Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1118809 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ancient incomplete inter-generic lineage sorting of Hyles and Rhodafra mitochondria (Lepidoptera: Sphingidae)
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Project description:The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.
2026-02-11 | GSE319137 | GEO
Project description:Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Incomplete Lineage Sorting
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Project description:Developmental gene function is conserved over deep time, but similar cis-regulatory sequence conservation is rarely found. However, rapid sequence turnover, paleopolyploidy, structural variation, and limited phylogenomic sampling have impeded conserved non-coding sequence (CNS) discovery. Using Conservatory, an algorithm that leverages microsynteny and iterative alignments to map CNS-gene associations over evolution, we uncovered ~2.3M CNSs, including over 3,000 predating angiosperms, from 284 plant species spanning 400 million years of diversification. Ancient CNSs were enriched near developmental regulators, and mutagenizing those near HOMEOBOX genes produced strong phenotypes. Tracing CNS evolution uncovered key principles: CNS spacing varies, but order is conserved; genomic rearrangements form new CNS-gene associations; and ancient CNSs are preferentially retained among paralogs but often are lost as cohorts or evolve into lineage-specific CNSs.
2025-11-24 | GSE307325 | GEO
Project description:Using Genomic Location and Coalescent Simulation to identify Paralogy, Hybridisation and Incomplete Lineage Sorting in nuclear loci
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Project description:Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
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Project description:Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus
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Project description:Bryophytes comprise mosses, liverworts and hornworts. The chromatin landscapes of mosses and liverworts are different, leaving open the question regarding the identity of the chromatin landscape of all bryophytes. To address this question we obtained a genome wide profile of 5-methylated cytosine from a model hornwort, Anthoceros agrestis.
2023-11-10 | GSE218877 | GEO