ABSTRACT: Phylogenomics of a genus of Great Speciators reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
Project description:Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus
Project description:Using Genomic Location and Coalescent Simulation to identify Paralogy, Hybridisation and Incomplete Lineage Sorting in nuclear loci
Project description:Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.
Project description:Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
| PRJNA576431 | ENA
Project description:Phylogenomics of the gymnosperm genus Abies
Project description:Transcriptome analysis was conducted to investigate the gene expression profiles of pDCs using bulk RNA-sequencing (RNA-seq). Peripheral blood mononuclear cells (PBMCs) from healthy donors (n=3) were stained with lineage markers (CD3, CD14, CD16, CD19, and CD56), and pDCs were identified via flow cytometry (fluorescence-activated cell sorting [FACS]) based on the co-expression of IL-3R (CD123) and BDCA-2 (CD303). mDCs were identified using CD11c and sorted from the same PBMC donor as a control. After sorting, mRNA was extracted from the sorted cells, including mDCs and pDCs. The whole transcriptome profile was analyzed via RNA-seq.
