Editor's Note: Some of the articles described below are not yet available at the PNAS site but are scheduled to be posted this week.
A Chinese Academy of Sciences-led team describes accelerated limb development gene evolution and other arboreal adaptations in Asian flying treefrogs known for their climbing and gliding abilities. After putting together de novo genome assemblies for a gliding treefrog species, Rhacophorus kio, and a related non-gliding species, R. dugritei, the researchers highlighted limb development and keratin cytoskeleton genes with apparent ties to climbing, using follow-up tadpole time series expression experiments to focus in on Wnt signaling and vascular remodeling pathways that are co-expressed during the development of fully webbed feet rather than weakly-webbed feet. "These findings highlight the molecular basis of phenotypes that facilitate expansion into new niches," the authors report, "and provide insights into the importance of local adaptation in shaping phenotypes and locomotion patterns."
Researchers in China and Israel retrace spiny mouse sympatric speciation in Mount Carmel's "Evolution Canyon I" (EC I). The area is known for its dramatically different microclimates, the team says, and has long been used as a site to study evolutionary events such as sympatric speciation — the potential development of a new species from an ancestral group that persists in roughly the same area. Using whole-genome sequencing, de novo genome assembly, DNA methylation profiling, and behavioral clues, the authors compared Acomys cahirinus spiny mice from a tropical EC I site known as the African Slope and from a more temperate EC I area dubbed the European Slope, uncovering SNP and structural variant difference in across hundreds of genome regions. Their results also pointed to waning gene flow between the tropical and temperate mouse populations as they split from one another, along with early DNA methylation differences, including epigenetic changes suspected of influencing circadian gene regulation.
A team from Monash University considers horizontal gene transfer (HGT) dynamics and their consequences on fitness in Helicobacter pylori populations. With the help of whole-genome sequencing and growth assays for following microbial fitness effects, the researchers tracked and analyzed the evolution of lab-grown H. pylori populations grown in the presence of transferred genetic variants, flagging more than 40,000 such variants obtained by the bugs via HGT. From these and other experiments, the authors saw that "natural transformation increases the rate of adaptation but comes at the cost of significant genetic load. We show that this cost is circumvented by recombination, which increases the efficiency of selection by decoupling deleterious and beneficial genetic variants."