Phylogenomic
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Related Articles from SNS
Cohort-HMM marker recruitment with per-OG orthology QC for phylogenomic supermatrices
OrthoFinder's all-vs-all DIAMOND step systematically misses single-copy orthogroups (SC OGs) at deep taxonomic divergence: a marker recovered cleanly within a tightly defined cohort is dropped when the same marker is searched against phylum-broad metagenome-assembled genome (MAG) sets, because pairwise sequence similarity falls below DIAMOND's detection threshold even when the underlying ortholog is present. The result is biased dropout - supermatrices that retain genomes near the cohort but...
Researchers use phylogenomics to identify cyanobacteria in Shenandoah River
You've probably seen slimy mats of brownish green clinging to rocks in streams or on lake beds, and perhaps not given it another thought. But George Mason University's Rosalina Stancheva Christova has. For more than 20 years, Christova, an assistant professor in the College of Science, has been researching Microcoleus, a common mat-forming cyanobacterium found in streams and lakes worldwide.
Genomic hallmarks of parasexual reproduction in three hybrid groups of the human pathogen Cryptococcus neoformans
Hybridization is a major driver of fungal evolution, yet knowledge of the molecular mechanisms underpinning hybridization and its genomic impact remain limited. Here, we analyse 197 Cryptococcus neoformans genomic sequences, including 13 newly sequenced strains, identifying three genetically clustered and distinct hybrid groups (H1, H2 and H3) each with unique parental origins and ecological associations. Using phylogenomics, population structure analyses, and long-read genome assemblies, we...
Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses
Grasses (Poaceae) dominate terrestrial ecosystems and sustain global food security, yet the genomic principles enabling their repeated adaptation to extreme environments remain unresolved. Combining dense phylogenomic sampling, global environmental data, and genomic large language models (gLLMs), we characterize the mutational targets underlying environmental adaptation across 707 genomes from 569 species spanning 17 climate zones. We identify 19-30 phylogenetically independent transitions...
Gene ancestries reveal diverse microbial associations during eukaryogenesis
Abstract The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4,5,6 and the role of interactions with viruses7,8,9 remain contentious.
Trichome and inflorescence evolution in the paleopolyploid tree genus Greyia Hook. & Harv.
The southern African endemic tree genus Greyia Hook. & Harv. (Francoaceae, Geraniales) comprises three species distinguished by striking variation in trichome morphology and floral architecture, yet the genomic and regulatory basis of these traits has remained largely unexplored. Here, we present chromosome-scale genome assemblies for all recognized Greyia species, namely Greyia radlkoferi, Greyia sutherlandii, and Greyia flanaganii, providing the first high-quality genomic resources for...
Tracing Sticky Trails: The Historical Biogeography of Australia's Glandular Goose-foots (Dysphania, Chenopodioideae, Amaranthaceae)
Abstract Aim The overarching aim of this study is to reconstruct the spatiotemporal evolutionary history of Australian Dysphania, including testing the littoral connection hypothesis, assessing the role of reticulation, and identifying the major drivers of diversification within the lineage. Location Australia and New Zealand Taxon Dysphania, Chenopodioideae, Amaranthaceae, Caryophyllales, Angiosperms Methods Using a DNA sequence dataset based on a target enrichment approach with custom...