This database contains ichthyoplankton data collected as part of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program and other cruises that were designed to assess the status coastal pelagic species and the California Current ecosystem from 1951 to present. The primary data are eggs and larvae captured in ring or bongo nets (oblique tows), Calvet or pairovet nets (vertical tows), and manta nets (surface tows).

The California Cooperative Oceanic Fisheries Investigations (CalCOFI)

In 1951, the Hopkins Marine Station of Stanford University became involved in the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program to collect oceanographic data in and near Monterey Bay. Hopkins staff conducted weekly sampling (more or less) continuously from March 1951 through June 1974. Moss Landing Marine Laboratories (MLML) took over the Monterey Bay sampling program in July 1974, and it appears to have ended in 1979. The aim of the initial program was to conduct joint fisheries-oceanographic cruises that would help researchers understand what contributed to the crash of the California sardine fishery. The Hopkins Marine Station CalCOFI dataset is an extremely important contribution to early oceanographic research in the Northeast Pacific Ocean, and extends our observations in this area decades into the past. The raw and aggregated data for most of these cruises currently resides in the library at the Hopkins Marine Station.

This portion of the dataset is a transcription of the zooplankton data that was collected from 1955 to 1963 (a subset of the full HMS CalCOFI program). These spreadsheets are the output of a crowdsourcing campaign on the 'From the Page' platform. We thank 58 contributors for transcribing over 1500 pages! See the dataset README file for detailed information about the data.

Dataset

This dataset was created by Gmastersixtyfo

Released under MIT

Contents

Original provider: PRBO Conservation Science

Dataset credits: The projects were conducted under the grants awarded to the following organizations and their scientists.

The principle investigators of the CalCOFI part of this dataset are (in the chronological order from 1987 to 2006): Richard Veit and John McGowan, Scripps Institution of Oceanography (1987-1994) David Hyrenbach, Scripps Institution of Oceanography (1994-2000) Bill Sydeman, PRBO Conservation Science (2000-2006)

The principle investigators of the Rockfish part of this dataset is Bill Sydeman, PRBO Conservation Science (1996-2006)

the affiliations are the ones they belonged to at the time of the surveys.

The data were contributed by PRBO Conservation Science. These two projects are on going. See [Supplemental information] for the information on the PIs and organizations in recent years.

Abstract: This dataset contains observation data of marine birds and mammals from California Cooperative Oceanic Fisheries Investigations (CalCOFI) from 1987-2006 and Rockfish cruises along the California coast from 1996-2006 by National Marine Fisheries Service (NMFS).

Data were collected aboard research vessels using standardized marine bird and mammal survey techniques (Tasker et al. 1984, Buckland et al. 1993). Marine birds and mammals were observed in a 90-degree arc from the bow to one side of the ship out to 300m. Counts are summarized by species and behavior along the transects in 3 km bins. Data span years 1987 - 2006.

Purpose: Relating changing ocean productivity patterns and upper-trophic predator (seabirds and marine mammals) distributions to the underlying physical oceanographic variability enhances our understanding of the ecological context of the CalCOFI and NMFS database, thereby aiding in the interpretation of large-scale hydrographic and ocean productivity patterns. An inter-disciplinary, ecosystem-level perspective will provide new insight into offshore California wildlife habitat associations and how apex marine organisms (including fish with diets similar to seabirds and/or mammals) respond to differences in ocean climate, productivity, and water mass properties, information needed to manage fisheries and wildlife under changing ocean conditions.

Supplemental information: [2020-09-30] The following invalid species names were corrected according to the Integrated Taxonomic Information System (ITIS). Black-footed Albatross: Diomedea nigripes (174516) => Phoebastria nigripes (554379) Bonaparte's Gull: Larus philadelphia (176839) => Chroicocephalus philadelphia (824040) Caspian Tern: Sterna caspia (176924) => Hydroprogne caspia (176935) Elegant Tern: Sterna elegans (176925) => Thalasseus elegans (176931) Franklin's Gull: Larus pipixcan (176838) => Leucophaeus pipixcan (824082) Great Egret: Casmerodius albus (174810) => Ardea alba (554135) Laughing Gull: Larus atricilla (176837) => Leucophaeus atricilla (824079) Laysan Albatross: Diomedea immutabilis (174517) => Phoebastria immutabilis (554378) Least Tern: Sterna antillarum (176923) => Sternula antillarum (824127) Red Phalarope: Phalaropus fulicaria (554376) => Phalaropus fulicarius (176734) Royal Tern: Sterna maxima (176922) => Thalasseus maximus (824142) South Polar Skua: Catharacta maccormicki (176801) => Stercorarius maccormicki (660062) Willet: Catoptrophorus semipalmatus (176638) => Tringa semipalmata (824147) Parula americana (178868) => Setophaga americana (950033) Dendroica petechia T(178878) => Setophaga petechia (950039) Dendroica townsendi (178897) => Setophaga townsendi (950058) Dendroica occidentalis (178902) => Setophaga occidentalis (950059) Dendroica coronata (178891) => Setophaga coronata (950046) Wilsonia pusilla (178973) => Cardellina pusilla (950080)

[UPDATE 2013-03-25] The following species codes had been associated with invalid species names. These were corrected to valid species names. WWSC White-Winged Scoter => Melanitta fusca deglandi STAL Short-Tailed Albatross => Phoebastria albatrus LAAL Laysan Albatross => Diomedea immutabilis LETU Leatherback Turtle => Dermochelys coriacea These data are publicly available without restriction. However, it is suggested that potential users contact the data contributor (Marine Division Director at PRBO Conservation Science, marinedirector@prbo.org) or PI Bill Sydeman (wsydeman@faralloninstitute.org) for questions concerning the use of dataset (methods, accuracy, help with interpretation etc.).

The dataset is also available at Ocean Informatics Data Zoo (http://oceaninformatics.ucsd.edu/datazoo/).

The CalCOFI and Rockfish projects are on going. The Principle Investigators of these projects are as follows (listed those in recent years only):

Rockfish survey 2008, Leg 1/2: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research 2008, Leg 3: Jaime Jahncke, PRBO Conservation Science 2009, Leg 1/2: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research 2009, Leg 3: Jaime Jahncke, PRBO Conservation Science

CalCOFI survey 2006-2007: Bill Sydeman, PRBO Conservation Science 2007-current: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research

These recent data are available from these individuals or organizations upon request. The recent data by Bill Sydeman will be also available through OBIS-SEAMAP in the near future.

Each sighting is a total of all of the birds/mammals of that species and behavior seen in an area (approx. 3 km long and 300m wide). The location is represented at the middle of the bin. Length may be less at the end of a transect, and width may be less depending on the weather. Each bin is temporally about 10 minutes in duration (depending on ship speed).

Tracklines on this map represent on-effort only. Off-effort tracks may be obtained from the data provider.

Summary information about sample locations for NOAA CalCOFI and related cruises.

Bottle data collected during CalCOFI cruises 1601, 1604, 1607, and 16011, January 2016 - November 2016. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service, and Scripps Institution of Oceanograhpy. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

Hydrographic data collected by bucket, CTD, or 10-m Niskin bottle as part of CalCOFI and related cruises. Note that most oxygen and salinity values in this table have not been calibrated with water samples. Most users will want to use the Scripps hydrographic data instead.

The data included in this dataset are bird and mammal observations from aboard research cruises. There are six tables of data: a transect log and observation log pairing for each of the three types of cruises. California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises are conducted quarterly off the coast of southern and central California. National Marine Fisheries (NMFS) cruises are a part of the Rockfish Recruitment Survey off the coast of southern and central California. Data were also collected aboard North Pacific Continuous Plankton Recorder (NPCPR) cruises from June 2002 through May 2006. Observations of birds and mammals include both number and behavior in addition to temporal and spatial information recorded along the cruise transect. Data are collected in order to research the interdependent aspects of the marine environment, including the effects of natural and human based climate change, and the broad implications and influences of ocean currents, weather patterns, fishing practices and coastal development on marine food webs and ecosystem processes.

Species and behavior definitions for data codes are available in the "Supplemental Documents" section.

Fish larvae counts and standardized counts for larvae captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and surface tows [Manta nets]). Surface tows are normally standardized to count per 1,000 m3 strained. Oblique tows are normally standardized to count per 10 m2 of surface sampled. This table includes all tows by species, even if zero larvae were captured for the species, i.e., negative tows. The "Larvae Counts Positive Tows" table includes only tows where one or more larvae were captured for the species selected by the user.

Jellyfish data from the California Cooperative Oceanic Fisheries Investigations (CALCOFI) were downloaded from http://data.calcofi.net/zooplankton.html. Data were formatted for the 'Jellyfish Database Initiative' (JEDI), a database of jellyfish data developed by the NCEAS Global Jellies Working Group. Data extend from 1951-1999 and cover the central and southern Califiornian shelf waters.

The (CalCOFI) are a unique partnership of the California Department of Fish and Game, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

2022-12-31

Bottle data collected during CalCOFI cruises 1203, 1207, 1210, and 1301, March 2012 - January 2013. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Niño and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

Original provider: Annie Douglas, Cascadia Research Collective Dataset credits: Annie Douglas, Cascadia Research Abstract: From July 2004 to April 2008 dedicated visual observers following consistent line-transect methods (Buckland et al., 1993; Kinzey et al., 2003) observed from the CalCOFI platforms on quarterly cruises. Observers used handheld 7X50 reticle Fujinon binoculars to sight, identify, and make school size estimates of cetaceans and pinnipeds encountered along the transect lines between CalCOFI water sampling stations. The southern water sampling stations are set along six, parallel lines running southwest to northeast, with lines increasing in length from north to south (470 – 700 km) and stations occurring every 37 km in coastal and continental shelf waters and every 74 km offshore. Three research vessels were used for the sixteen surveys, Scripps Institution of Oceanography Roger Revelle (2 surveys) and New Horizon (8 surveys) and, NOAA David Starr Jordan (6 surveys), vessel height varied from 8.1-13.2m and survey speed varied from 10 to 12 knots. Purpose: The waters off southern California are remarkably diverse and species rich, but they are also an area of swift commercial development, navy training activity, population growth and climate change. Continued visual marine mammal and seabird surveys working in concert with oceanographic ecosystem investigations are essential for monitoring the health and changes of the California current system. Supplemental information: Effort tracklines may overlap with data published in the CalCOFI and NMFS Seabird and Marine Mammal Observation Data, 1987-2006 dataset. However, data collected for this dataset used different methods and observers. Please contact the primary contact listed for more details.

Since 1949, hydrographic and biological data of the California Current System have been collected on quarterly CalCOFI cruises. The 59+ year hydrographic time-series includes weather, temperature, salinity, oxygen and phosphate observations. In 1961, nutrient analysis expanded to include silicate, nitrate and nitrite; in 1973, chlorophyll was added; in 1984, C14 primary productivity incubations were added.

These data are being provided here in collaboration with CalCOFI-SIO in order to provide an additional queriable interface to the data. The data are updated on a regular basis from the CalCOFI hydrographic database.

This site contains hydrographic data from 1949-2002. It also has ongoing oceanographic, weather, abiotic and invertebrate (e.g. zooplankton) data and research projects details. Database can be downloaded and PUBLICATIONS link also has a search option to find results and data. Of the multiple ocean transects surveyed only one pertains to the central coast.

This accession includes data from the CalCOFI ichthyoplankton database and data from publicly available ERDDAP servers hosted at Southwest Fisheries Science Center. The data include fish species occurrence and distribution, identification and developmental staging of fish and egg stages as well as information about cruises, instruments and platforms used in the CalCOFI program from 1951-10-01 to 2017-04-22. The ERDDAP data is available in CSV format. The raw files were extracted from the SWFSC CalCOFI database and includes documentation that explains each table and how to reconstruct the database schema.

Fish egg counts and standardized counts for eggs captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and surface tows [Manta nets]). Surface tows are normally standardized to count per 1,000 m3 strained. Oblique tows are normally standardized to count per 10 m2 of surface sampled. This table includes all tows by species, even if zero eggs were captured for the species, i.e., negative tows. The "Egg Counts Positive Tows" table includes only tows where one or more eggs were captured for the species selected by the user.

The fish larvae (ichthyoplankton) survey is conducted through the California Cooperative Fisheries Investigations program (CALCOFI, http://www.calcofi.org/). These data are a time series of fish larvae counts (or density, as number per 10 m2 of ocean surface) collected in the area of the California Current between San Diego and Avila Beach, California, during the period of 1966 to 2015. Original data were filtered to facilitate consistent comparisons over time and space.

The original CalCOFI fish larvae count data is available from the CoastWatch West Coast Regional Node (WCRN) at NOAA’s Pacific Fisheries Environmental Laboratory, http://coastwatch.pfeg.noaa.gov/erddap/tabledap/index.html. The dataset presented here is an aggregation of 31 data files, originally divided alphabetically by taxon (named “CalCOFI Larvae Counts, Scientific Names * to *”). The data were filtered to include only the 66 core stations with a maximum of 1 cruise per season. These 66 core stations have been most frequently sampled in the past and sampling is ongoing.

CalCOFI sampling began in 1949. However, the dataset presented here begins in 1966 to include only samples that were analyzed with techniques that apply the most current and accurate identification of larvae to the species level. As the backlog of samples (i.e., before 1966) is re-examined, this dataset will be augmented with that additional, earlier data.

SIO Hydrographic data. See https://wp.calcofi.org/wp/sampling-info/methods/bottle-sampling-methods/