NeoDarwinian Review

The article "Crossovers are associated with mutation and biased gene conversion at recombination hotspots" by Kong et al. presents direct evidence that crossing over, a key process in meiosis , is mutagenic . The authors sequenced large numbers of single crossover molecules obtained from human sperm for two recombination hotspots and found that crossovers carried more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The authors also found that GC alleles, which are more likely to be methylated (epigenetics), were preferentially transmitted during crossing over, opposing mutation. This GC-biased gene conversion (gBGC) predominated over mutation in the sequence evolution of hotspots. These findings suggest that gBGC may be an adaptation to counteract the mutational load of recombination. The article's findings are significant because they provide direct evidence that crossing over is an important source of new mu...

The article "Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes" by Dingle et al. (2023) investigates how the set of all possible RNA secondary structure (SS) shapes is populated in nature.  The authors argue that a strong phenotype bias, which limits evolutionary dynamics to a subset of structures that are easy to "find," is the primary explanation for this pattern. Phenotype bias is the tendency of certain phenotypes to arise more readily than others due to the constraints of development. It is also referred to as developmental bias. To support their argument, Dingle et al. use a combination of theoretical and computational methods. They first show that the number of possible RNA SS shapes is extremely large, far exceeding the number of shapes that have been observed in nature.  RNA SS shapes, or RNA secondary structure shapes, are the two-dimensional representations of RNA molecules. They a...

"In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. … Most of the genome that we used to think was there for spacer turns out to be doing stuff.” - Francis Collins, head of the Human Genome Project The journal article "Overcoming challenges and dogmas to understand the functions of pseudogenes" by Cheetham, Faulkner, and Dinger (2020) discusses the growing body of evidence that pseudogenes play important biological roles, despite their previous classification as "junk DNA." The authors argue that this misclassification is due in part to the pejorative inference of the term "pseudogene" itself, as well as to the limitations of traditional genome annotation practices. Pseudogenes are defined as regions of the genome that contain defective copies of genes. They can arise through a vari...

A morphospace derived from all 548 characters for 248 extant taxa. The axes summarize morphological disparity derived from the observed dissimilarity between living taxa  The article "Evolution of phenotypic disparity in the plant kingdom" by James Clark et al. was published in Nature Plants on September 4, 2023. The article presents a comprehensive analysis of the evolution of plant diversity, using a dataset of over 25,000 species and 100 phenotypic traits. The authors found that plant phenotypic disparity has increased episodically throughout evolutionary history. Phenotypic disparity is the variation in form presented by a group of organisms. It is a measure of the diversity of physical characteristics within a clade, such as body size, shape, and color. Phenotypic disparity can be studied at different taxonomic levels, from within a single species to across all of life. This pattern is mirrored by the evolution of new reproductive innovations and the extinc...