The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation

Table 1 Parameter settings of the model.

parameter	default value	alternative values
grid size	60 by 140	-
initial nr organisms	1500	-
total evolutionary time	500000	-
death rate	0.1	-
nr different niches	20	2/7/14
nr of types of TF genes	4	-
nr of types of phenotype genes	20	-
nr of network iterations	10	30/60
initial network connectivity	2	-
α	0.8	0.4
HD_th	6	only nearest
β	250	25/100
γ	1.	0.6
tfbs duplication rate	0.0001	0.001/0.00001
tfbs deletion rate	0.000165	0.00165/0.0000165
tfbs innovation rate	0.00005	0.0005/0.000005
tfbs type change rate	0.00005	0.0005/0.000005
tfbs weight switch rate	0.00005	0.0005/0.000005
gene duplication rate	0.0003	0.003/0.00003
gene deletion rate	0.00045	0.0045/0.000045
macromutation rate	0.005	0.05/0.0005
gene state mutation rate	0.003	-
assortativeness mutation rate	0.075	0.0075
assortativeness mutation std.	0.15	-
reproduction radius	2	1/4/global
competition radius	2	1/4/global

The table shows the default parameter settings we used for the simulations described in the article. In addition, alternative parameter values used for the additional simulations described in Additional file 1 are shown. The number of network iterations refers to the maximum number of times the state of the gene regulatory network is updated starting from the birth state of the organism to determine it's phenotype. TFBS mutation rates are per TFBS, gene mutation rates are per gene. Macromutations, assortativeness mutations and TFBS innovation rates are per genome. The ratios between the different mutation rates where chosen such that macromutations, which occur per genome, have a rate that is an order of magnitude larger than that of TFBS and gene mutations, which occur per TFBS or gene. To prevent either gene evolution or TFBS evolution from dominating the dynamics of our model, we aim for similar overall gene and TFBS mutation rates. Therefore, as a single gene usually has multiple TFBS, and more types of mutations occur on TFBS than on genes, TFBS mutation rates are kept somewhat lower than gene mutation rates. Finally, to prevent excessive genome growth, TFBS and gene deletion rates are chosen to be approximately 1.5 times larger than their duplication rates.

ISSN: 2730-7182