W.R. Congleton

A C++ implementation of an individual/landscape model

Abstract Dynamic models of biological systems are diverse, but have components in common. The description of a system may involve multiple databases which change and interact (individuals, populations, the landscape). A clock is required to advance the system description through time. In addition, the generation of random variates from different probability distributions, interpolation of values from tabular data, and the collection of statistics on system components may be required. All of these tasks can be effectively achieved through object oriented programming (OOP). The C++ programming language is the object oriented language utilized in the implementation described. Object oriented programming can be utilized to facilitate the organization and development of dynamic models of biological systems. A C++ hierarchy of classes describing objects in the system can start at the level of machine processing. A binary object can use individual bits of memory to represent binary data. Computer memory requirements can be minimized by using a linked list class to place objects in a list whose composition and size vary as the program executes. The C++ feature of runtime linking can connect a general base class with the data required for a specific application. These machine oriented classes can then be inherited into an individual animal class with binary data (male/female, diseased/nondiseased) and a population class which is a linked list of individuals. The binary arithmetic and memory pointers involved in these base classes can be completely transparent to the user of the individual and population classes which are described in biological rather than machine terms. OOP can facilitate the development of a description of the individual, population, landscape and their interactions. A landscape object can be described by a grid of rectangular cells linked on four sides to adjoining cells by memory pointers. These memory pointers to adjoining cells can be utilized to describe flows and movement of objects over the grid. This base class grid description can be inherited into a derived habitat class with additional data. The location or coordinates of objects located on the grid can be utilized to access the data for the cell in which it is located. Since grids describing landscapes can be large and heterogeneous, GIS can be utilized for grid initialization and for analysis of spatial data in the simulation output. A simulation clock is required to advance the description of the objects in the system and their interactions through time. A base clock class advances time in specified increments, or between events, or in specified increments until an event occurs. Events can be either scheduled long term or triggered by a change in the system and stored in an event queue by using the same base linked list class used to describe populations. The type of events which occur in a system are specified in a derived clock class which is accessed by the base clock class when the program executes through run-time linking. An example application is developed to describe winter kill of deer. Analysis of the simulation output in a GIS showed simple rules for individual animal behavior affected the pattern of landscape usage through time. Source code and documentation are available.

Mariculture siting : a GIS description of intertidal areas

Variations in habitat parameters greatly affect the physiological state and the growth of bivalves. To achieve success in shellfish mariculture, environmental parameters favorable to the cultured species must be determined and then characteristics of potential grow-out sites evaluated. An intertidal bay in Eastern Maine was described in a GIS (geographical information system), which incorporated infrared aerial photographs and maps of bottom types, topography and bathymetry. Data layers included elevations from both nautical charts and GPS measurements made in the bay. From the elevation data, a series of programs was developed to generate a triangulated irregular network and a grid of elevations. A numerical flow model used the elevation grid to simulate a time series of tidal current vectors and free surface elevations. Gridded data from the numerical model were imported into the GIS and displayed as false color images of elevations, maximum current velocities and tidally averaged current velocities. Current vectors were layered over aerial photos showing sediment transport in the water. The GIS can be queried to identify sites for mariculture. A sample query identified sites for shellfish grow-out.

Regional differences in initial settlement and juvenile recruitment of Mya arenaria L. (soft-shell clam) in Maine.

ABSTRACT Clam landings have dramatically decreased in eastern Maine since 1982. Earlier studies demonstrated that densities of 0-y-old individuals of Mya arenaria L. were lower in Washington County on the eastern Maine coast than in Cumberland County on the southern Maine coast. Reduced juvenile recruitment could result from reduced larval abundances, high postsettlement mortality, or a combination of these factors. Attempts to assist recovery of populations experiencing reduced recruitment would vary depending on which combination of factors inhibited recruitment. In this study we measured initial settlement, short-term (<4 wk) postsettlement densities, and longer term (several months) postsettlement densities of 0-y-old juvenile M. arenaria in both eastern and southern Maine. Although there were seasonal and spatial differences, densities of juvenile clams were significantly greater in southern Maine over eastern Maine at each of these life history stages (initial settlement, and early and later postsettlement), generally by one or more orders of magnitude. These results suggest the low number of M. arenaria recruits in eastern Maine is a consequence primarily of reduced densities of larvae in near-shore waters rather than processes affecting postsettlement survival differentially between southern and eastern Maine. Because of the very low abundance of competent clam larvae in eastern Maine, restoration of clam populations there will require intensive efforts, such as seeding mudflats with hatchery-reared juvenile clams and managing subsequent clam survival.