Introduction

SPLATCHE (for SPatiaL And Temporal Coalescences in Heterogenous Environment) is a program that allows to incorporate the influence of environment in the simulation of migration of a given species from one origin. In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated.

Geographic area and environmental information have to be specified by the program user in a series of input files. Basically, the virtual world where migrations take place is constituted by a matrix of demes. Each deme has its own environmental characteristics according to the input files. A coalescent-based approach allows to generate the molecular diversity of any population sample. The molecular data obtained can then be analyzed in order to study the signature of the simulated demographic scenario.

The goal of this online manual is to describe the technical aspects of the software SPLATCHE (version 1.0). This manual complements the article from Currat, Ray and Excoffier, published in 2004. Further details on the methodology can also be found in Ray (2003) and Currat (in prep). The pdf version of the user manual could also be download there.

Authors and related papers

This software was developped by Mathias Currat, Nicolas Ray and Laurent Excoffier and the reference to cite is:

Currat M, Ray N, & Excoffier L (2004) SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity, Molecular Ecology Notes, Volume 4, Issue 1, Page 139-142 [PDF file]
 

About SPLATCHE

SPLATCHE user manual ( pdf version)

Related applications

Ray N, Currat M, Excoffier L (2003) Intra-deme molecular diversity in spatially expanding populations.Mol Biol Evol. 2003 Jan;20(1):76-86

Currat M, Excoffier L (2004) Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe. PLoS Biol 2(12): e421

Data sets

Square data set

Africa data set

Demographic and spatial expansion module

Principles:
The demographic and spatial expansion module allows to simulate a demographic and spatial expansion from one or many initial populations. The simulation uses discrete time and space. The unit of time is the generation, while the unit of the 2D space is a cell, also called a deme. Each deme has the same size and can be considered as a homogeneous subpopulation. The spatial model used in SPLATCHE is the 2D stepping-stone model (Kimura and Weiss 1964), which defines a regularly spaced array of demes. Each deme undergoes an independent population growth and can exchange emigrants with its four direct neighboring demes.
Each deme is also considered as a sub-unit of the environment. The environment can influence the local demography through its carrying capacity (maximum number of individuals) and its friction (facility to migrate through). These two environmental characteristics can be defined for the entire array of demes through the input of maps. Variations, through time, of carrying capacity and/or friction values are also possible.
 

Available demographic models:
The logistic population growth of each deme follows a standard logistic curve, of the form