6:01 PM
phypapers.bsky.social
Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes https://pubmed.ncbi.nlm.nih.gov/40809096/
August 15, 2025 at 12:02 AM
chercheurjuteux.com
Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics

academic.oup.com/mbe/article/...
Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics
Abstract. Recent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales.
academic.oup.com
August 12, 2025 at 3:41 PM
pflieglerlab.bsky.social
group.szbk.u-szeged.hu/minikonf/ We just registered to the Genetics mini-conference in Szeged! If you are based in Hungary, the deadline is today, there is still some time:) @balintnemeth.bsky.social will present on Saccharoymces phylogenomics, and I'll show our student #kveik and #mead projects.
Genetikai Műhelyek Magyarországon
Genetika minikonferencia
group.szbk.u-szeged.hu
July 15, 2025 at 4:05 PM
plantgenomics.bsky.social
A novel transformer-based platform for the prediction and design of biosynthetic gene clusters for (un)natural products
doi.org/10.1101/2025...

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis
doi.org/10.1101/2024...
A novel transformer-based platform for the prediction and design of biosynthetic gene clusters for (un)natural products
Biosynthetic gene clusters (BGCs), comprising sets of functionally related genes responsible for synthesizing complex natural products, are a rich source of bioactive compounds with pharmaceutical pot...
doi.org
June 13, 2025 at 4:28 AM
biogeopapers.bsky.social


Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
April 8, 2025 at 12:30 AM
biogeopapers.bsky.social


Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
April 1, 2025 at 12:18 AM
biogeopapers.bsky.social


Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
March 25, 2025 at 12:10 AM
dnarnaresearch.bsky.social
PlastidHub: an integrated analysis platform for plastid phylogenomics and comparative genomics
doi.org/10.1101/2025...

Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
doi.org/10.1101/2023...
Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
Objective Eutrophication poses a mounting concern in today’s world. Ceratophyllum submersum L. is one of many plants capable of living in eutrophic conditions, therefore it could play a critical role ...
doi.org
March 21, 2025 at 4:56 AM
biogeopapers.bsky.social


Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning

https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
March 18, 2025 at 12:40 AM
phypapers.bsky.social
Correction: Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships https://pubmed.ncbi.nlm.nih.gov/40075454/
March 15, 2025 at 6:34 AM
phypapers.bsky.social
Correction: Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships https://pubmed.ncbi.nlm.nih.gov/40075454/
March 15, 2025 at 2:52 AM
phypapers.bsky.social
Correction: Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships https://pubmed.ncbi.nlm.nih.gov/40075454/
March 14, 2025 at 5:48 AM
phypapers.bsky.social
Correction: Phylogenomics of angiosperms based on mitochondrial genes: insights into deep node relationships https://pubmed.ncbi.nlm.nih.gov/40075454/
March 14, 2025 at 1:48 AM
phypapers.bsky.social
Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
March 13, 2025 at 1:43 AM
phypapers.bsky.social
Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
March 12, 2025 at 3:17 AM
biorxivpreprint.bsky.social
Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning https://www.biorxiv.org/content/10.1101/2025.03.06.641773v1
March 11, 2025 at 2:05 PM