DOI: 10.5061/dryad.g79cnp5vk
title: Demographic mechanisms and anthropogenic drivers of contrasting population dynamics of hummingbirds

description: 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 (Calypte anna) 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.
description: 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).
description: Data can be opened in R and analyzed using Nimble.
description: ## Hummingbird IPM data file This data file contains a list of lists named
 for each of the four species in our analysis: Anna's (ANHU; *Calypte
 anna*), black-chinned (BCHU; *Archilochus alexandri*), calliope (CAHU;
 *Selasphorus calliope*), and rufous hummingbirds (RUHU; *Selasphorus*
 rufus). Each of these lists contains the required mark-recapture inputs
 for integrated population modelling in R/Nimble. Raw covariates of human
 population density, land cover classification, as well as Breeding Bird
 Survey data can be accessed as described under **Sharing/Access
 information**. To load the file in R from the current working directory:
 *load("./IPM.shared.Rdata")* ### Description of the data and
 file structure Within each named list, there are data for mark-recapture
 records (NA = station not active, 0 = not captured, 1 = captured; **y**),
 the known state, either alive (1) or unknown (NA) , of each individual in
 each year (**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** (0 = not yet marked, 1 = juvenile, 2 = adult)
 membership for each individual, the observed residency information (NA =
 station not active, 0 = not observed as resident, 1 = observed as
 resident) for each individual in each year (**r**), the partially observed
 residency state information (NA = residency state unknown, 1 = known
 resident) for each individual (**u**), the standardized human population
 density (people per square kilometer) and proportion of 300 meter crop
 pixels 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**), a matrix of indicator flags for years
 of active banding for each station (0 = not active, 1 = active;
 **active**), an indicator for each station and year signifying whether
 banding occurred on at least two occasions separated by more than 5 days
 that year (no = 0, yes = 1; **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 (**lam0**).
 \*Not in Rda file due to preexisting licensing and must be accessed from
 original data provider. ### Sharing/Access information Breeding Bird
 Survey (BBS) data used in these analyses can be accessed from the USGS
 site () or from within R
 using bbsBayes package: ().
 Unconstrained human population densities from Canada and the USA at a 1
 kilometer resolution in the 3 kilometers surrounding banding stations can
 be downloaded from WorldPop.org
 (). Annual 300 meter
 land cover classification gridded maps can be downloaded from the Climate
 Data Store of the Copernicus Climate Change Service at
 . ### Code/Software This data
 file is loaded and analyzed in the R script ***AppendixD.R***. We
 conducted these analyses using R version 4.2.3 (2023-03-15). The NIMBLE
 MCMC compiler version interfaced through R was *nimble_0.13.1*.