RangeShifter 2.0: An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species’ responses to environmental changes

Abstract

Process-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes.Here we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, the genetic and evolutionary capabilities have been strengthened, notably by introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement rules can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0’s new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition.RangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows GUI has been enhanced. Furthermore, the recoding of the package has supported the development of a new version running under the R platform, RangeShiftR.RangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community.

RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental change

“…The tutorials include adaptations of the three original RangeShifter examples (Bocedi et al, 2014), accompanied by sample code for analysis and visualisation. Additionally, we provide a fourth tutorial that demonstrates novel features of RangeShifter 2.0 (Bocedi et al, 2020) by simulating the range dynamics of a species in a changing landscape. Here, we present its shortened form to introduce the RangeShiftR syntax.…”

“…The genetics module is optional and we leave it disabled here (but see Bocedi et al (2020) for an example of this functionality). Although this implies missing inter-individual variation in dispersal traits, individuals are still characterised by their sex, stage and age.…”

“…RangeShifter is a Windows application that can be used via a graphical user interface (GUI) or in a batch mode. The new version 2.0 (Bocedi et al, 2020) adds novel features including the option for dynamic landscapes and a completely revised genetics module. Here, we present RangeShiftR, a package that implements the RangeShifter 2.0 simulation in R (R Core Team, 2020), making it a multi-platform software.…”

“…Below, the main modules are described briefly. For comprehensive documentation, covering all parameters and options, we refer to the package documentation and the RangeShifter manual (Bocedi et al, 2014, 2020).…”

“…Individuals can carry a genome that they inherit from their parents at birth. The genome may consist of multiple autosomal loci that can either be neutral or coding for traits (Bocedi et al, 2020). Most dispersal parameters can optionally be treated as heritable traits thus allowing evolution of dispersal strategies.…”