The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders

On the impact of an offshore bathymetric anomaly on surf zone rip channels

We use a nonlinear morphodynamic model to demonstrate that the presence of a single persistent offshore bathymetric anomaly strongly affects the formation, nonlinear evolution and saturation of surf zone rip channels. In the case of an offshore bump or trough and waves with oblique incidence, a rip channel shoreward of the anomaly is enforced by the more seaward alongshore variability in depth. The degree of rip channel enforcement is controlled by the strength of the rotational nature of surf zone rip current circulations, which is, in turn, driven by differential broken wave energy dissipation induced by wave refraction across the offshore bathymetric anomaly. The alongshore location of this forced\ud rip channel is more stable with increasing offshore anomaly amplitude, decreasing offshore wave obliquity and decreasing bathymetric anomaly distance to the shore. Simulations show that rip channel behavior downdrift and updrift of the offshore perturbation are different. In our numerical experiments, downdrift rip channels have systematically larger alongshore scales, smaller alongshore migration rates and more erosive megacusps than those updrift. Rip channels therefore self-organize into patterns of different alongshore scales and migration rates as a result of an alongshore perturbation in the wave forcing enforced by wave refraction across an offshore bathymetric anomaly. These simulations are qualitatively corroborated by video observations of sandbar behavior during a down-state sequence at a site with a persistent offshore trough

Regulation of single-cell genome organization into TADs and chromatin nanodomains.

Super-resolution microscopy identifies sub-topologically associating domain (TAD) nanodomains and intercellular heterogeneity in TAD conformation and insulation. Cohesin or CTCF depletion regulates distinct types of chromatin contacts at the TAD but not nanodomain level.The genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs)(1-4). However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy. TAD structures and physical insulation associated with their borders are variable between individual cells, yet chromatin intermingling is enriched within TADs compared to adjacent TADs in most cells. The spatial segregation of TADs is further exacerbated during cell differentiation. Favored interactions within TADs are regulated by cohesin and CTCF through distinct mechanisms: cohesin generates chromatin contacts and intermingling while CTCF prevents inter-TAD contacts. Furthermore, TADs are subdivided into discrete nanodomains, which persist in cells depleted of CTCF or cohesin, whereas disruption of nucleosome contacts alters their structural organization. Altogether, these results provide a physical basis for the folding of individual chromosomes at the nanoscale