Point count and location records from: Agricultural and urbanized avian communities diverge via nestedness and turnover in a heterogenous urban-agroecosystem
Data files
Jun 17, 2026 version files 2.55 MB
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Count_File_Refined_Manuscript.csv
2.53 MB
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Point_LatLong.csv
1.84 KB
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README.md
20.28 KB
Abstract
The data that was collected from year-round point count surveys of avian communities at 54 sites across a gradient of natural, agricultural, and urbanized landscapes in Southern California. These data contain all of the recorded information associated with every individual that was observed as a part of this study. These data have been used to assess differences in species richness, abundance, beta diversity, and association between five different habitats. All survey data were collected between March 7th 2021 and December 9th 2022 by author Rachel Bockrath.
Dataset DOI: 10.5061/dryad.brv15dvqs
Description of the data and file structure
Accompanies the paper “Agricultural and urbanized avian communities diverge via nestedness and turnover in a heterogenous urban-agroecosystem”
Rachel Elise Bockrath; California State Polytechnic University, Pomona / North Dakota State University; rachel.bockrath@ndsu.edu
Data Collected from March 7th 2021 to December 9th 2022
Collected in the Santa Clara River Valley, California, United States
This Read Me refers to the wide format data that contains a record of every individual bird that was counted as part of this experiment, and all the associated information for that individual bird. This file was finalized on April 26th, 2026.
Files and variables
File: Count_File_Refined_Manuscript.csv
Description:
Variables
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Species: The species for whom the data is about, recorded based on their Banding Code circa 2020. Full chart of codes, common English names, and species names:
Species Code Species Common Name Species Scientific Name XXDU Duck Anus XXGU Gulls Laridae XXHB Hummingbirds Trochilidae XXSP Sandpipers Scolopacidae XXWP Woodpecker Picidae ACWO Acorn Woodpecker Melanerpes formicivorus ALHU Allen's Hummingbird Selasphorus sasin AMCO American Coot Fulica americana AMCR American Crow Corvus brachyrhynchos AMGO American Goldfinch Spinus tristis AMKE American Kestrel Falco sparverius AMRO American Robin Turdus migratorius ANHU Anna's Hummingbird Calypte anna ATFL Ash-throated Flycatcher Myiarchus cinerascens BARS Barn Swallow Hirundo rustica BCHU Black-chinned Hummingbird Archilochus alexandri BCNH Black-Crowned Night Heron Nycticorax nycticorax BEKI Belted Kingfisher Megaceryle alcyon BEVI Bell's Vireo Vireo bellii BEWR Bewick's Wren Thryomanes bewickii BGGN Blue-gray Gnatcatcher Polioptila caerulea BHCO Brown-Headed Cowbird Molothrus ater BHGR Black-headed Grosbeak Pheucticus melanocephalus BLPH Black Phoebe Sayornis nigricans BRBL Brewer's Blackbird Euphagus cyanocephalus BRCR Brown Creeper Certhia americana BRPE Brown Pelican Pelecanus occidentalis BTPI Band-tailed Pigeon Patagioenas fasciata BUOR Bullock's Oriole Icterus bullockii BUSH Bushtit Psaltriparus minimus CAGN California Gnatchatcher Polioptila californica CAGU California Gull Larus californicus CAHU Calliope Hummingbird Selasphorus calliope CAKI Cassin's Kingbird Tyrannus vociferans CALT California Towhee Melozone crissalis CANG Canada Goose Branta canadensis CAQU California Quail Callipepla californica CASJ California Scrub-Jay Aphelocoma californica CATH California Thrasher Toxostoma redivivium CEDW Cedar Waxwing Bombycilla cerdrorum CLSW Cliff Swallow Petrochelidon pyrrhonota COHA Cooper's Hawk Accipiter cooperii CORA Common Raven Corvus corax COYE Common Yellowthroat Geothlypis trichas DCCO Double-crested Cormorant Phalacrocorax auritus DEJU Dark-eyed Junco Junco hyemalis DOWO Downy Woodpecker Picoides pubescens EUCD Eurasian Collared-Dove Streptopelia decaocto EUST Euopean Starling Sturnus vulgaris FOSP Fox Sparrow Passeralla iliaca GBHE Great Blue Heron Ardea herodias GCKI Golden-crowned Kinglet Regulus satrapa GREG Great Egret Ardea alba GRSP Grasshopper Sparrow Ammodramus savannarum GTGR Great-tailed Grackel Quiscalus mexicanus GWTE Green-Winged Teal Anas crecca HAFL Hammond's Flycatcher Empidonax hammondii HAWO Hairy Woodpecker Picoides villosus HERG Herring Gull Larus argentatus HETH Hermit Thrush Catharus guttatus HEWA Hermit Warbler Setophaga occidentalis HOFI House Finch Haemorhous mexicanus HOOR Hooded Oriole Icterus cucullatus HOSP House Sparrow Passer domesticus HOWR House Wren Troglodytes aedon HUVI Hutton's Vireo Vireo huttoni JUTI Juniper Titmouse Baeolophus ridgwayi KILL Killdeer Charadrius vociferus LAGO Lawrence's Goldfinch Spinus lawrencei LASP Lark Sparrow Chondestes grammacus LEGO Lesser Goldfinch Spinus psaltria LISP Lincoln's Sparrow Melospiza lincolnii LOSH Loggerhead Shrike Lanius ludovicianus MALL Mallard Anas platyrhynchos MERL Merlin Falco columbarius MGWA MacGillivray's Warbler Geothlypis tolmiei MODO Mourning Dove Zenaida macroura NOFL Northern Flicker Colaptes auratus NOMO Northern Mockingbird Mimus polyglottos NRWS Northern Rough-winged Swallow Stelgidopteryx serripennis NUWO Nuttall's Woodpecker Picoides nuttalii OATI Oak Titmouse Baeolophus inornatus OCWA Orange-crowned Warbler Oreothlypis celata OSFL Olive-sided Flycatcher Contopus cooperi OSPR Osprey Pandion haliaetus PHAI Phainopepla Phainopepla nitens PISI Pine Siskin Spinus pinus PSFL Pacific-slope Flycatcher Empidonax difficilis PUFI Purple Finch Haemorhous purpureus RBNU Red-breasted Nuthatch Sitta canadensis RBSA Red-Breasted Sapsucker Sphyrapicus ruber RCKI Ruby-crowned Kinglet Regulus calendula RSHA Red-shouldered Hawk Buteo lineatus RTHA Red-tailed Hawk Buteo jamaicensis ROPI Rock Pigeon Columba livia ROWR Rock Wren Salpinctes obsoletus RUHU Rufous Hummingbird Selasphorus rufus RWBL Red-winged Blackbird Agelaius phoeniceus SAPH Say's Phoebe Sayornis saya SAVS Savannah Sparrow Passerculus sandwichensis SBMU Scaly-breasted Munia Lonchura punctulata SNEG Snowy Egret Egretta thula SOSP Song Sparrow Melospiza melodia SPTO Spotted Towhee Pipilo maculatus SSHA Sharp-shinned Hawk Accipiter striatus SWTH Swainson's Thrush Catharus ustulatus TRES Tree Swallow Tachycineta bicolor TUVU Turkey Vulture Cathartes aura VATH Varied Thrush Ixoreus naevius VESP Vesper Sparrow Pooecetes gramineus WAVI Warbling Vireo Vireo gilvus WBNU White-breasted Nuthatch Sitta carolinensis WCSP White-crowned Sparrow Zonotrichia leucophrys WEBL Western Bluebird Sialia mexicana WEGU Western Gull Larus occidentalis WEKI Western Kingbird Tyrannus verticalis WEME Western Meadowlark Sturnella neglecta WETA Western Tanager Piranga ludoviciana WIFL Willow Flycatcher Empidonax traillii WIWA Wilson's Warbler Caridellina pusilla WREN Wrentit Chamaea fasciata YBCH Yellow-breasted Chat Icteria virens YRWA Yellow-rumped Warbler Setophaga coronata YWAR Yellow Warbler Setophaga petechia -
Activity: The type of behavior the individual was performing the moment they were counted. Full chart of codes and explanations:
Symbol Defined H Hear Only FO Forage FL Fly P Perch W Walk M Mobbing N nest building/attending/nestlings DI Displaying DR Drink HUN Hunting/Hunted -
Substrate: The surface that the individual was on the moment they were counted. Full chart of codes and explanations:
Symbol Define S Shrub T Tree B Building P Pole C Car G Ground W Water F Feeder -
Plant_Type: If an individual was interacting with vegetation, this records the type of vegetation. Note that plants that are “wild” indicate that they were not intentionally planted by humans, while “planted” indicates that the plant was clearly part of a landscaping effort. Full chart of codes and explanations:
Symbol Define A Avocado O Orange L Lemon W Wild P Planted NA undefined -
Diet: The typical diet of the species for that individual, as defined by the AVONET database. Full chart of codes and explanations:
Symbol Defined I Insectavor (invertabrate consumption) P Preditor (vertabrate consumtion) G Granivore (any type of seed predation) FR Frugivore (fruits) FO Folivore (plant vegetation) N Nectavore (necture/feeders) O Omnivore (No dominance in the other food catagories described/large swings based on season) -
Date: The data of the survey.
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Time: The starting time of the five-minute point count for that observation.
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Station_Name: The name of the location group that a survey occurred in.
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Point_Num: The point number information that designates the specific point within a Station that the survey occurred in.
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Point_Name: The full name of the specific survey location. This is the combination of the Station_Name and Point_Num columns.
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Habitat: The designation of which of the five habitat types the survey point belongs to.
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Season: The original organization of the seasonal component of the data (Spring, Summer, Fall, Winter). These seasonal designations are not used in the final analysis.
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Year_Season: A designation of both the season (Spring, Summer, Fall, Winter), and if the survey occurred in the First or Second year of the project.
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Temp: The temperature, in Fahrenheit, that was recorded when the observer arrived at the Station.
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Wind_Speed: The wind speed, measured in mph, that was recorded when the observer arrived at the Station.
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Noise_Level: A qualitative assessment of the relative amount of noise, both produced abiotically (e.g. cars driving, wind rustling trees) and biotically (e.g. noise from non-target species such as coyotes), that could mask birdcalls. Four levels.
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Visit_Ord: The order within a day that the Station was visited on that given day.
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Visit_Num: How many visits into the survey the current visit was for a particular point. (For example, the nineth time a point was surveyed is designated nine.)
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Julian_Day: The Julian date that a survey occurred, with a designation of either one=first year of surveys, and two=second year of surveys.
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Visit_Group: A combination of the information from the "Season" and "Visit_Num" columns.
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Observer: The initials of the individual who conducted the survey. They are all REB, designating the first author Rachel Elise Bockrath.
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Invasive: Indicating whether a species is native to Southern California (N) or non-native (I).
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Seen_or_Heard: Designating wither an individual was seen and identified by sight (Seen) or was only identified by sound (Heard).
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Behavior: A more condensed version of the behavior data reflected in Activity. Some are an exact match to the activity column, these are the particularly common behaviors. Uncommon behaviors have been condensed into “Other”.
Activity Behavior H Not_Seen FO Foraging FL Flying P Perched W, M, N, DI, DR, HUN Other -
Comp_Behavior: A third designation of bird behavior data. This designated the common actions taken by birds that are interacting with a solid substrate.
Activity Comp_Behavior FO Feed H, FL, M, N, DI, DR, HUN No_Match P Perch W Move -
Cultivated: Designates whether a plant was intentionally planted (Planted) or grew wild (Wild). Non-foliage substrates were labeled as NA.
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Plant_Status: Designating wether a plant was not native to Southern California (Non-Native_Plant), native to Southern California (Native_Plant), or was not a plant (NA). In instances where the observer was not certain about the origin of the plant, resources such as iNaturalist and people familiar with the plants of the region were consulted.
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Detailed_Plant: Adding further detail to the plant descriptions, whether the plant growth form fit into shrub or tree.
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Size: Designating species into one of five size categories, based on their average body mass measurements from the AVONET database. Full chart of codes and explanations:
Symbol Size Range Very Small < 10 g Small 10-30 g Medium 31-60 g Large 61-500 g Very Large > 500 g -
Site: Location designations for survey locations. In some cases where Stations are in close proximity and/or share a high level of similarity between them they are condensed into one Site here.
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Breeding_Season: The season designation that is used in the analysis, combining the data from Season so that there are only two designations, when most species are breeding and when they are not. Full chart of codes and explanations:
Season designation Breeding_Season designation Spring, Summer Breeding Fall, Winter NonBreeding
File: Point_LatLong.csv
Description: Accompanies the paper “Agricultural and urbanized avian communities diverge via nestedness and turnover in a heterogenous urban-agroecosystem”
Rachel Elise Bockrath; California State Polytechnic University, Pomona / North Dakota State University; rachel.bockrath@ndsu.edu
Data Recorded on April 9th 2026
Collected in the Santa Clara River Valley, California, United States
This Read Me refers to the data containing information about the specific location of the survey points in the form of latitude and longitude values. Each point that was ever surveyed as a part of this study is included. This file was finalized on April 26th, 2026.
Variables
- Point_Name: The full name of the specific survey location. Matches Point_Name in the “Count_File_Refined_Manuscript” file.
- latitude: The latitude of the survey point, in signed degree format with five decimal places. Taken from survey points labeled on Google Maps.
- longitude: The longitude of the survey point, in signed degree format with five decimal places. Taken from survey points labeled on Google Maps.
Code/software
All Data files are .cvs and should not require any additional software to be downloaded or opened.