**2. Methods**

We used NEWGARDEN to model the population growth and genetic diversity of newly establishing chestnut populations. This program simulates natural population development based on a set of user-specified initial input conditions (Rogstad & Pelikan, 2011). One set of input conditions constitutes a "trial" and input between trials may vary as to founder number and geometric patterning, preserve characteristics, and with regard to various lifehistory characteristics (see below). For each age (bout of mating with mates chosen randomly as conditioned by the input) of the developing population, NEWGARDEN provides output statistics (for each new cohort and for the entire population; only the latter are given here) concerning the population size, the number of founding alleles retained, heterozygosity (observed and expected), and Fit (a measure reflecting deviation from Hardy-Weinberg expectations due to subdivision and/or inbreeding; hereafter referred to as F value). For each set of input trial conditions, the user can specify the number of replicate runs of those conditions to be used to calculate a mean and standard deviation for each of the listed output statistics. The user can thus compare whether means of statistics differ for populations of contrasting trials that differ in one or more input conditions.

#### **2.1 Input parameters held constant**

376 Genetic Diversity in Plants

include propagule generation and collection, storage, treatment, site preparation, planting, protecting, provisioning, travelling to and from the introduction site, monitoring, and future

One approach to optimizing restoration of the American chestnut is to use computer programs to model the population growth and genetic effects of restoring plant populations in different ways. While restoration programs have been widely undertaken for a number of plant species, we lack the tools to analyze how factors like founder number and geometry of placement within a restoration habitat interact with varying founder or species life history characteristics, and whether these factors impact resultant population growth rates and preservation of genetic diversity. While ecological edge effects have been documented as being evident at the borders and edges of restoration preserves due to altered microenvironments in terms of wind-speeds, light availability and organismal composition among other factors (Primack, 2010), less is known about whether placement of founders at varying distances from the preserve edge impacts the population dynamics and genetic diversity measures of establishing populations. Further, can differing founder placement patterns interact with other life-history characteristics such as pollen and offspring dispersal distances to bring about different population growth rates and genetic diversity levels? Exploring these potential demographic and genetic edge effects in the field with *C. dentata* would not be feasible due to the costs associated with carrying out such experiments on a wide-scale to ensure statistical reliability of data, especially since blight-resistant individuals are expensive and time-consuming to produce, and thus must be used judiciously. In this case modeling virtual populations through computer simulations represents a more tractable alternative to field experiments, potentially providing valuable insight for restoration managers on how best to re-introduce the American chestnut into preserves.

In this study, the computer program NEWGARDEN (Rogstad & Pelikan, 2011) was used to model blight-resistant American chestnut population restoration in a virtual preserve to explore the population growth and genetic effects of placing founders at different distances from preserve borders under differing patterns of gene dispersal. Our null hypothesis is: Varying American chestnut founder placement at various diagonal distances from the preserve border, while altering offspring and pollen dispersal distances, will have no effect on population growth rates or retention of founding genetic diversity. We used comparative trials to examine the degree to which some patterns of introduction might be preferable over others.

We used NEWGARDEN to model the population growth and genetic diversity of newly establishing chestnut populations. This program simulates natural population development based on a set of user-specified initial input conditions (Rogstad & Pelikan, 2011). One set of input conditions constitutes a "trial" and input between trials may vary as to founder number and geometric patterning, preserve characteristics, and with regard to various lifehistory characteristics (see below). For each age (bout of mating with mates chosen randomly as conditioned by the input) of the developing population, NEWGARDEN provides output statistics (for each new cohort and for the entire population; only the latter are given here) concerning the population size, the number of founding alleles retained, heterozygosity (observed and expected), and Fit (a measure reflecting deviation from Hardy-Weinberg expectations due to subdivision and/or inbreeding; hereafter referred to as F

manipulations of individuals (Rogstad & Pelikan, 2011).

**2. Methods** 

The input parameters common to all experimental runs are described following their order in the NEWGARDEN input file. These constant input parameters are based on population development data obtained from the only known chestnut restoration stand which is naturally developing at West Salem, Wisconsin (for details, see Pierson *et al.,* 2007; Rogstad & Pelikan, 2011).

### **2.1.1 The preserve grid system**

Populations for all trials develop on a Cartesian grid system defined by the user. Individuals can only establish on grid points, the spacing of which represents the average minimum distance that can exist between reproductive trees. In our simulations, the grid system represents a restoration preserve (a 5 km x 5 km square), comprising a 1000 x 1000 grid point system with 5 m between grid points. This simple model represents an approximate average minimum distance spacing needed between two reproductive trees based on a mature chestnut community at the carrying capacity.
