The changing physical and ecological meanings of North Pacific Ocean climate indices.

Climate change is likely to change the relationships between commonly used climate indices and underlying patterns of climate variability, but this complexity is rarely considered in studies using climate indices. Here, we show that the physical and ecological conditions mapping onto the Pacific Decadal Oscillation (PDO) index and North Pacific Gyre Oscillation (NPGO) index have changed over multidecadal timescales. These changes apparently began around a 1988/1989 North Pacific climate shift that was marked by abrupt northeast Pacific warming, declining temporal variance in the Aleutian Low (a leading atmospheric driver of the PDO), and increasing correlation between the PDO and NPGO patterns. Sea level pressure and surface temperature patterns associated with each climate index changed after 1988/1989, indicating that identical index values reflect different states of basin-scale climate over time. The PDO and NPGO also show time-dependent skill as indices of regional northeast Pacific ecosystem variability. Since the late 1980s, both indices have become less relevant to physical-ecological variability in regional ecosystems from the Bering Sea to the southern California Current. Users of these climate indices should be aware of nonstationary relationships with underlying climate variability within the historical record, and the potential for further nonstationarity with ongoing climate change.

Exoskeleton dissolution with mechanoreceptor damage in larval Dungeness crab related to severity of present-day ocean acidification vertical gradients.

Ocean acidification (OA) along the US West Coast is intensifying faster than observed in the global ocean. This is particularly true in nearshore regions (<200 m) that experience a lower buffering capacity while at the same time providing important habitats for ecologically and economically significant species. While the literature on the effects of OA from laboratory experiments is voluminous, there is little understanding of present-day OA in-situ effects on marine life. Dungeness crab (Metacarcinus magister) is perennially one of the most valuable commercial and recreational fisheries. We focused on establishing OA-related vulnerability of larval crustacean based on mineralogical and elemental carapace to external and internal carapace dissolution by using a combination of different methods ranging from scanning electron microscopy, energy dispersive X-ray spectroscopy, elemental mapping and X-ray diffraction. By integrating carapace features with the chemical observations and biogeochemical model hindcast, we identify the occurrence of external carapace dissolution related to the steepest Ω calcite gradients (∆Ωcal,60) in the water column. Dissolution features are observed across the carapace, pereopods (legs), and around the calcified areas surrounding neuritic canals of mechanoreceptors. The carapace dissolution is the most extensive in the coastal habitats under prolonged (1-month) long exposure, as demonstrated by the use of the model hindcast. Such dissolution has a potential to destabilize mechanoreceptors with important sensory and behavioral functions, a pathway of sensitivity to OA. Carapace dissolution is negatively related to crab larval width, demonstrating a basis for energetic trade-offs. Using a retrospective prediction from a regression models, we estimate an 8.3% increase in external carapace dissolution over the last two decades and identified a set of affected OA-related sublethal pathways to inform future risk assessment studies of Dungeness crabs.

Development of a CRISPR-Cas9 System for Efficient Genome Editing of Candida lusitaniae.

Candida lusitaniae is a member of the Candida clade that includes a diverse group of fungal species relevant to both human health and biotechnology. This species exhibits a full sexual cycle to undergo interconversion between haploid and diploid forms. C. lusitaniae is also an emerging opportunistic pathogen that can cause serious bloodstream infections in the clinic and yet has often proven to be refractory to facile genetic manipulations. In this work, we develop a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (Cas9) system to enable genome editing of C. lusitaniae. We demonstrate that expression of CRISPR-Cas9 components under species-specific promoters is necessary for efficient gene targeting and can be successfully applied to multiple genes in both haploid and diploid isolates. Gene deletion efficiencies with CRISPR-Cas9 were further enhanced in C. lusitaniae strains lacking the established nonhomologous end joining (NHEJ) factors Ku70 and DNA ligase 4. These results indicate that NHEJ plays an important role in directing the repair of DNA double-strand breaks (DSBs) in C. lusitaniae and that removal of this pathway increases integration of gene deletion templates by homologous recombination. The described approaches significantly enhance the ability to perform genetic studies in, and promote understanding of, this emerging human pathogen and model sexual species. IMPORTANCE The ability to perform efficient genome editing is a key development for detailed mechanistic studies of a species. Candida lusitaniae is an important member of the Candida clade and is relevant both as an emerging human pathogen and as a model for understanding mechanisms of sexual reproduction. We highlight the development of a CRISPR-Cas9 system for efficient genome manipulation in C. lusitaniae and demonstrate the importance of species-specific promoters for expression of CRISPR components. We also demonstrate that the NHEJ pathway contributes to non-template-mediated repair of DNA DSBs and that removal of this pathway enhances efficiencies of gene targeting by CRISPR-Cas9. These results therefore establish important genetic tools for further exploration of C. lusitaniae biology.

Temporal Stability of Genetic Structure in a Mesopelagic Copepod.

Although stochasticity in oceanographic conditions is known to be an important driver of temporal genetic change in many marine species, little is known about whether genetically distinct plankton populations can persist in open ocean habitats. A prior study demonstrated significant population genetic structure among oceanic gyres in the mesopelagic copepod Haloptilus longicornis in both the Atlantic and Pacific Oceans, and we hypothesized that populations within each gyre represent distinct gene pools that persist over time. We tested this expectation through basin-scale sampling across the Atlantic Ocean in 2010 and 2012. Using both mitochondrial (mtCOII) and microsatellite markers (7 loci), we show that the genetic composition of populations was stable across two years in both the northern and southern subtropical gyres. Genetic variation in this species was partitioned among ocean gyres (FCT = 0.285, P < 0.0001 for mtCOII, FCT = 0.013, P < 0.0001 for microsatellites), suggesting strong spatial population structure, but no significant partitioning was found among sampling years. This temporal persistence of population structure across a large geographic scale was coupled with chaotic genetic patchiness at smaller spatial scales, but the magnitude of genetic differentiation was an order of magnitude lower at these smaller scales. Our results demonstrate that genetically distinct plankton populations persist over time in highly-dispersive open ocean habitats, and this is the first study to rigorously test for temporal stability of large scale population structure in the plankton.

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod.

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.