SHIBAcombines information about i) the changing spatial conformation of land areas through time with ii) a dated phylogeny and iii) a contemporary distribution of terminal taxa in the land areas, in order to produce likelihoods of the spatial distribution of ancestral taxa. It achieves this through simulating the movement of ancestral taxa based on a simple model of island biogeography.
SHIBAmodels the history of a landscape as discrete ‘cells’ of time-
lineage’ that begins and ends contemporaneously with the beginning and end of a time
periodwith on edge and leaves with two, the two ‘new’ lineages will be reconciled to appear at the beginning of the subsequent
period. If a clade enters a
periodwith on edge and branches twice, thus leaving with three edges, the three ‘new’ lineages will appear at the beginning of the subsequent
period; information about the branch within a
perioddoes not persist).
lineagewith a starting distribution,
spaces, with a probability based on the distance between
spaces, and ii) survive or go extinct in each
spaceit is in, with a probability based on the area of the
lineagesmake it to the present, without dying out in all
lineagesbeing in different places.
SHIBAcan best be seen as an experimental ‘sandbox’ to explore likelihoods of hypotheses about lineage movement. Varying parameter values and historical area details can then be used to assess the sensitivity of ones biogeographic conclusions.
SHIBA you will need:
See Input File Format for more details on encoding your input data.
SHIBA uses a simple model to determine the spatial distribution of daughter lineages that maximizes allopatric speciation. When, at the transition of one period to the next, a lineage splitting occurs (as specified by the input phylogeny):
Hence, with two daughter lineages and two areas, the outcome will be simple allopatry. With two daughter lineages and one area, the outcome will be simple sympatry. With two daughter lineages and three areas, the outcome will be one area with one daughter lineage and two areas with the other daughter lineage, indicating that the ancestral species grew in spatial distribution, perhaps with little evolutionary change, while the population in one area underwent divergence and allopatry. Et cetera...
See Pseudocode for more details of the biogeographical algorithm.
Both the size of an ancestral area and its degree of isolation from other areas will strongly influence the likelihood that an ancestral taxon distribution included it or not. To incorporate these data,
SHIBA contains a basic Island Biogeography model, with functions similar to those proposed in the classic MacArthur and Wilson model: extinction of a lineage on an island is inversely related to its area, while dispersal probability into and out of an island is inversely related to its isolation.
Please see Island Biogeography functions for more details on the functions.
SHIBAwith the first phylogeny:
shiba -l -p 0(the
-loption give the input data printout). Look at the distribution of Lineage 0 and Lineage 2 (marked with a ‘
*’ in the ascii-graphic).
SHIBAwith the second phylogeny:
shiba -p 1. Look again at the distribution of the Lineage 0 and 2.
-son the command line, or in the
shibaInput.xmlfile), our confidence in these interpretations can be further strengthened.
SHIBA use a ‘brute-force’ approach to finding successful solutions, running each simulation until the present and then comparing observed and simulated distributions. This is very inefficient, in terms of the number of solutions found relative to the number of runs initiated. The code has been parallelized using
pthreads to make use of all the cores of a multi-core CPU. Nevertheless, with large trees and/or large space-time grids, the program may take several hours to run. By directing the output to another file, and using
nohup, the program can be left to run on powerful servers:
$ nohup shiba > out
We are working to optimize the code further and to incorporate alternative search heuristics.
Please see Webb & Ree (2012) for more details.