Month: September 2022

CLONAL SMALL POPULATIONS. "Star-like trees arise because viruses are more likely to share a recent common ancestor when the population is small, and a growing population has an increasingly smaller population size towards the past." https://lnkd.in/dDjCWve View in LinkedIn

AIDS STAR. "The phylogeny of HIV provides a good example of a star-like tree, as the prevalence of HIV infection rose rapidly throughout the 1980s." https://lnkd.in/dDjCWve View in LinkedIn

CONFOUNDED TRADITIONAL TREES. "The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees." https://lnkd.in/dkR5NBx View in LinkedIn

VERTICAL VS HORIZONTAL EVOLUTION. "Evolution is mediated not only by random mutations over a number of generations (vertical evolution), but also through the mixture of genomic material between individuals of different lineages (horizontal evolution)." http://www.pnas.org/content/110/46/18566.full View in LinkedIn

VERTICAL TREES MISS RELATIONSHIPS. "Phylogenetic trees, however, cannot capture horizontal, or reticulate, events, which occur when distinct clades merge together to form a new hybrid lineage." http://www.pnas.org/content/110/46/18566.full View in LinkedIn

SO ENDS this first weekend on viruses. These enigmatic and talented creatures have been maligned by biologists who either have only focused on their disease roles, or who have stubbornly refused to drop a Victorian mindset that assumed that they are not alive. Alive they are, in an extreme version of outsourcing. And causing diseases is a minor part of the full spectrum of these creatures. Undoing these two biases is underway but may take decades more to sink into the general consciousness. View in LinkedIn

CHIMERIC GENES. “More interestingly, MULE-derived putative genes tended to arise from multiple parental sequences, which could potentially form novel chimeric gene structures. This is consistent with our previous discovery that the formation of chimeric ORFs is the general mode of new gene origination in Oryza species.” (MULEs = Mutator-like transposable elements; ORF = open reading frame; Oryza = crop plants). http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0954-8 View in LinkedIn

EPIGENETIC LINKS. “We showed that the methylation level in three cytosine contexts of MULE internal sequences increases and that the CHH context of MULE TIRs decreases over evolutionary time. This result implies that genic-MULEs which acquired potentially functional coding sequences and were maintained in the multiple Oryza species over millions of years might acquire epigenetic marks in their internal and TIR sequences that are needed to maintain their stability in the genome.” (MULEs = Mutator-like transposable elements; TIR = terminated inverted repeats). http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0954-8 View in LinkedIn

EPIGENETICS AND NOVELTY. “Our results suggest that DNA methylation may play an important role in the origination and survival of MULE-derived genes through modulation of their stability and expression, which might be a general mechanism for all the TE-derived genes, thereby contributing to the evolution of gene novelty.” (MULEs = Mutator-like transposable elements; TE = transposable element). https://lnkd.in/dPzCkty View in LinkedIn

NONCODING REGULATORY VARIANTS. "It is now well established that noncoding regulatory variants play a central role in the genetics of common diseases and in evolution. However, until recently, we have known little about the mechanisms by which most regulatory variants act." https://lnkd.in/dFv6Tsi View in LinkedIn