The processes that control diversification and speciation in deep-sea species are poorly known. Here, we analyzed data produced by Restriction-Site Associated DNA Sequencing (RAD-Seq) of octocorals in the genus Paramuricea to elucidate diversification patterns and examine the role of environmental gradients in their evolution. The genus Paramuricea evolved around 8 MYA, with a high probability of a broad ancestral depth range from mesophotic depths to the deep sea. At around 1-2 MYA, the genus diversified across the continental slope of the deep North Atlantic, supporting the depth-differentiation hypothesis, with no invasions back into shallower depths (< 200 m). Diversification in the deep sea generally occurred from shallower, warmer waters to deeper, colder depths of the lower continental slope. We also found that the vertical structure of water masses was influential in shaping phylogeographic patterns across the North Atlantic Ocean, with clades found in either upper/intermediate or intermediate/deep water masses. Our data suggest that species diverged first because of environmental conditions, including depth, temperature, and/or water mass, and then diversified into different geographical regions multiple times. Our results highlight the role of the environment in driving the evolution and distribution of Paramuricea throughout the deep sea. Furthermore, our study supports prior work showing the utility of genomic approaches over the conventionally-used DNA barcodes in octocoral species delimitation.

The alternative sigma factor RpoS regulates transcription of over 1000 genes in Escherichia coli in response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of RpoS for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured RpoS levels at various times during the entry to stationary phase, or in response to high osmolarity or low temperature, and found that the time required to reach maximum levels varied by several hours. We quantified the transcriptome across these stresses using RNA-seq. The number of differentially expressed genes differed among stresses, with 1379 DE genes were identified in in stationary phase, 633 in high osmolarity, and 302 in cold shock. To quantify the timing of gene expression, we fit sigmoid or double sigmoid models to differentially expressed genes in each stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS. The timing of individual genes' expression was not correlated across stresses. Taken together, our results demonstrate E. coli activates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response to each stress.