An Individual-Based Model for Metapopulations on Patchy Landscapes-Genetics and Demography (IMPL-GD)

Abstract

The model described in this chapter addresses the risk of metapopulation extinction when a habitat parcel is eliminated from a patchy landscape. The authors describe the Individual-Based Model for Metapopulations on Patchy Landscapes-Genetics and Demography (IMPL-GD), an agent-based simulation model developed using NetLogo (http://ccl.northwestern.edu/netlogo/). This model is intended to provide a better understanding of how ecological variables such as landscape physical characteristics, population genetic and demographic traits, and network relationships between habitat parcels relate dynamically to metapopulation viability. The IMPL-GD places generic organisms on a landscape that consists of habitable and non-habitable patches, including traversable but non-habitable terrain. The agents, called “whatsits,” were designed to reflect the characteristics of small, solitary animals that defend small, circular territories in the landscape. They are defined in the model by a unique identification number, age, sex, lineage, and other characteristics. The IMPL-GD model enables the user to rapidly execute thousands of simulations in which a random parcel of habitable terrain is eliminated from the landscape after a given number of time steps and the impact on whatsit population viability is recorded. The output from a large number of IMPL-GD simulations can statistically analyzed to identify associations between the independent ecological variables and quantify their relation to the dependent variable of whatsit survival in the form of a conservation utility index.

Appendix

User-specified setting	Description	Range or options
patch-seed	Seeds the random number generator for initial placement of seed patches, to ensure that runs are replicable	Any number
Landscape_Specs?	If true, user-defined parameters constrain acceptance of randomly generated landscapes	True or false
#Habitats?	If true, acceptance of randomly generated landscapes is based on the number of discrete habitat parcels	True or false
seed-patches	The number of patches that will be designated “habitable” or “not habitable” to begin landscape initialization	0–350 Patches
seed-good	The percentage of seed patches that will be designated “habitable”	Any whole number percentage
#-Habitats	The number of discrete habitat parcels that will comprise an acceptable landscape	Any whole number
Parcel_Size?	If true, acceptance of randomly generated landscapes is constrained by the area of habitat parcels	True or false
min-terr/hab	The minimum number of whatsit territories available in each acceptable habitat parcel	Any whole number
max-terr/hab	The maximum number of whatsit territories available in each acceptable habitat parcel	Any whole number
%_Good/Bad?	If true, acceptance of randomly generated landscapes is constrained by the proportions of habitable and non-habitable patches	True or false
min%good	The minimum percent habitable patches in an acceptable landscape created via the “seed-all” algorithm	Any whole number percentage
max%good	The maximum percent habitable patches in an acceptable landscape created via the “seed-all” algorithm	Any whole number percentage not  >  (min%good)
min%bad	The minimum percent non-habitable patches in an acceptable landscape created via the “seed-all” algorithm	Any whole number percentage
max%bad	The maximum percent non-habitable patches in an acceptable landscape created via the “seed-all” algorithm	Any whole number percentage not  >  (min%bad)
whatsit-seed	Seeds the random number generator for initial placement of whatsits, to ensure that runs are replicable	Any number
initial-whatsits	The number of founder whatsits created to begin the run	Any whole number
#_Steps	The total number of steps included in the replicate	To extinction
		1
		10
		25
		50
		100
		150
step#	The step on which habitat elimination will occur	Any whole number
#	The number of habitat parcels that are eliminated at the scheduled step	Any whole number
criteria	Determines the order in which habitat parcels are selected for elimination	Highest or lowest
attribute	The characteristic by which habitat parcels are chosen for elimination	Random
		#-of-whatsits
		Births-previous-year
		Deaths-previous-year
		Net-population-change-previous-year
		#-outmigrants-previous-year
		Area
		Edge-to-area-ratio
		Distance-to-closest-habitat
		Female:male_ratio
		#-founders-represented
		#-founders-represented-­only-here
		#-alleles
		#-private-alleles
		Heterozygosity
		Abs-diversity
		Relative-diversity
		Differentiation-relative
		Contribution-to-total-diversity
		Allelic-richness
		Contribution-to-total-allelic-richness
		Node-degree
		Connectivity-contribution
		Bonacich’s-centrality
		Node-strength
		Sum-of-linked-nodes’-strengths
		Contribution-to-connectivity-strength
		#-of-founders-represented
survival_to_age_1	The mortality rate for individuals in the first year of life	0–1 (increment 0.001)
annual-survival_>age_1	The mortality rate for individuals at least 1 year of age	0–1 (increment 0.001)
death-rate-grn	The odds that a dispersing whatsit will die while traveling one cell-length through habitable terrain	0 to (death-rate-red) (increment 0.0001)
death-rate-red	The odds that a dispersing whatsit will die while traveling one cell-length through non-habitable terrain	(death-rate-grn) to 1 (increment 0.0001)
territory-radius	The distance (in patches) from a whatsit’s location to the boundary of its territory in all directions	1–20 Cells (whole numbers)
allow-M/F-terr-overlap	This setting determines whether or not a patch may be included simultaneously in both a male and a female territory	True or false
first-repro-age	The minimum age at which whatsits are capable of reproducing	0–5 Steps
superior-repro-age	The age at which individuals become more likely to reproduce than younger whatsits	0–25 Steps
last-repro-age	The maximum age at which whatsits are capable of reproducing	(superior-repro-age) to 100 steps
lineage-depth	The number of generations contained in each whatsit’s lineage	0–20 Levels
mating-radius	The maximum distance (in patches) at which whatsits are able to mate	1–10 Cells (whole numbers)
Avg_lethal_­equivalents	The average number of lethal equivalents for the population	0–20 (Increment 0.1)
avg-litter-size	The minimum average litter size	0–20
#_Loci	The number of loci for which genetic information is recorded	0–449