A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups. The evolutionary events inferred are: speciation, gene duplication and loss, horizontal gene transfer retaining the original gene copy. A transfer event with the loss of original gene copy is considered a combination of gene transfer and loss. The model maps gene evolution events onto the species phylogeny.
Download full-text PDF |
Source |
|---|
Publication Analysis
Top Keywords
Similar Publications
Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.
PLoS Comput Biol
January 2025
Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, United States of America.
Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response.
View Article and Find Full Text PDFPlant diversity across dimensions: Coupling biodiversity measures from the ground and the sky.
Sci Adv
January 2025
Department of Ecology, Evolution and Behavior, University of Minnesota, 1479 Gortner Ave., Saint Paul, MN 55108, USA.
Tracking biodiversity across biomes over space and time has emerged as an imperative in unified global efforts to manage our living planet for a sustainable future for humanity. We harness the National Ecological Observatory Network to develop routines using airborne spectroscopic imagery to predict multiple dimensions of plant biodiversity at continental scale across biomes in the US. Our findings show strong and positive associations between diversity metrics based on spectral species and ground-based plant species richness and other dimensions of plant diversity, whereas metrics based on distance matrices did not.
View Article and Find Full Text PDFLow oxygen but dynamic marine redox conditions permitted the Cambrian Radiation.
Sci Adv
January 2025
School of GeoSciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK.
Whether metazoan diversification during the Cambrian Radiation was driven by increased marine oxygenation remains highly debated. Repeated global oceanic oxygenation events have been inferred during this interval, but the degree of shallow marine oxygenation and its relationship to biodiversification and clade appearance remain uncertain. To resolve this, we interrogate an interval from ~527 to 519 Ma, encompassing multiple proposed global oceanic oxygenation events.
View Article and Find Full Text PDFChromosome-scale genome dynamics reveal signatures of independent haplotype evolution in the ancient asexual mite .
Sci Adv
January 2025
Institute of Zoology, University of Cologne, Cologne, Germany.
Some unique asexual species persist over time and contradict the consensus that sex is a prerequisite for long-term evolutionary survival. How they escape the dead-end fate remains enigmatic. Here, we generated a haplotype-resolved genome assembly on the basis of a single individual and collected genomic data from worldwide populations of the parthenogenetic diploid oribatid mite to identify signatures of persistence without sex.
View Article and Find Full Text PDFAn ancient apical patterning system sets the position of the forebrain in chordates.
Sci Adv
January 2025
Department of Zoology, University of Cambridge, Cambridge, UK.
The evolutionary origin of the vertebrate brain remains a major subject of debate, as its development from a dorsal tubular neuroepithelium is unique to chordates. To shed light on the evolutionary emergence of the vertebrate brain, we compared anterior neuroectoderm development across deuterostome species, using available single-cell datasets from sea urchin, amphioxus, and zebrafish embryos. We identified a conserved gene co-expression module, comparable to the anterior gene regulatory network (aGRN) controlling apical organ development in ambulacrarians, and spatially mapped it by multiplexed in situ hybridization to the developing retina and hypothalamus of chordates.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!