https://oceaninformatics.ucsd.edu/zoodb/

## About this Project

### Overview

The ZooDB zooplankton data module provides a queriable interface to extensive zooplankton data from the California Current System covering 1951 to the present. The plankton samples analyzed originate from [CalCOFI](http://calcofi.org/) (the California Cooperative Oceanic Fisheries Investigations), a long-term ocean observing program that began in 1949 and continues actively today. Most of the data originate from springtime cruises (February, March, April or May), 1951-2008 from two distinct geographical areas off California: Southern California (CalCOFI lines 80-93) and Central California (lines 60-70). Only the nighttime samples were analyzed. In two years (1969 and 1984), nearly monthly cruises were analyzed. See [Table 1 - Southern California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_SoCA_Coverage_Table.pdf) and [Table 2 - Central California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_CenCA_Coverage_Table.pdf) for coverage and sample processing by cruise.

Dr. Mark Ohman initiated and directed this project with support from NSF (via the U.S. GLOBEC NE Pacific program and currently the CCE-LTER site). People involved in the analysis of the samples include the following. Dr. Bertha Lavaniegos, of CICESE in Ensenada, Mexico, analyzed the majority of samples from both southern and Central California for all taxa except euphausiids (in the separate Brinton and Townsend Euphausiid Database) and copepods by species. Ginger Rebstock, then a graduate student, enumerated 33 species of copepods for the Southern California region, 1951-1999. Connie Fey continued the counts from 2000-present and the 1969 and 1984 seasonal samples. Chris Martin enumerated aplot.php?mode=abundancell taxa for the Central California area for a number of cruises. Since 2006, Annie Townsend has been responsible for the analysis of all taxa, except copepods. Erin Rempala-Kim, Patricia Brommer and Annie Townsend helped with the pooling, subsampling and data entry. This database is a contribution from the [SIO Pelagic Invertebrate Collection](http://sio2020-stage.ucsd.edu/pelagic-invertebrate-collection).

### Design and Implementation

The ZooDB database is part of the SIO Ocean Informatics environment. For details on the database schema and interface implementation, see the [technical notes page](https://oceaninformatics.ucsd.edu/zoodb/#). Programming and design by Mason Kortz and Karen Baker.
## Help

### Instructions

Use the search form to specify the parameters of your search. Some parameters are only available for unpooled data. The parameters available are:

-   **Year:** Specify a range of years to search. Samples start in 1951.
-   **Month:** Choose one or more months to search.
-   **Time of Day:** Choose day, night, or all sampling times, or enter a custom time range. Day is defined as the period from the beginning of nautical twilight in the morning to the end of nautical twilight in the evening. Night is defined as the period from the end of nautical twilight in the evening to the beginning of nautical twilight in the morning.
-   **Location:** Choose all locations, or enter a bounding box in CalCOFI line/station numbers or latitude/longitude coordinates. Latitude and longitude should be entered in a decimal degree format.
-   **Higher Taxa:** Optionally, select one of more higher taxa (class, order, and/or family) to search for (default is all higher taxa). Multiple taxa can be selected by holding down the Ctrl key (for PCs) or Command key (for Macs).
-   **Genus/Species:** Optionally, select one of more species to search for (default is all species). Multiple species can be selected by holding down the Ctrl key (for PCs) or Command key (for Macs).
-   **Phase/Stage:** Optionally, select one of more phases to search for (default is all phases). Multiple phases can be selected by holding down the Ctrl key (for PCs) or Command key (for Macs). Note that while all species on all cruises were enumerated to phase, only select species on select cruises were to stage. Selecting a stage may cause some years to return less data points, and other year to be excluded entirely.
-   **Size:** Optionally, enter a size range, in millimeters. Only select species were sized, and only on a limited number of cruises. Selecting a size range may cause some years to return less data points, and other year to be excluded entirely.
-   **Calculation:** Choose pooled (per cruise), unpooled (per station), or combined data points. Choose individual points (one measurement per station), yearly means, or monthly means. Choose either 1000m3 or m2 as the unit of measurement. Optionally, check the boxes to apply a correction factor or convert measurements to a log10 scale. Choose to Display Data as an HTML table, Plot Data (abundance vs. time), or Save Data as comma separated value (CSV) text file.

### Contact

If you encounter a problem with the Zooplankton Euphausiid Database, or have a question about the content, design, or use of the database, please email the [database administrator](mailto:ccelter-im@ucsd.edu).

## Methods Notes

### Changes in Sampling Methods and Geographic Coverage

The user should be aware that both the geographic coverage and temporal frequency of CalCOFI cruises have changed since the program was initiated in 1949. **It is essential that users of ZooDB carefully consider the changing spatial coverage of cruises (see [CalCOFI station occupation](https://calcofi.org/history/#Survey%20Coverage)), as well as the cruises for which particular taxa have been analyzed ([Table 1 - Southern California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_SoCA_Coverage_Table.pdf) and [Table 2 - Central California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_CenCA_Coverage_Table.pdf)), prior to generating time series of abundance of any organisms.**

Lack of a plotted symbol indicates no data present.

The maximum zooplankton sampling depth in the CalCOFI time series increased from 0-70 m (1949-1950) to 0-140 m in 1951. It was maintained at 0-140 m from 1951-1968, and then increased to 0-210 m in 1969, where it has since remained (see Ohman and Smith 1995). A 1-m diameter ring net was used from 1949 - late 1977, which was then replaced with a 0.71-m diameter bongo net in December 1977 (Ohman and Smith 1995). Effects of these changes have been analyzed by Brinton and Townsend (1981), Ohman and Smith (1995), Rebstock (2001), and Ohman and Lavaniegos (2002). Results suggest that only some species of euphausiids (Brinton and Townsend 1981) and salps (Ohman and Lavaniegos 2002) are caught differentially by the two nets. A net correction factor can be applied if desired. See [ZooDB Correction Factors](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_Correction_Factors.pdf).

M.D. Ohman's retrospective studies have focused on interannual variability in springtime cruises, hence more up-to-date temporal coverage is available for springtime cruises than at other times of year.

The zooplankton samples for this study were enumerated as either individual samples ("unpooled") or after combining aliquots corresponding to 50 m3 of water filtered from each of several samples taken in a common geographic area ("pooled" samples). Pooled samples were composed only from nighttime stations (i.e., between nautical sunset and nautical sunrise), from two regions defined as Southern California (CalCOFI lines 80 through 93, from shore through station 70) and Central California (CalCOFI lines 60 through 70, from shore through station 90; see [coverage map](https://oceaninformatics.ucsd.edu/zoodb/docs/Map_SoCA_CenCA.png)) by Lavaniegos and Ohman (2007). See Rebstock (2001) and Lavaniegos and Ohman (2002) for pooling techniques and [Table 1 - Southern California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_Coverage_SoCA_20171204.pdf) and [Table 2 - Central California Coverage](https://oceaninformatics.ucsd.edu/zoodb/docs/ZooDB_Coverage_CCA.pdf) for taxa analyzed for each cruise.

In the spring of 2012, CalCOFI 1203SH sampled from lines 76.7 through 93.3 out to station number 120. Due to a coast-wide salp bloom, all salps and pyrosomes were removed from each station’s sample and enumerated individually by station. The cruise designation for these unpooled data is CALCOFI 1203SH. A subset of nighttime stations from lines 80 through 93.3 out through line 70 was selected and pooled. These samples were enumerated for copepods and other taxa. The cruise designation for these pooled data is CALCOFI 1203.

A coast-wide survey was also conducted in the spring of 2012 with two legs, CalCOFI 1204OS and CalCOFI 1204SH. Together these cruises sampled station 50.49, and also lines 63.3 to 90, out to station 120. All salps and pyrosomes were removed from 58 stations and enumerated. The cruise designation for these unpooled data is CALCOFI 1204SH OS. Due to a wire read out issue, some of these bongo net tows were taken to approximately 100m depth rather than to the typical 210m depth. Two subsets of nighttime stations from lines 60 through 70 out to station number 90 were selected and pooled for depth intervals of (a) ≤ 100m and (b) ≥ 200m. The cruise designation for this ≤ 100m pooled sample is CALCOFI MONTEREY 1204 shallow. The cruise designation for this ≥ 200m pooled sample is CALCOFI MONTEREY 1204.

Literature citations are available at the [References tab](https://oceaninformatics.ucsd.edu/zoodb/#).

## Data Use Policy

The data available here are intended for scholarly use by the research community, with the express understanding that (1) all data users will properly acknowledge the originating investigators' efforts, as indicated below and (2) reprints of any reports, articles, or other publications resulting from use of these data will be deposited in the Pelagic Invertebrate Collection, Scripps Institution of Oceanography. Use or reproduction of any materials herein for any commercial purpose is prohibited without prior written permission from Dr. Mark D. Ohman.

## Data Acknowledgement Policy

The following citation should be included in any use of the data or figures from this database: "Plankton sample analysis supported by NSF grants to M.D. Ohman and the CCE-LTER site, and by the SIO Pelagic Invertebrate Collection." The originating investigator (Dr. Mark Ohman, [mohman@ucsd.edu](mailto:mohman@ucsd.edu)) should be contacted to determine whether co-authorship is warranted for any materials arising from use of these data.

## Selected References

### Sampling Methods

Ohman, M. D., and B. E. Lavaniegos 2002. Comparative zooplankton sampling efficiency of a ring net and bongo net with comments on pooling of subsamples. _CalCOFI Reports_ **43**: 162-173.

Ohman, M. D., and P. E. Smith 1995. A comparison of zooplankton sampling methods in the CalCOFI time series. _CalCOFI Reports_ **36**: 153-158.

Brinton, E., and A. W. Townsend 1981. A comparison of euphausiid abundances from bongo and 1-M CalCOFI nets. _CalCOFI Reports_ **22**: 111-125.

Rebstock, G. A. 2001. Long-term changes in the species composition of calanoid copepods off Southern California. Ph.D thesis. University of California, San Diego. 240 p.

### Other

Brinton, E., and A. Townsend 2003. Decadal variability in abundances of the dominant euphausiid species in southern sectors of the California Current. _Deep-Sea Research II_ **50**: 2469-2492.

Hsieh, C.-H., and M. D. Ohman 2006. Biological responses to environmental forcing: The Linear Tracking Window hypothesis. _Ecology_ **87**: 1932-1938.

Lavaniegos, B. E., and M. D. Ohman 1999. Hyperiid amphipods as indicators of climate change in the California Current, p. 489-509. _In_ \[eds.\], F. R. Schram and J. C. von Vaupel Klein Crustaceans and the Biodiversity Crisis. Proceedings of the Fourth International Crustacean Congress, Amsterdam, The Netherlands, July 20-24, 1998, Vol. I. Brill.

Lavaniegos, B. E., and M. D. Ohman 2003. Long term changes in pelagic tunicates of the California Current. _Deep-Sea Research II_ **50**: 2493-2518.

Lavaniegos, B. E., and M. D. Ohman 2007. Coherence of long-term variations of zooplankton in two sectors of the California Current System. _Progress in Oceanography_ **75**: 42-69.

Mackas, D. L., W. T. Peterson, M. D. Ohman, and B. E. Lavaniegos 2006. Zooplankton anomalies in the California Current system before and during the warm ocean conditions of 2005. _Geophysical Research Letters_ **33**: Art. L22S07 Nov 18 2006.

Rau, G. H., M. D. Ohman, and A. C. Pierrot-Bults 2003. Linking nitrogen dynamics to climate variability off Central California: A 51 year record based on 15N/14N in CalCOFI zooplankton. _Deep-Sea Research II_ **50**: 2451-2467.

Sydeman, W. J., R. W. Bradley, P. Warzybok, C. L. Abraham, J. Jahncke, K. D. Hyrenbach, V. Kousky, J. M. Hipfner, and M. D. Ohman 2006. Planktivorous Auklet _Ptychoramphus aleuticus_ responses to ocean climate, 2005: Unusual atmospheric blocking? _Geophysical Research Letters_ **33**: Art. L22S09 Oct 21 2006.

See also the extensive CalCOFI Atlas series, as well as the web sites of the [SIO Pelagic Invertebrate Collection](http://sio2020-stage.ucsd.edu/pelagic-invertebrate-collection) and [CalCOFI](http://www.calcofi.org/).