Bird Curatorial Manual | Organization of the Collection

Organization of Specimens

Skins in the MVZ bird collection are organized in the following hierarchy:

    1. Taxonomic down to species or subspecies (if polytypic)
    2. Geographic within the lowest taxonomic unit to the level of states/counties
    3. Geographic within a state/county from north to south and west to east
    4. Elevationally from low to high within an identical specific locality
    5. Chronologically within the same locality (including elevation) by day and month regardless of year
    6. Numerically by collector or MVZ catalog number if the locality and date are identical for a given taxon

The geographic arrangement is intended to allow curators and researchers to see how phenotypes (e.g., size, color, pattern) change in different geographic areas and associated environments. The chronological arrangement within a locality provides organization of skins by annual cycle (e.g., breeding, molting, wintering).

For more detail, see the section on skins under Installing Birds.

Refer to the following documents for guidance:

Skeletons, eggs, and nests are housed separately from the skins, and are organized in a different hierarchy that is similar to MVZ amphibians, reptiles, and mammals:

    1. Taxonomic down to family or subfamily (see Arrangement of Bird Families in the next section)
    2. Alphabetical within a family/subfamily by genus, then species within a genus, then subspecies within a species
    3. Alphabetical within the lowest taxonomic unit by country, then state/province within a country, then county within a state (for USA)
    4. Numerical within the lowest geographic unit by collector or MVZ catalog number

Fluid-preserved whole organisms in the MVZ bird collection are organized in the following hierarchy:

    1. Taxonomic down to family or subfamily
    2. Alphabetical within a family/subfamily by genus, then species within a genus, then subspecies within a species
    3. Alphabetical within the lowest taxonomic unit by country (non-USA), state, or county
    4. Numerical within the lowest geographic unit by collector or MVZ catalog number

The level of organization depends on how many jars there are for a given taxon. If all specimens of a taxon fit in one jar, then they are put in the same jar regardless of their geographic locality or number. If there are multiple jars of a given taxon, the specimens are divided among jars geographically and, if necessary, numerically to make it easy to find them.

Fluid-preserved parts are arranged strictly numerically by MVZ catalog number. Parasites are stored separately from other kinds of parts such as syrinx or stomach contents.

Tissues are barcoded and stored in liquid nitrogen tanks, where they are organized in boxes by MVZ catalog number within a given accession. Barcodes for tissue vials are scanned into Arctos and organized in a hierarchy of barcoded containers:

    1. Freezer
    2. Rack
    3. Rack slot
    4. Box
    5. Position
    6. Vial

Taxonomic Arrangement

The arrangement of bird families in the MVZ collection in based primarily on the American Ornithological Society Check-list of North American Birds, Clements Checklist, and IOC World Bird List. In cases where there was conflict, MVZ Curators made an executive decision based on the best available evidence.

To view the MVZ’s arrangement of bird families and subfamilies, click Arrangement of Bird Families. This document is updated in realtime to reflect yearly taxonomic updates.

To view the MVZ’s arrangement of birds down to the subspecies level, click MVZ Bird Taxonomic Checklist. This spreadsheet is updated in realtime to reflect yearly taxonomic updates.

Note: Non-passeriformes and Passeriformes are on separate tabs to facilitate faster load times.

Gallery Layout: Orders

Gallery Layout: Passeriformes

Geographic Order for Bird Skins

Organization of California Counties

Del Norte
Humboldt
Siskiyou
Shasta
Trinity
Mendocino
Lake
Sonoma
Napa
Marin
Modoc
Lassen
Plumas
Sierra
Nevada
Placer
El Dorado
Amador
Alpine
Calaveras
Tuolumne
Mariposa
Tehama
Glenn
Butte
Colusa
Sutter
Yuba
Yolo
Solano
Sacramento
San Joaquin
Stanislaus
Merced
Madera
Fresno
Tulare
Kings
Kern
San Francisco
San Mateo
Contra Costa
Alameda
Santa Clara
Santa Cruz
San Benito
Monterey
San Luis Obispo
Santa Barbara
     San Miguel Island
     Santa Rosa Island
     Santa Cruz Island
Ventura
     San Nicolas Island
Los Angeles
     Santa Barbara Island
     Santa Catalina Island
     San Clemente Island
Orange
Mono
Inyo
San Bernardino
Riverside
San Diego
Imperial

Taxonomic Updates

Yearly Updates

At least once per year the supplement/update pages of the American Ornithological Society, Clements Checklist, and the IOC World Bird List should be consulted to determine what changes should be made to the MVZ bird collection. The MVZ Bird Taxonomic Checklist must also be updated with any changes made to Arctos and the physical collection.
 

Physically moving specimens

Relabeling

Skins, Eggs, and Nests: The process for updating the scientific names on skin tags and egg and nest labels is the same. Using a #4H pencil, place the old name in brackets. If only the species or subspecies identification is changing, place the brackets around that part of the name. 

For example:

    • Genus name change: [Oceanodroma] matsudairae
    • Species name change: Oceanodroma [matsudairae
    • Genus species name change: [Oceanodroma matsudairae]

Write the new identification directly above or below the bracketed obsolete name. Press down hard to ensure that the identification is legible and visible. 

Fluids: To update fluid tags, the process is the same as for skins, eggs, and nests, but you must use a 01 or 02 archival micron pen instead of a pencil. For skin tags and labels, remove the item from the jar and blot the tag dry with paper towel before attempting to write.

Shelves and Cases: Updates to the collection will often require the printing of new labels for drawers, cases, and aisles. Label templates can be downloaded from the Installing Birds page.

Updating Taxonomy in Arctos

When updating the collection, it is useful to search for all specimens within a taxonomic level. For example, you may wish to search for all specimens within family Hydrobatidae so that you can update species with genus name Oceanodroma to genus name Hydrobates. Displaying the search results by scientific name enables quick bulk updates.
To search for all specimens within a family, grouped by scientific name:
    1. To the right of the Search button on the main search page is See results as followed by a drop-down menu. From the menu, select Specimen Summary.
    2. A new drop-down menu will appear called Group by. Scroll down the menu and click the box next to Scientific Name.
    3. Within Identifiers you can select a Collection to search. Click the small arrows to expand the menu, then click the check box(es) next to the collection(s) needed for your task: Bird specimens (MVZ:Bird), Bird eggs/nests (MVZ:Egg), and/or Bird observations (MVZObs:Bird). 
    4. Within Identification and Taxonomy, type Hydrobatidae into the Family field. Click Search.
    5. The search results page will display a list of all scientific names in which records for family Hydrobatidae exist. Click on any of the blue specimens links next to a scientific name to generate a new page containing those specimen records.
When creating a new taxon, Arctos allows the cloning of an existing taxon in order to replicate classification data (kingdom, phylum, class, etc.) and metadata (source_authority, taxon_status, etc.). Choosing a closely related taxon to clone can expedite the creation process and minimize data entry errors.
To create a new taxon from an existing taxon name:
    1. From the main Search drop-down menu, select Taxonomy.
    2. In the Taxon Name field, type in a related name to the one you are trying to create. For example, to add the new species name Hydrobates matsudairae, search for the genus name Hydrobates.
    3. Under Taxonomy Search Results you will see one or more names listed. Click Hydrobates.
    4. Scroll down the page until you find a record with the heading Data from source Arctos. This is an existing Arctos taxonomy record for genus name Hydrobates, and its classification hierarchy should be filled with the following information: kingdom, phylum, class, order, family, genus. Ensure that the classification data is correct and complete, then click Clone Classification as new name.
    5. In the New Namestring/Scientific Name field, type the new taxon name you want to add to Arctos (for this example, Hydrobates matsudairae). Arctos taxonomy is case sensitive and genus names must be capitalized. Be sure to double-check the spelling for accuracy! Copy and pasting the name from a reputable list, such as Clements, is recommended.
    6. From the drop-down Clone into Source, select Arctos.
    7. Click create name with entire classification.
    8. The classification data and metadata from Hydrobates has now been cloned and added to a new taxon name Hydrobates matsudairae. At this point, the record may be edited to customize it for species matsudairae. Under Classification Metadata, ensure that the following fields are filled correctly:
      • nomenclatural_code: ICZN
      • source_authority: the name of the publication recommending the use of this name (e.g., Clements Checklist 2019, IOC World Bird List 10.2)
      • taxon_status: valid (in current use) or invalid (obsolete or a common misspelling)
      On the record page, code table provides further description of the Term Types available in Arctos.
    9. All of the classification terms from Hydrobates will have been cloned into this new record, but perhaps not perfectly. Under Classification Terms, ensure that all classification data are present and correct (kingdom, phylum, class, order, family, genus, and species). Due to a quirk of Arctos, you may need to move the row for species from above kingdom to below genus. The first column is labeled Drag Handle. Click and hold (drag row here) in the row for species, then drag the row below genus before releasing the mouse button. The species row should now appear below the genus row.
    10. Click Save Edits. The page will reload after saving.
Specimen identification can be updated in the Identifications module on an individual specimen’s record page in Arctos. However, if there is a taxonomic revision at the genus or species level you may need to update many records at once. For example, all specimens with the identification Oceanodroma castro need to be revised to Hydrobates castro.
To search for and revise the identification for all specimens currently identified as Oceanodroma castro:
    1. To the right of the Search button near the top of the page is See results as, followed by a drop-down menu. From the menu, select Specimen Summary.
    2. The new drop-down menu Group by will appear. Scroll down the menu and click the box next to Scientific Name.
    3. Within Identifiers you can select a Collection to search. There are three collections associated with birds in the MVZ: Bird specimens (MVZ:Bird), Bird eggs/nests (MVZ:Egg), and Bird observations (MVZObs:Bird). Click the small arrows to expand the menu, then click the check boxes next to all three collection names. This ensures that all bird records within Arctos will receive the update.
    4. Within Identification and Taxonomy, type Oceanodroma into the Any taxon, ID, common name field and click Search.
    5. The Specimen Summary page will display all taxa with MVZ records within genus Oceanodroma. Click the blue specimens link to the left of Oceanodroma castro.
    6. The Specimen results page will display all records using the identification Oceanodroma castro. Click the Manage… pull-down menu near the center of the page.
    7. Within the Manage… menu under Change Stuff, click Identification.
    8. On the Add Identification page, fill in the fields to re-identify the specimens. Fields highlighted yellow are required. ID Formula should match the specimens being re-identified (in this example, A is the appropriate selection). If you have questions about the appropriate use of ID Formula, please consult with a Staff Curator.
    9. Type in a partial or full scientific name in the Taxon A field, then press tab. If a partial name is used, a pop-up will be generated that will allow you to choose from a list of potential names (note: the name must already exist within Arctos). Fill in the ID by field in the same manner (full or partial name, then press tab).
    10. The ID Date field is not required, but it is generally only left blank if a date is truly impossible to determine. Click the ID Date field to generate a calendar, then select the appropriate date.
    11. Select the appropriate Nature of ID from the pull down menu. In this example, the identification change is due to revised taxonomy.
    12. Take a look at the list of specimens to be re-identified near the bottom of the page, and ensure they are the correct specimens (there is no undo button!). Click the Add Identification to all listed specimens button to re-identify all listed specimens. Please note, there is no confirmation page. The Add Identification page will reload and the field contents will be emptied when the re-identification process has completed.
When a name becomes obsolete and a new name is added, Arctos has a function that allows the taxa to be linked together. That way a search will return specimens using either name. Additionally, sometimes there is disagreement between authorities on which name is most “valid”. In such a case, there may be multiple equally valid synonyms.
To link synonymous terms within Arctos:
    1. From the main Search drop-down menu, select Taxonomy.
    2. In the Taxon Name field, type in either the new or the obsolete name. For example, to link Hydrobates matsudairae and Oceanodroma matsudairae, either name can be selected to begin the linking process.
    3. Under Taxonomy Search Results you will see one or more names listed. Click Hydrobates matsudairae.
    4. Under Taxonomy Details for Hydrobates matsudairae are several links. Click [Edit Name + Related Data].
    5. From the drop-down menu under Relationship >> Add Relationship, select synonym of.
    6. In the Related Taxa field type in the synonymous term, then press the tab button.
    7. A pop-up window with valid Arctos selections will appear. Choose the appropriate term (Oceanodroma matsudairae) and click [ use ].
    8. In the Authority field, type in the name of the source authority for the synonymous use of these terms. In this example the source authority is Clements Checklist 2019. This field is optional but highly recommended.
    9. Click the Create button.
At this time, Arctos does not automatically create reciprocal links. Repeat steps 1 through 9 for taxa Oceanodroma matsudairae to create a reciprocal link to taxa Hydrobates matsudairae.