NEWGARDEN: a computer program to model the population dynamics and genetics of establishing and fragmented plant populat
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APPLICATION ESSAYS
NEWGARDEN: a computer program to model the population dynamics and genetics of establishing and fragmented plant populations Stephan Pelikan • Steven H. Rogstad
Received: 21 July 2012 / Accepted: 22 January 2013 / Published online: 3 February 2013 Ó The Author(s) 2013. This article is published with open access at Springerlink.com
Abstract Conservation of plants often involves isolated in situ or ex situ protective restoration or supplemental plantings. Plant preservation also frequently involves maintenance of recently fragmented populations. The effects of the spatial patterning of the initial target species individuals in such situations on future population growth and genetic diversity maintenance are commonly difficult to predict, especially given that plants have varying life history characteristics. NEWGARDEN allows users to create a virtual preserve or fragment of specified size, place initial individuals at designated locations (the program is spatially explicit using a grid system), and follow population development stemming from bouts of mating influenced by user-specified life history characteristics (e.g., genetic diversity of the initial individuals; age-specific mortality; age-specific reproduction; gene dispersal distances; etc.). Output, which can be reported for the entire population data set and/or specified regions of the preserve or fragments after each bout of mating, includes total population and individual newest cohort data on the number of individuals, total number of founding alleles retained, observed heterozygosity, expected heterozygosity, and FIT. Use of the program is illustrated with a NEWGARDEN analysis of the effects of varying founder pattern and gene dispersal distance on population growth and genetic diversity for an annual plant.
S. Pelikan Department of Mathematical Sciences ML25, University of Cincinnati, Cincinnati, OH 45221, USA S. H. Rogstad (&) Department of Biological Sciences ML6, University of Cincinnati, Cincinnati, OH 45221, USA e-mail: [email protected]
Keywords Conservation genetics Founder effects Fragmentation Plant population genetics Population establishment Restoration genetics
Introduction If current trends continue, conservation of numerous plant species will increasingly involve the creation and management of limited rescue or maintenance populations that will need to be manipulated in small, fragmented habitats. Several costs are associated with such management, and thus modeling population establishment, development, and consequent changes in genetic diversity under different conditions can assist in determining best practices for plant conservation efforts (e.g., Rogstad and Pelikan 2011). NEWGARDEN is a computer program designed to model the growth and population genetics of plant populations developing from different founding and life history conditions. Although several other programs exist to simulate and analyze population characteristics and gene flow within, between, and among plant populations (e.g., see Ball
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