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The Portal Project: a long-term study of a Chihuahuan desert ecosystem

S. K. Morgan ErnestiD, Glenda M. YenniiD, Ginger R. H. AllingtoniD, Ellen K. BledsoeiD, Erica M. ChristenseniD, Renata M. DiaziD, Patricia Kaye T. DumandaniD, Keith Geluso, Jacob R. GoheeniD, Qinfeng GuoiD, Edward Heske, Douglas A. KeltiD, Samantha Lamb, Joan M. MeinersiD, Jim Munger, Raven Padgett, Carla RestrepoiD, Douglas A. Samson, Michele R. Schutzenhofer, Marian Skupski, Sarah R. SuppiD, Katherine M. ThibaultiD, Shawn TayloriD, Ethan P. WhiteiD, Hao YeiD, , Thomas J. ValoneiD

Abstract

This is a data paper for the Portal Project, a long-term ecological study of rodents, plants, and ants located in southeastern Arizona, U.S.A. This paper contains an overview of methods and information about the structure of the data files and the relational structure among the files. This is a living data paper and will be updated with new information as major changes or additions are made to the data. All data - along with more detailed data collection protocols and site information - is archived at: https://doi.org/10.5281/zenodo.1215988.

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In-depth summary

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Claude Opus 5.5 · xhigh effort · 2 Nov 2026 · from the full text of version 4 (14 Apr 2026) · CC BY 4.0

The Portal Project archives over 40 years of continuous monthly rodent, biannual plant, multi-decade ant, and automated weather data from 24 experimentally manipulated Chihuahuan Desert plots with automated quality control.

Fewer than 9% of ecological studies use data spanning more than a decade, and typical ecological datasets cover less than 3 years and are rarely made publicly available. Initiated in 1977 near Portal, Arizona, this living data paper and continuously updated GitHub/Zenodo archive provide over 40 years of relational data on granivore competition, community dynamics, and grassland-to-shrubland conversion across 24 experimental plots.

Key results

  1. ShownThe Portal Project archive provides 27 relational tables across 7 directories documenting experimental manipulations and multi-taxon monitoring on 24 fenced plots since 1977.

    Across a 20-hectare site with twenty-four 50 m x 50 m plots (11 kept in original treatments since 1977), the dataset spans monthly rodent trapping (49 traps/plot since 1977), biannual plant censuses (16 permanent 0.25 m2 quadrats/plot since 1981) and shrub transects, annual July ant counts (1977-2009), local weather (since 1980), remotely sensed NDVI, and daily PhenoCam images (since March 2017). · Site Information; Rodent sampling; Quadrats; Data overview

  2. ShownMulti-step manual and automated quality assurance and quality control (QA/QC) pipelines validate field records, resolve tag reuse across decades, and automatically update supplementary tables and semantic Zenodo releases.

    Field datasheets are double-entered into restricted Excel templates and checked via R scripts for species-specific measurement bounds, duplicate stake records, and individual recapture consistency (assigning unique IDs when ear or PIT tags repeat after > 3 years), with every GitHub update triggering automated tests and a semantically versioned Zenodo release. · Overview; Rodents; Data versions

  3. ShownHistorical protocol shifts and biological changes at the site require specific filtering and effort corrections when analyzing multi-decadal time series.

    Key documented discontinuities include Banner-tailed kangaroo rat (Dipodomys spectabilis) local extinction in the late 1990s (phasing out its exclosures in 2004), treatment flips on 12 of 24 plots in March 2015, discontinuing ant sampling after July 2009, surveying 8 vs 16 plant quadrats in 1981-1982, omitting perennial plants from quadrats prior to 1989, and partial single-night (12-plot) rodent trapping events. · Rodent treatments; Ant treatments; Quadrats; Data usage recommendations

Methods, data and reproducibility

Across twenty-four 50 m x 50 m fenced plots with size-selective rodent gates, ant poison treatments (1977-2009), and temporary seed/herbicide manipulations (1977-1987), researchers conduct monthly Sherman live-trapping, biannual plant quadrat and shrub transect surveys, weather logging, and NDVI/PhenoCam tracking. Double-entered field data undergo automated R QA/QC checks before release in 27 relational tables.

  • Monthly rodent live-trapping records (species, sex, reproductive status, weight, hind foot length, ear/PIT tags) across 24 plots (49 stakes per plot) since 1977 · multiple species · n = 24 plots (49 permanent stakes per plot), sampled monthly since 1977 · 10.5281/zenodo.1215988
  • Biannual winter and summer plant quadrat censuses (since 1978/1981; percent cover since 2015) and shrub transects (1989-2009 every 3 years; 2015-present annually) · plant (other) · n = 16 permanent 0.25 m2 quadrats and 2-4 transects per plot across 24 plots · 10.5281/zenodo.1215988
  • Annual July monsoon ant colony counts (within 2 m radius of 49 stakes or whole-plot for large-bodied species) and crushed-millet bait pile abundance counts (25 stakes per plot) from 1977 to 2009 · multiple species · n = 33 years (1977-2009) across 24 plots · 10.5281/zenodo.1215988
  • Site weather station logs (1980-1989 daily; 1989-present hourly; 5-min storms), regional GHCN-Daily stations, satellite NDVI (Landsat, GIMMS, MODIS), and PhenoCam images (since March 2017) · none · n = 4 generations of site weather stations (since 1980) plus 2 regional stations · 10.5281/zenodo.1215988, US1AZCH0005, USC00026716
Methods & tools
portalr, Landsat, GIMMS, MODIS, PhenoCam Network, SEINet
Code
http://github.com/weecology/PortalDatahttp://github.com/weecology/portalr
Data & accessions
https://doi.org/10.5281/zenodo.1215988https://phenocam.sr.unh.edu/webcam/sites/portal/http://swbiodiversity.org/seinet/http://www.ncdc.noaa.gov/ghcn-daily-description
Software & environment
R, devtools (devtools::install_github("weecology/portalr")), Git, Excel
Limitations (5)
  • Experimental treatments shifted on short-term plots in 1988, 2004, and 2015 (including flipping 12 of 24 plots in March 2015), and ant monitoring and treatments were discontinued after July 2009. · stated by the authors
  • Rodent trapping is occasionally only partially completed (12 of 24 plots trapped over one night due to weather or travel), and untagged animals removed from exclosure plots are assumed to be new individuals upon recapture. · stated by the authors
  • Plant quadrat protocols changed over time: quadrat size decreased from 0.5 m2 to 0.25 m2 in summer 1981, only 8 of 16 quadrats per plot were surveyed in 1981-1982, and perennial species were omitted from quadrats prior to 1989. · stated by the authors
  • Shrub transect recording methods between 1989 and 2009 were highly variable across years in which non-shrub species were recorded, lacked location points in 2004 and 2009, had a 2010-2014 sampling gap, and changed protocol in 2015. · stated by the authors
  • Seed addition (1977-1985) and Roundup annual plant removal (1985-1987) manipulations had no significant detected effect on the plant community and were discontinued. · stated by the authors

Who should read:Read this if you analyze long-term ecological time series, species interactions, regime shifts, or desert community dynamics and need a continuously updated, quality-controlled multi-decadal field dataset.

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