DOI: 10.5061/dryad.qjq2bvqpw
title: Predator-prey time series: Monthly densities of least Killifish and Eastern Mosquitofish over five years

description: Individual predator and prey species exhibit coupled population dynamics
 in simple laboratory systems and simple natural communities.  It
 is unclear how often such pairwise coupling occurs in more complex
 communities, in which an individual predator species might feed on several
 prey species and an individual prey species might be attacked by several
 predators.  To examine this problem, we applied multivariate
 autoregressive state-space (MARSS) models to five-year time series of
 monthly surveys of a predatory fish, the Eastern Mosquitofish (Gambusia
 holbrooki), and its littoral zone prey species, the least Killifish
 (Heterandria formosa), in three locations in north Florida.  The
 MARSS models were consistent with coupled predator-prey dynamics at two of
 the three locations.  In one of these two locations, the
 estimated densities of the two species displayed classic predator-prey
 oscillations.  In the third location, there was a positive effect
 of Killifish density on Mosquitofish density but no detectable effect of
 Mosquitofish density on Killifish density.  In all three
 locations, increased submergent vegetation cover was associated with
 increased prey density but not increased predator density. 
 Eigenvalues analyses for the joint dynamics indicated that all three
 systems would return to their respective stationary distributions of
 density if perturbed.  The three different patterns demonstrate
 that the dynamics of a pairwise predator-prey interaction emerge not only
 from the characteristics of the prey and the predator, but also those of
 the habitat and trophic web in which the predator and prey are
 embedded.    
description: Data collected in rivers and ponds via monthly throw-trap
 census.
description: # Predator-prey time series: Monthly densities of least Killifish and
 Eastern Mosquitofish over five years
 [https://doi.org/10.5061/dryad.qjq2bvqpw](https://doi.org/10.5061/dryad.qjq2bvqpw) The dataset contains the summary means and variances of several variables estimated from the throw-trap data collected in three locations in north Florida, two in Jefferson County and one in Leon County. The data were used to assess whether monthly densities of a species of prey, Heterandria formosa, display a reciprocal relationship with monthly densities of a predator, Gambusia holbrooki. The data come from three separate locations, with monthly censuses over a five-year period at each month. ## Description of the data and file structure The datafile is entitled TimeSeriesLogMeans.csv. The first row is a heading with the variable names. Each subsequent row corresponds to a sampling date at each of three locations. LOCATION: There are three locations, TP (Trout Pond), WRHW (headwaters of Wacissa River), WRGP (Goose Pasture campground along the Wacissa River). DATESEQ: This is the ordinal designation for the samples. They are listed as numbers 1, 2, etc. with the first sample, DATESEQ=1, taken in September 1999. Samples were taken every four weeks so usually, but not always, correspond with successive months. Within some periods, there were two samples in the same calendar month and on occasion there was no sample in February. COVER1: The average percent vegetative cover within a 0.71 m x 0.71 m throw trap, taken over three replicate throws at that location on that sampling date. VA1COVER: The variance in percent vegetative cover among the three replicate throws. ME1LOGHETADS: The average log density of adult Heterandria formosa (adults per 0.5 sq. meter) taken over three throws. VA2LOGHETADS: The variance in log density of adult Heterandria formosa (adults per 0.5 sq. meter) taken over three throws. ME4LOGGAMBO: The average log density of adult Gambusia holbrooki (adults per 0.5 sq. meter) taken over three throws. VA4LOGGAMBO: The variance in log density of adult Gambusia holbrooki (adults per 0.5 sq. meter) taken over three throws. Several cells are blank. In these cases, data are not available. These cases reflect sampling periods when the site was not accessible due to flooding on the roads leading to the site. ## Code/Software There are two R files. Each one implements code found in Holmes, E.E., Scheuerell, M.D., and Ward, E.J. 2021. Analysis of multivariate time-series using the MARSS package Version 3.11.4. NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA, pp. 1-341. The MARSS package can be downloaded through any of the CRAN centers for the R language and computing environment. FINAL.R contains the code used to fit the state-space models to the data provided in TimeSeriesLogMeans.csv. These models examine the dynamics of the two species with and without vegetative cover as a covariate. Bootstrap.R contains the code used to calculate eigenvalues of the dynamic system at each site and perform bootstap simulations as surrogate hypothesis tests for cyclicity.