Open Collections

Description

<b>Abstract</b><br/><p id="docs-internal-guid-166be8cf-7fff-07d1-d701-4946a923cb3f" dir="ltr">Conserving species requires knowledge of demographic rates (survival, recruitment) that govern population dynamics to allow the allocation of limited resources to the most vulnerable stages of target species' life cycles. Additionally, quantifying drivers of demographic change facilitates the enactment of specific remediation strategies. However, knowledge gaps persist in how similar environmental changes lead to contrasting population dynamics through demographic rates. For sympatric hummingbird species, the population of urban-associated partial-migrant Anna's hummigbird (<em>Calypte anna</em>) has increased, yet the populations of Neotropical migrants including rufous, calliope, and black-chinned hummingbirds have decreased. Here, we developed an integrated population model to jointly analyze 25 years of mark-recapture data and population survey data for these four species. We examined the contributions of demographic rates on population growth and evaluated the effects of anthropogenic stressors including human population density and crop cover on demographic change in relation to species' life histories. While recruitment appeared to drive the population increase of urban-associated Anna's hummingbirds, decreases in juvenile survival contributed most strongly to population declines of Neotropical migrants and highlight a potentially vulnerable phase in their life-history. Moreover, rufous hummingbird adult and juvenile survival rates were negatively impacted by human population density. Mitigating threats associated with intensively modified anthropogenic environments is a promising avenue for slowing further hummingbird population loss. Overall, our model grants critical insight into how anthropogenic modification of habitat affects the population dynamics of species of conservation concern.</p>; <b>Methods</b><br />

This R data file contains a named list for each species in our study. It has been processed to remove covariates and data that are not public domain but are available for download at the links provided (indicated with * in the readme file). Each species list contains mark-recapture records (y), the known-state records (z), number of years spanned by the analysis (n.years), numbers banded individuals (n.ind), banding station membership (sta), number of banding stations (n.sta), year of first encounter for each individual (first), year of last possible encounter of each individual if it were to be alive (last), first and last years of mark recapture data (first_yr / last_yr), sex (1 = male, 2 = female) and age (1 = juvenile, 2 = adult) membership for each individual, the observed residency information for each individual in each year (r), the partially observed residency state information for each individual (u), the standardized human population density and crop data in the 3 kilometers around each banding station (HPD / crop), the unstandardized HPD and crop data (HPD_raw / crop_raw), the number of days of operational banding activity at each station each year (effort), and indicator for each station and year signifying whether banding occurred on at least two occasions separated by more than 5 days that year (kappa_shrink), the BBS survey year (year), an indicator of whether the BBS surveyor was suveying on their first year or not (firstyr), the number of BBS surveys (ncounts), the species tally on a given survey (count), the number of individual transects surveyed over the study period (nrte), the BBS transect membership for each count (rte), the number of observers contributing data over the study period (nobserver), the anonymized observer ID on a given transect for each count (rte.obser), and the initial abundance estimate given as the mean count across all transects and years, inflated by 100 for precise estimation of demographic rates (lam0).</p>; <b>Usage notes</b><br />

Data can be opened in R and analyzed using Nimble.</p>