Biodynamica Beta Version
Parameters of the Advanced Version
INTERNAL Variables
Unless the variable is declared as fixed, the value will range between 0 and the value entered with the slider
MISCELLANEOUS:
Max Movement: Maximum number of pixels the agent may move each time step
Life span (gene 2) Indicates the maximum possible life expectancy (in number of time steps) of the individual.
Free (gene 20): Neutral unless target of pesticide is 8, or gene 18 has a value of 2 or 3:
If Target of pesticide = 8 then value of this gene will indicate who will pay the cost for parental investment. The value of this gene + 5 will give the sex targeted following the rules defined in "Target of pesticide", and genes 16-17.
If g18 is set or allowed to have values of 2 or 3, then the value of gene 20 will indicate the gene targeted for sexual selection.
If Target of pesticide = 10 then simulation of Batesian mimicry is activated using genes 11 = 31, genes 12 = 32, and genes 20= 33.
Neutral gene (gene 1): Has no effect on the fitness of the organism
Mutation control (9): Induces mutation rates at probabilities according to formula: p = 0.2 ^ (iv9/2 +1); where iv9 is the randomly assigned value with a maximum possible value of MV. Max and Min Values of 0 give the best results.
INDIVIDUAL FITNESS
Clutch size (gene 3): Indicates the maximum possible number of offspring at each reproductive act. Actual phenotypes will be constraint by life history parameters.
Reproductive age for females (4): Age at which reproduction starts.
Reproductive age for males (15): Defines reproductive maturity for males.
Parental investment (16) fixed: Degree of investment determined by gene 17 and cost to parent will be determined by the parameter "Cost of parental investment". If value of PI =
0: No parental investment/ no cost to fitness of parent
1: Communal care of offspring: Parent will invest equally in all newborns at a cost to its own fitness. Fitness of offspring = mean(g17)/10
2: Open parents: Parent will invest in their offspring and in others at a cost to its own fitness. Fitness of offspring = (mean(g17) + value of g17 of parent) / 20
3: Closed but opportunistic parents: Parent invest in own offspring, but without investing in others, at a cost to its own fitness. Fitness of offspring as in 2, but the parent's value of gene 17 do not contribute to the mean.
4: Closed and exclusive parents: Parent invest in own offspring without investing in others, at a cost to its own fitness. Similar to 3 but fitness of offspring = value of g17 of parent/10
Sex realizing the investment is defined by “Target of pesticide”
(the meaning of the values differ when Batesian mimicry is simulated)
Degree of parental investment (17): Gives the amount of fitness increase/reduction it will provide to its offspring and its cost to the mother, father or both. Benefit = v17/10, cost (v17/10)*cost of parental investment. (unless Batesian mimicry is simulated)
Resistance 1 (10): Indicate a continuous range of susceptible alleles. Resistance is given in a continuous range so that allele 0 is the most resistant (i.e. is immune) and allele 10 is the least resistant to biocide 1
Resistance 2 (11): Indicate the distribution of resistant alleles. Only allele 0 is resistant and all other alleles are susceptible to biocide 2. The larger the value of MV, the lower the occurrence of resistant organism possessing allele 0 (except when Batesian mimicry is simulated)
Resistance 3 (12): Idem gene 11 but at a different loci and susceptible to biocide 3 (except when Batesian mimicry is simulated)
SEX LIFE
Sex ratio at birth or SRB (5): Values 1 to 10 produces a variable random female/male ratio, according to sex determination parameter (gene 14) chosen. Value = 0 produces 1/1 ratio (See below)
Sex (6): Values = 0 produce asexual populations. Values of 2 produce males and females.
Allele = 1 is female, 2 is male.
Sexual Strategy (7) simulation produces organisms with values that range between min and max value:
0: Asexuals
1: Monosexuals
2: Bisexuals
3: Trisexuals
4: Sexual-Asexual (as in haplodiploidy): females are produced sexually and males asexually. Produces haplo-polyploid populations (for example if polyploidy is 3 then females are triploid and males haploid)
5: Sexual hermaphrodites (hermaphrodites mate only with other hermaphrodites)
6: Sexual hermaphrodites (Hermaphrodites mates with any female)
7: Bisexual with spermatozoa selection with crossover during mitosis
8: Bisexual with spermatozoa selection without crossover during mitosis
9: Produces mixes of mono-bi- and tri-sexuals, and haplo-polyploids.
10: Produces mixes of mono and bi-sexuals.
Ploidy (8): Value = 3 produces mixes of haplo-diplo and triploids. Minimum is 1.
Max and Min Values of 1, 2 and 3 produce pure populations of haploids, diploids and triploids respectively. Variable ploidy produces unreliable values with hyperBD.
Sex appeal (13) of males: Values of gene 13 is used as a sexual selection criteria depending on the type of sexual selection defined.
Sex determination (14) fixed:
0 = Sex is determined randomly in a 1/1 ratio. Gene 5 is neutral
1 = Sex is determined randomly but biased according to allele in gene 5. If rnd * 10 > gene 5, then female, else male. Values of 1 produce 10 % males, of 9, 90 % males, etc.
2 = Sex is determined by gene 6 (incompatible with haplo-diploids), following random recombination of alleles. Gene 5 is neutral
3 = Sex is determined by meiosis of females sex gene (g6). Gene 5 is neutral
4 = Sex is determined by meiosis of male sex gamete (g6). Gene 5 is neutral
5 = Sex is determined according to environment given by Biocide 1 and Gene 5
If phen(i, 5)* 10 * pe1 * Rnd < Rnd Then female else male
6 = Sex is determined according to environment given by Biocide 1 and Gene 5
If phen(i, 5) * 10 * pe1 * Rnd > Rnd Then female else male
If gene 14 (SD) > 0 then make g5 (SRB) > 0
Mate selection criteria (18) fixed: Value of individual indicates what gene it will use to select its mate. All females above reproductive age (RA) will mate with males of same species, which are adult, and above the reproductive age given by genes 4 and 15. The number of mates searched will depend on the value of gene 19. Values code for :
0 (or > 13): Random selection of mates. Female mates with the first male encountered if it is an adult of its species (see gene 15)
1: Sexual Selection: prefers males with high sex appeal, i.e. high values of gene 13
2: Handicap : prefers males with high values of the gene indicated by Nr in g20
3: 1 gene : prefers males with high fitness (Str)
4: 1 gene : prefers males with low values of the gene indicated by Nr in g20
5: 2 genes : prefers phenotypes 0 of R2 or R3
6: 3 genes : female prefers mates with resistant phenotype of R1, R2 and R3 (phenotype 0)
7: prefers young males
8: prefers old males
9: Assortative mating, prefers males similar to her in genetic composition, except Neutral gene (g1) and sex (g6) (CMS included):
10: Dissortative mating, prefers males different to her in genetic composition, else as 9 (CMS not included)
11 prefers males similar to her in genetic composition, else as 9 (CMS not included)
12: prefers males with the same CMS
13: prefers males with the same value of gene indicated by gene 20
14: Females prefer males with sex appeal (1), 3 good genes (6) and mate assortatively (9)
(unless Batesian mimicry is simulated)
Mating efficiency (19): Number of males (or females in hermaphrodites), screened for mating according to criteria defined by gene 18. MV = 0 or = 1 will screen just 1 individual.
Sperm number (21): Determines the number of spermatozoa produced by the male
Sperm genes (22): Determines the number of resistance genes screened for allele 0 in the spermatozoa (1 to 3) and 4 screens lowest age for reproduction of female and 5 the lowest for males. The best spermatozoa is used for fecundation using the bisexual reproductive strategy
EXTERNAL Variables:
MISCELLANEOUS
Number of agents or organisms: Indicates the number of virtual organisms used to randomly create the population
Max Tsteps: Gives the number of time steps or iterations the simulation will run.
Target:
Indicate which sex is susceptible to illness or pesticide 2 and 3:
0 = pesticides inactivated
1 = only females are targeted
2 = only males are targeted
3 = both sexes are targeted
4 = only young (age < 2) from both sexes are targeted
5-9= pesticide 2 (R2) targets females and pesticide 3 (R3) targets males
6 = both females and males invest in offspring and pay the cost
7 (or 0-5, 9-10) = only females invest in offspring and pay the cost
8 = only males invest in offspring and pay the cost
9= strategies 6 to 8 are defined by the value of gene 20 + 6, i.e. allele 0 of gene 20 will code for 0+6 = target 6, allele 1 for target 7 and allele 2 for target 8.
Biocide 1 efficiency:
0 = no effect, 1 = 100% probability for non resistant organisms to die varies randomly each time step with maximum defined by the value given.
Biocide 2 efficiency:
0 = no effect, 1 = 100% probability for non resistant organisms to die. Affected by Environmental Change
Biocide 3 efficiency:
0 = no effect, 1 = 100% probability for non resistant organisms to die. Affected by Environmental Change
Special population dynamics: not implemented (Batesian mimicry and others)
Environmental change: Indicates the pattern of change of external parameters:
0 = No change, no occurrence for biocides (constant environment)
1 - 10 = Indicate the frequency (in time steps) biocides 2 and 3 will occur at efficiencies given below.
11 = random changes in ops (between 100-1000) each 5 tsteps
12 = At tstep = 10 ops = ops/2
13 = At tstep > 11 ops = 200; pe2 <> 0; tstep>15 pe3 <>0
14 = At tstep= 5 pe2<>0 else pe2 = 0, tstep<10 pe3 <> pe3 else pe3 = 0
15 = pe2<>0, each 5 tsteps pe3<>0
16 = alternatively pe2 or pe3 = 0
17= pe2 and pe3 have changing random values after tstep 3 (maximum 0.9)
18= pe2 and pe3 have changing random values after tstep 2 with maxima as given by external parameters
19= As 18 plus Deleterious effect = 0 until t-step 5, then = 10. Ops = 200 after t-step 20
pe1 is not affected by any of those choices
PARENTAL INVESTMENT
Cost/Benefit of parental investment:
Gives the ratio between the cost to the parent (reduced fitness) to invest in the offspring and the benefit to its offspring in increased fitness, according to gene 16 and 17 coding for type and degree of investment.
0 indicates no cost
1 indicates that cost = 100%
Cost may be assigned any intermediate values
If "Target of pesticide" <= 5 then investment and cost will be paid only by females
If "Target of pesticides" = 6 then investment and cost will be paid by both sexes
If "Target of pesticide" = 7 then investment and cost will be paid only by males
Social Synergy:
Gives the increased relative benefit of parental investment when investment is social, i.e. for all offspring equal (for parents having gene 16 = 1) or half that amount for parents having gene 16 = 2, benefiting all offspring from parents with alleles 1 to 3 in gene 16. Values of 1 give equal benefits for all parental investment strategies. Values < 1 make social behavior to be detrimental.
Life history for Clutch Size: For ages > than Reproductive age of female, the Clutch Size will be (only parameters of the mother are used):
0: = value given by gene 3 (vg3)
1: = vg3 * age / 2, Max = MV(3)
2: truncated normal (as 3 but = 0 if age > oar x 2 or >oar/2)
3: normal distribution with maximum = vg3 at age = oar
4: normal distribution with maximum = ocs at age = oar
Fitness function of Clutch Size: Indicates the probability of reduction in fitness (only parameters of the mother are used ), i.e. value will be multiplied by the fitness of offspring at birth:
0: = 1 (no reduction)
1: = 1 if clutch size (cs) into it was born to is < ocs;
= 0 (offspring dies) if cs > ocs
2: = 1/ cs
3: = 1/ normal distribution of cs
4: = 1 if cs < ocs;
= (ocs/cs)^3 if cs > ocs
5: = 1 if cs * age < ocs * oar ; else = ocs * oar / (cs * age)
6: Parental investment: = 1.5 if cs < ocs; = (ocs/cs)^2 if cs > ocs
7: Maximum as defined in 3, but following a normal distribution
maximized at age = oar
Optimal clutch size: Clutch size conferring maximal fitness to offspring according to Fitness function
SEX-LIFE
Living Cost Female or Female reduction in next clutch size after the reproductive act: implies a cost in the reproduction of females so that if = 1: = 0 % reduction; 0:= 100 % reduction; etc
Living Cost Male or Male reduction in next clutch size after each reproductive act: implies a cost in the reproduction of males so that if = 1: = 0 % reduction; 0:= 100 % reduction; etc
Reproductive Age (Optimal): Age at which maximal number of offspring is produced according to Life history value
Female reduction in life span after each reproductive act (0 - 1) real, FLS:
implies a cost in the reproduction of females so that if = 1: = 0 % reduction; 0:= 100 % reduction; 0.5:= 50 %, etc.
Male reduction in life span after each reproductive act (0 - 1) real, MLS:
implies a cost in the reproduction of males so that if = 1: = 0 % reduction; 0:= 100 % reduction; etc
Reproductive constraints:
0 or 2: a- Polyploids transmit their genes to offspring according to rules of meiosis
1 or 3: b- Polyploids transmit their alleles completely random, i.e. several copies of the same allele may be transmitted
0 or 1: c- Only females reproduce and have 0 offspring if they mate with a sterile males
2 or 3: d- Females reproduce independently of males clutch size
(Value: 0 = a + c 1 = b + c 2 = a + d 3 = b + d)
4 : As 2 but asexuals and monosexuals produce only females and males are bisexuals (alle 1 of gene 7 = 2)
5: As 0 but the alleles for sexual reproductive system (gene 7) are fixed in the offspring according to the reproductive system they were created.
That is, sexual females produce sexual offspring.
OTHERS:
RSt loads original values for the simulation
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