The deep sea is a vast and essentially continuous environment with few obvious barriers to gene flow. How populations diverge and new species form in this remote ecosystem is poorly understood. Phylogeographical analyses have begun to provide some insight into evolutionary processes at bathyal depths (<3000 m), but much less is known about evolution in the more extensive abyssal regions (>3000 m). Here, we quantify geographical and bathymetric patterns of genetic variation (16S rRNA mitochondrial gene) in the protobranch bivalve Ledella ultima, which is one of the most abundant abyssal protobranchs in the Atlantic with a broad bathymetric and geographical distribution. We found virtually no genetic divergence within basins and only modest divergence among eight Atlantic basins. Levels of population divergence among basins were related to geographical distance and were greater in the South Atlantic than in the North Atlantic. Ocean-wide patterns of genetic variation indicate basin-wide divergence that exceeds what others have found for abyssal organisms, but considerably less than bathyal protobranchs across similar geographical scales. Populations on either side of the Mid-Atlantic Ridge in the North Atlantic differed, suggesting the Ridge might impede gene flow at abyssal depths. Our results indicate that abyssal populations might be quite large (cosmopolitan), exhibit only modest genetic structure and probably provide little potential for the formation of new species.

The deep ocean supports a highly diverse and mostly endemic fauna, yet little is known about how or where new species form in this remote ecosystem. How speciation occurs is especially intriguing in the deep sea because few obvious barriers exist that would disrupt gene flow. Geographic and bathymetric patterns of genetic variation can provide key insights into how and where new species form. We quantified the population genetic structure of a protobranch bivalve, Neilonella salicensis, along a depth gradient (2200-3800 m) in the western North Atlantic using both nuclear (28S and calmodulin intron) and mitochondrial (cytochrome c oxidase subunit I) loci. A sharp genetic break occurred for each locus between populations above 2800 m and below 3200 m, defining two distinct clades with no nuclear or mitochondrial haplotypes shared between depth regimes. Bayesian phylogenetic analyses provided strong support for two clades, separated by depth, within N. salicensis. Although no morphological divergence was apparent, we suggest that the depth-related population genetic and phylogenetic divergence is indicative of a cryptic species. The frequent occurrence of various stages of divergence associated with species formation along bathymetric gradients suggests that depth, and the environmental gradients that attend changes in depth, probably play a fundamental role in the diversification of marine organisms, especially in deep water.

The ocean absorbs about one-third of anthropogenic carbon dioxide (Sabine et al., 2004), resulting in a decrease in oceanic pH. As pH drops, the concentration of carbonate ions decreases. Together, carbonate ion availability and pH exert a strong influence over the rates of calcification in organisms that use calcite or aragonite for skeletal, test, and shell formation (Georgian, DeLeo, et al., 2016;Melatunan, Calosi, Rundle, Widdicombe, & Moody, 2013;Waldbusser et al., 2015). The aragonite saturation horizon (ASH) is the boundary between waters saturated and undersaturated with respect to aragonite and is a potential boundary between net calcification and net dissolution of coral skeleton. The ASH currently lies between approximately 200 and 2,000 m in the world's ocean . This is deeper than the depth range that corals with photosynthetic symbionts can live, but nearly all cold-water AbstractCold-water corals (CWCs) are important foundation species in the world's largest ecosystem, the deep sea. They support a rich faunal diversity but are threatened by climate change and increased ocean acidification. As part of this study, fragments from three genetically distinct Lophelia pertusa colonies were subjected to ambient pH (pH = 7.9) and low pH (pH = 7.6) for six months. RNA was sampled at two, 4.5, and 8.5 weeks and sequenced. The colony from which the fragments were sampled explained most of the variance in expression patterns, but a general pattern emerged where upregulation of ion transport, required to maintain normal function and calcification, was coincident with lowered expression of genes involved in metabolic processes; RNA regulation and processing in particular. Furthermore, there was no differential expression of carbonic anhydrase detected in any analyses, which agrees with a previously described lack of response in enzyme activity in the same corals. However, one colony was able to maintain calcification longer than the other colonies when exposed to low pH and showed increased expression of ion transport genes including proton transport and expression of genes associated with formation of microtubules and the organic matrix, suggesting that certain genotypes may be better equipped to cope with ocean acidification in the future. While these genotypes exist in the contemporary gene pool, further stresses would reduce the genetic variability of the species, which would have repercussions for the maintenance of existing populations and the ecosystem as a whole. K E Y W O R D S coral, deep sea, ocean acidification, RNAseq, stress response, transcriptomics S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section.

Resource extraction from the ocean comes with ecosystem-wide risks, including threats to its biota such as the habitat forming corals that support elevated biomass and biodiversity. Despite catastrophic incidents like the Deepwater Horizon oil spill (DWHOS) disaster that occurred in 2010, offshore oil and gas drilling continues to occur around the world. Previous work investigating the toxicity of oil and the chemical dispersant used in an attempt to mitigate the effects of the DWHOS revealed that the dispersant elicits a stronger, negative physiological response than oil alone. However, little is known regarding the specific ways in which these anthropogenic pollutants impact organisms at the cellular level. To investigate the impacts of each pollutant and their synergistic effects on corals, we analyzed the transcriptional responses of the deep-sea octocorals Callogorgia delta and Paramuricea type B3 following 12 h of exposure to oil, dispersant, and mixtures of oil and dispersant. Analyses revealed that the highest levels of significant differential gene expression were found among the treatments containing dispersant, which corresponds to the significant effects observed in physiological experiments. Functional analyses of annotated transcripts further suggest both species- and colony-specific responses to the exposures, likely due to underlying cellular and physiological differences. However, some commonalities were observed among the responses to chemical stress across treatments and species, including immune and cellular stress responses, altered energy metabolism, and oxidative stress, elucidating how corals respond to chemical pollutants. As resource extraction is an ongoing threat, this study demonstrates the importance of considering the varied and diverse responses of biota to anthropogenic disturbances and the implications of introducing chemicals into vulnerable ecosystems like those associated with deep-sea corals.

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