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opencc-zeroOct 2020View details →

Data for: Performance of a high-frequency (180 kHz) acoustic array for tracking juvenile Pacific salmon in the coastal ocean

Background Acoustic telemetry is now a key research tool used to quantify juvenile salmon survival, but transmitter size has limited past studies to larger smolts (>130 mm fork length). New, smaller, higher-frequency transmitters ("tags") allow studies on a larger fraction of the smolt size spectrum (>95 mm); however, detection range and study duration are also reduced, introducing new challenges. The potential cost implications are not trivial. With these new transmitters in mind, we designed, deployed, and tested the performance of a dual-frequency receiver array design in the Discovery Islands region of British Columbia, Canada. We double-tagged 50 juvenile steelhead (Oncorhynchus mykiss) with large 69 kHz tags (VEMCO model V9-1H) and small 180 kHz tags (model V4-1H). The more powerful 69 kHz tags were used to determine fish presence in order to estimate the detection efficiency (DE) of the 180 kHz tags. We then compared the standard error of the survival estimate produced from the tracking data using the two tag types which has important implications for array performance and hypothesis testing in the sea. Results Perfect detection of the 69 kHz tags allowed us to determine the DE of the 180 kHz tags. Although the 180 kHz tags began to expire during the study, the estimated DE was acceptable at 76% (SE = 9%) when we include single detections. However, confidence intervals on steelhead survival (64%) were 1.5x larger for the 180 kHz tags (47-85% vs. 51-77% for 69 kHz) because of the reduced DE. Conclusions The array design performed well; however, single detections of the 180 kHz tags indicates that under slightly different circumstances the DE could have been compromised, emphasizing the need to carefully consider the interaction of animal migration characteristics, study design, and tag programming when designing telemetry arrays. To increase DE and improve the precision of 180 kHz-based survival estimates presented here requires either an increase in receiver density, an increase in tag sample size (and modified transmitter programming), or both. The optimal solution depends on transmitter costs, array infrastructure costs, annual maintenance costs, and array use (i.e., contributors). Importantly, the use of smaller tags reduces potential tag burden effects and allows early marine migration studies to be extended to Pacific salmon populations that have been previously impossible to study.

opencc-zeroDec 2020View details →

Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean

Stony corals (Scleractinia) form the basis for some of the most diverse ecosystems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals, we here investigated phylogenetic relationships between morphologically defined species and genetic lineages in the genus Galaxea (Euphyllidae) using a combined phylogenomic and phylogeographic approach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differentiated lineages (L, S & L+) in the western Pacific, but their distribution and relationship to other species in the genus were unknown. Based on genomic (RAD-seq) and mitochondrial sequence data (non-coding region between cytb and ND2) we investigated whether the morphological taxa represent genetically coherent entities and what is the phylogenetic relationship and spatial distribution of the three lineages of G. fascicularis throughout the observed species range. Using the RAD-seq data, we find that the genus Galaxea is monophyletic and contains three distinct clades: an Indo-Pacific, a Pacific, and a small clade restricted to the Chagos Archipelago. The three lineages of G. fascicularis were associated with different RAD-seq clades, with the 'L' lineage showing some morphological distinction from the other two lineages (larger more asymmetrical polyps). In addition to these, three more genetic lineages in G. fascicularis may be distinguished – a Chagossian, an Ogasawaran, and one from the Indian-Red Sea. Among nominal taxa for which we have multiple samples, G. horrescens was the only monophyletic species. The mitochondrial non-coding region is highly conserved apart from the length polymorphism used to define L, S & L+ lineages and lacks the power to distinguish morphological and genetic groups resolved with genomic RAD-sequencing. The polyphyletic nature of most species warrants a careful examination of the accepted taxonomy of this group with voucher collections and their comparison to type specimens to resolve species boundaries. Further insight to the speciation process in corals will require international cooperation for the sharing of specimens to facilitate scientific discovery.

opencc-by-4.0Jan 2021View details →

Assessing sedimentary detrital Pb isotopes as a dust tracer in the Pacific Ocean

Dataset in Support of Manuscript "Assessing sedimentary detrital Pb isotopes as a dust tracer in the Pacific Ocean", in review at Paleoceanography and Paleoclimatology.  Data includes Pb isotopes of detrital fractions from ocean sediments and source regions.

opencc-zeroJan 2021View details →

Large-scale patterns of green turtle trophic ecology in the eastern Pacific Ocean

Trophic position and niche width are fundamental components of a species' ecology, reflecting resource use, and influencing key demographic parameters such as somatic growth, maturation, and survival. The present data file contains results of stable isotope analysis (stable-carbon, δ13C; stable-nitrogen, δ15N values) that was conducted on bulk skin tissue of 718 green sea turtles (Chelonia mydas) distributed among 16 foraging areas in the eastern Pacific from the US to Chile, a range spanning ~10,000 km. These study sites were distributed across a latitudinal range from 33.736 °N to 23.098°S in the Eastern Pacific (Site Code): Long Beach, USA (LB); San Diego Bay, USA (SDB); north Gulf of Ulloa, Mexico (NGU); Magdalena Bay, Mexico (BMA); Los Angeles Bay, Mexico (BLA); Infiernillo Channel, Mexico (CIN); Navachiste Bay, Mexico (NAV); Dulce Gulf, Costa Rica (DUL); Cocos Island, Costa Rica (COC); Gorgona Island, Colombia (GOR); Punta Espinosa, Galapagos Islands, Ecuador (IGP); Bahia Elizabeth, Galapagos Islands, Ecuador (IGE); Caleta Derek, Galapagos Islands, Ecuador (IGD); oceanic waters, Peru (PPE); Pisco Paracas Bay, Peru (PAR); and Mejillones Bay, Chile (MEJ). Substantial variability in bulk tissue δ13C and δ15N values was found within and among sites. These data were also used to calculate the isotope niche space (used as a proxy for ecological niche space) using the Bayesian ellipse approach, and we found that isotope niche space varied among sites, likely influenced by the diversity of prey types and relative input of terrestrial- vs. marine-derived nutrients. In addition to providing additional spatial resolution for δ13C and δ15N isoscapes in the eastern Pacific, especially in coastal habitats, this study and resultant dataset further establish stable isotope analysis as an effective tool to study the trophic ecology of sea turtles across a variety of food webs and habitats.

opencc-zeroDec 2016View details →

Data from: Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird

Human-induced ecological change in the open oceans appears to be accelerating. Fisheries, climate change and elevated nutrient inputs are variously blamed, at least in part, for altering oceanic ecosystems. Yet it is challenging to assess the extent of anthropogenic change in the open oceans, where historical records of ecological conditions are sparse, and the geographical scale is immense. We developed millennial-scale amino acid nitrogen isotope records preserved in ancient animal remains to understand changes in food web structure and nutrient regimes in the oceanic realm of the North Pacific Ocean (NPO). Our millennial-scale isotope records of amino acids in bone collagen in a wide-ranging oceanic seabird, the Hawaiian petrel (Pterodroma sandwichensis), showed that trophic level declined over time. The amino acid records do not support a broad-scale increase in nitrogen fixation in the North Pacific subtropical gyre, rejecting an earlier interpretation based on bulk and amino acid specific δ15N chronologies for Hawaiian deep-sea corals and bulk δ15N chronologies for the Hawaiian petrel. Rather, our work suggests that the food web structure in the NPO has shifted at a broad geographical scale, a phenomenon potentially related to industrial fishing.

opencc-zeroDec 2017View details →

Data from: Rare long-distance dispersal of a marine angiosperm across the Pacific Ocean

Aim: Long-distance dispersal (LDD) events occur rarely but play a fundamental role in shaping species biogeography. Lying at the heart of island biogeography theory, LDD relies on unusual events to facilitate colonisation of new habitats and range expansion. Despite the importance of LDD, it is inherently difficult to quantify due to the rarity of such events. We estimate the probability of LDD of the seagrass Heterozostera nigricaulis, a common Australian species, across the Pacific Ocean to colonise South America.Location: Coastal Chile, Australia and the Pacific Ocean. Methods: Genetic analysis of H. nigricaulis collected from Chile and Australia were used to assess the relationship between the populations and levels of clonality. Ocean surface current models were used to predict the probability of propagules dispersing from South East Australia to Central Chile and shipping data used to determine the likelihood of anthropogenic dispersal. Results: Our study infers that the seagrass H. nigricaulis dispersed from Australia across the entire width of the Pacific (~14,000 km) to colonise South America on two occasions. Genetic analyses reveal that these events led to two large isolated clones, one of which covers a combined area of 3.47 km2. Oceanographic models estimate the arrival probability of a dispersal propagule within 3 years to be at most 0.00264%. Early shipping provides a potential alternative dispersal vector, yet few ships sailed from SE Australia to Chile prior to the first recording of H. nigricaulis and the lack of more recent and ongoing introductions demonstrate the rarity of such dispersal. Main Conclusion: These findings demonstrate LDD does occur over extreme distance despite very low probabilities. The large number of propagules (100s of millions) produced over 100s of years suggests that the arrival of propagules in Chile was inevitable and confirms the importance of LDD for species distributions and community ecology.

opencc-by-4.0Feb 2017View details →

Figure 1. - World map representing all the locations mentioned in the dataset. Areas of particular interest are represented with the same colour (⬤ Madagascar, ⬤ Western Indian Ocean, ⬤ Papuasia, ⬤ New Caledonia, ⬤ South Pacific). Grey spots gather all the other locations.

Figure 1. - World map representing all the locations mentioned in the dataset. Areas of particular interest are represented with the same colour (⬤ Madagascar, ⬤ Western Indian Ocean, ⬤ Papuasia, ⬤ New Caledonia, ⬤ South Pacific). Grey spots gather all the other locations.

opencc-by-4.0Nov 2023View details →

Figure 72 in Diversity and distribution of species of the planktonic dinoflagellate genus Alexandrium (Dinophyta) from the tropical and subtropical Mexican Pacific Ocean

Figure 72: Distribution map of Alexandrium species from this study in the Mexican Pacific.

opencc-by-4.0Jan 2022View details →

Surface Ocean Biogeochemistry Regulates the Impact of Anthropogenic Aerosol Fe Deposition on the Cycling of Iron and Iron Isotopes in the North Pacific

Monthly-average (year 2014) netcdf output files of NEMO/PISCES Fe isotope model experiments on the ORCA2 grid for experiments with updated iron deposition fields; "ptrc" files contain model outputs for heavy and light iron tracers, "diad" files contain diagnostic model outputs for iron uptake (of light and heavy iron), primary production (for diatoms and nanophytoplankton), and iron deposition fluxes (from dust, anthropogenic, and fire sources).

opencc-by-4.0Mar 2022View details →

Sr isotope variations in Oligocene–Miocene and modern biogenic carbonate formations of Koko Guyot (Emperor Seamount Chain, Pacific Ocean)

Tables for manuscript "Sr isotope variations in Oligocene–Miocene and modern biogenic carbonate formations of Koko Guyot (Emperor Seamount Chain, Pacific Ocean)" by Irina A. Vishnevskaya, Marc Humblet, Yasufumi Iryu, Davide Bassi, Tatiana G. Okuneva, Daria V. Kiseleva, Andrey V. Vishnevskiy, Natalia G. Soloshenko, Pavel E. Mikhailik. Abstract: The Hawaiian-Emperor Seamount Chain, a major topographic feature of the Pacific Ocean floor, is composed of seamounts capped with fossil coral reef deposits formed originally close to sea level but lying today hundreds of meters in water depth due to prolonged subsidence. These fossil reef deposits are important archives of paleoenvironmental changes and yield information on the subsidence history of the seamounts. We studied Sr isotope composition of Oligocene–Miocene coral reef limestone from Koko Guyot in the southern part of the Emperor Seamount Chain in order to assess the subsidence dynamics. The age of the studied samples with coral fragments established by Sr isotope stratigraphy varies from 26.3 to 20.1 Ma, while the youngest samples deposited at water depth of > 120 m, barren in corals and composed exclusively of bryozoans and coralline algae, are 15.3 Ma in age. The subsidence rate of the Koko Guyot volcanic structure was not uniform. Combining data of previous studies and those obtained in this study, the assessed subsidence rate was 0.046 ± 0.005 mm/yr during the first 25–30 Myr (from about 49–44 Ma ago). During this period of time, Koko Guyot was in bathymetric interval favourable for coral reef development and its subsidence was compensated by rapid vertical reef growth. Successively, the subsidence rate decreased to an average value of 0.019 ± 0.003 mm/yr from 20 to 15 Ma. The decrease in bottom subsidence coincided with unfavourable environmental conditions for coral reef development, leading to the disappearance of corals. The subsidence rate reached a value of 0.015 ± 0.002 mm/yr in the last 15 Ma, comparable to the present-day subsidence rate. The change in the sedimentary setting is also confirmed by the study of δ88/86Sr.

Fig. 6 in A new species of Breviconia Conroy-Dalton & Huys, 2000 (Copepoda: Harpacticoida: Ancorabolidae Sars) from the Bering Sea, northern Pacific Ocean (Russia)

Fig. 6. Breviconia andrei sp. nov., ♀. A. P3. B. P4.

Fig. 5 in A new species of Breviconia Conroy-Dalton & Huys, 2000 (Copepoda: Harpacticoida: Ancorabolidae Sars) from the Bering Sea, northern Pacific Ocean (Russia)

Fig. 5. Breviconia andrei sp. nov., ♀. A. P1. B. P2.

Fig. 9 in A new species of Breviconia Conroy-Dalton & Huys, 2000 (Copepoda: Harpacticoida: Ancorabolidae Sars) from the Bering Sea, northern Pacific Ocean (Russia)

Fig. 9. Breviconia andrei sp. nov., ♂. A. P3. B. P4.

Fig. 7 in A new species of Breviconia Conroy-Dalton & Huys, 2000 (Copepoda: Harpacticoida: Ancorabolidae Sars) from the Bering Sea, northern Pacific Ocean (Russia)

Fig. 7. Breviconia andrei sp. nov., ♂. A. Habitus, dorsal view. B. Abdomen, ventral view. C. P6.

opencc-zeroJun 2022View details →

Population structure and demographic analyses of Acanthocybium solandri from the Indo-Pacific and Atlantic oceans

This repository contains scripts, data and results for a populaton genomics study of genetic structure and demography of wahoo, Acanthocybium solandri, published in Journal of Biogeography: Haro-Bilbao et al. (2021) Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. In this work, we generated population allele frequencies for wahoo sampled at 11 locations around the globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs, we demonstrated a significant (but subtle) genetic divide between wahoo from the Indo-Pacific and those from the Atlantic. This genetic differentiation likely occurs against a background of high gene glow throughout the evolutionary history of wahoo, as we inferred from demographic analysis of select population pairs within and between oceanic regions. Analyses contained in this repository are for: (1) Filtering pooled ezRAD allele counts (assembled with dDocent and imputed using poolne_estim); (2) Estimation of genetic differentiation among globally sampled wahoo populations; (3) Estimation of site frequency spectra from joint allele frequencies among select population pairs; (4) Inference of demographic parameters (using δaδi); and (5) Generations of demographic simulation summary statistics. Most of the analyses are performed in R and can be run directly from within the repository directory, this includes: allele filtering, estimation of genetic differentiation, estimaiton of site frequency spectra, and generation of demographic summary statistics. Demographic inference using δaδi requires setup of a Unix environment: input data files and execution scripts are provided, but their implementation needs to be customised.

opencc-by-4.0Jul 2022View details →

Ocean-atmosphere changes in the midlatitude North Pacific over the last 330 ka: Dust, biogenic sediment and authigenic uranium accumulation at Shatsky Rise — Dataset

Title: Ocean-atmosphere changes in the midlatitude North Pacific over the last 330 ka: Dust, biogenic sediment and authigenic uranium accumulation at Shatsky Rise — Dataset Version: 1.0 Date of Release: July 03, 2022 Last Update: July 03, 2022 Identifier: 10.5281/zenodo.6791726 Permalink: <a href="https://doi.org/10.5281/zenodo.6791725">https://doi.org/10.5281/zenodo.6791725</a> Associated publication:  Link to publication preprint:  Suggested citation: Please reference the associated publication above when using any datasets or materials in this repository. Contact information: Christopher W. Kinsley, ckinsley@mit.edu OR cwkinsley@gmail.com Dates of data collection and generation:  --------------- DESCRIPTION OF DATA This data repository contains the following dataset. We refer the user to the original manuscript (see above) and the text of the Supporting Information published alongside this manuscript for additional general information regarding the collection and generation of these data. DATA TABLES FOR ALL CORE SITES <ul> <li> Kinsley et al. (2022) P&P - Data Tables for ODP 198-1208A core - v1: This Excel workbook contains all data used in the study for the ODP 198-1208A core site, taken by the R/V JOIDES Resolution close to the center of the Central High of Shatsky Rise in the western North Pacific Ocean during Ocean Drilling Program Leg 198. This includes the age control and age model, biogenic %s, U-Th isotopic measurements, and 230Th-normalized flux data. All previously published data is noted as such and referenced. </li> </ul>

opencc-zeroJun 2024View details →

Low molecular weight reduced sulfur substances: a major component of non-volatile dissolved organic sulfur in the Pacific Ocean

The low molecular weight (LMW) reduced sulfur substances (RSS) composition of dissolved organic matter (DOM) was examined along the GEOTRACES US-GP15 section in the Pacific Ocean. We demonstrate that LMW RSS constitutes a significant fraction of non-volatile dissolved organic sulfur (DOS). While thiols such as glutathione were below our detection limit (300 pM), RSS containing two carbon (C) sulfur (S) bonds were present at concentrations in the hundreds of nM range. RSS accumulation was observed in subtropical waters. The most likely source of these RSS is microbial alteration of sulfurized DOM with production of secondary thioamidated metabolites. RSS are initially produced by cyanobacteria to mitigate copper and oxidative stress induced by UV-B irradiance. A preferential remineralization of RSS over dissolved organic carbon (DOC) in the upper 350 meters suggests a partial lability of LMW DOS. Deeper, homogeneous concentrations and C:S ratio indicate increasing stability of this LMW DOS.

opencc-by-4.0Dec 2009View details →

Figure 16 in New and poorly described stenothoids (Crustacea, Amphipoda) from the Pacific Ocean.

Figure 16: Metopa cf. clypeata:?sex. 8mm, Japan Sea.