NetLogo User Community Models

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## WHAT IS IT?

According to Gauss competitive exclusion principle (Gauss, 1932) two species cannot exist in a same environment. However, thousands of species found coexists in tropical forests. This model discribes combined Hubbell's (2001) neutral model with non-neutral processes (e.g. disturbances, intra-specific competition, negative density dependence, demographic-trade offs (_e.g._ shade tolerance and shade intolerance) etc. see Wright, 2002) to explains the two macro-ecological patterns, species abundance distribution (SAD) and species area relationship (SAR). The model consists of two parts.

### Meta-community
Meta-community (size _J__M) is very large compared to local community (size _J__L). Meta-community is saturated. That is there is no vacant sites (space). Meta-community has demographic fluctuations (stochastic drift). This is one of the main assumptions of neutral theroy. Trees dies and rebirth every time step. It has also mechanisam called speciation. Speciation allows new species to appear. When a tree dies the vacant space is occupied by offsprings of a randomly selected individual or from a new species (speciation is a rare event. Probability of happening that event is very very small). Number of species in the meta community depends on the fundemental bio-diversity number (theta) and the meta-community size (_J__M). Species are generated at the beginning using the Hubbell's (2001) species generating flow chart (pg. 291). Each species has _J__i number of individuals.

### Local community
Local community has demographic fluctuations (death and birth of trees). Local community is saturated. That is there is no vacant sites (space). This is one of the main assumptions of neutral theroy. Original version of the Hubbell's neutral model assumes single death in each time steps. When a tree dies randomly the vacant space is occupied by a offspring of a randomly selected individual. This randomly selected individual is either from a local community or meta-community. If its from meta-community then offspring immigrates from meta-community to local community to occupy the vacant site. If there is no immigration (_m_ = 0) local community undergoes mono-dominance (all the sites occupied by one species). Therefore to maintain the species diversity immigration is necessary. Local community has _S_ number of species. Species are generated at the beginning using the Hubbell's (2001) species generating flow chart (pg. 291). Number of species in the local community depends on the fundemental bio-diversity number (theta2) and the local community size (_J__L). Each species has _J__i number of individuals.

## HOW IT WORKS

Each agent has a properties called 'species, species-trait'. Species have different colors. When an agent dies an offspring of an randomly selected agent is occupied that empty space. Only agent exists in a patch.

**(1) Meta-community:** When an agent dies the vacant space is occupied by offsprings of a randomly selected agent or from a new type of agent (probailities are 1-_v_ and _v_ respectively).

**(2) Local community:** When an agent dies randomly the vacant space is occupied by a offspring of a randomly selected agent. This randomly selected agent is either from a local community or meta-community (probabilites are 1-_m_ and _m_ respectively). If its from meta-community then offspring agent immigrates from meta-community to local community to occupy the vacant site.

Maximum number of conspecific trees that can be allowed to exists around focal tree within a certain radius (called 'crowd-radius') from a focal tree for a minimal stable system is called 'conspeciifc-crowd'. Conspecific-crowd can be used to find the maximum proportion of conspecific trees that can be allowed to exists around a focal tree within crowd-radius from the focal tree. This is called 'conspecific-density' around a focal tree.

Trees die not fully randomly (not a fully stochastic model). Each time step tree in a patch is randomly selected. If number of conspecific trees within crowd-radius around the randomly selected tree exceeds conspecific-crowd then tree dies and patch is vacant. The vacant patch is replaced by a offspring of a randomly selected existing individual.

If the species have no dispersal limitation then offspring of a any individual can come to the vacant site. If species have dispersal limitation then an offspring can come to the vacant site only if the vacant patch is inside radius of the dispersal limitation of its parent.

Local community may undergoes disturbances due to tree falls. Tree fall gaps can be vary (called Disturbance-Size). The frequency of tree falls can be also vary (called Disturbance-rate-per-year). If trees fall and gap created then offsprings of randomly selected individuals come into vacant patches.

However, if shade tolerance and shade intolerance mechanisms exist then individuals from shade intolerance species within dispersal radius come to vacant sites.

## HOW TO USE IT

### Sliders
1. **w1:** Used to change meta-community size. J_M = (w1+1)²
2. **w2:** Used to change the local community size. J_L = (w2+1)²
3. **theta:** Fundamental biodiversity numbers used for meta-community.
4. **theta2:** Fundamental biodiversity numbers used for local-community.
5. **immigration-rate:** Used to control the immigration rate (0-1).
6. **D:** Used to defines the number of death per each time step in the local community. Hubbell's (2001) original model _D_ = 1. Here it can takes any value from 1 to JL.
7. **speciation-initiation-rate:** Defines the speciation rate in the Hubbell's (2001) model. Hubbell used Wright-Fisher equation to define the point mutation speciation. In this model it has additional three additional switches (off-on) that used to set the speciation rates according to either Hubbell (2001) or Moran or Etinne-Alonso-Hubbell.
8. **tau-protracted:** Hubbell (2001) used only point mutation (instant specitation). However, this model has an slider called tau-protracted to shift from Hubbell's (2001) point mutation to Rosindell et al. protracted speciation. When tau-protracted is 0 it is Hubbell's instant point speciation, else it is protracted speciaiton (Rosindell et al. 2010).
9. **Equilibrium-run:** use to decide the number of runs before stop the process.
10. **dispersal-radius:** Use to decide the maximum radius offspring of an individual can move.
11. **Disturbance-rate-per-year:** Number of disturbance cycles per year.
12. **Disturbance-Size:** Number of patches vacant after a disturbance.
13. **conspecific-crowd:** Maximum number of conspecific individuals exists around a focal tree within a radius called 'crowd-radius'.
14. **crowd-radius:** Radius around focal tree.

### Switches
1. **graphic?:** switch is used to switch on-off graphics. Off graphics? speeds the process.
2. **Moran?:** _J_²_M. _v_
3. **Etienne-Alonso-Hubbell?:** theta = _J__M.(_J__M-1). _v_
4. **Hubbell-200-Wright-Fisher?:** theta = 2._J__M. _v_
5. **limited-dispersal?:** If switch on then then species have limited dispersal else species have no dispersal limitation.
6. **light-sensitivity?:** If switch is on only light-sensitive species come to vacant patches.
7. **intra-specific-competition?:** If switch is on intraspecific competition is presents within the community. Else no intraspecific competition.
8. **immigration-number?:** If switch is on then theta2 = _m_._J__L / (1 - _m_)

## THINGS TO NOTICE

### Monitor:
1. **Meta-community size:** Shows the meta-community.
2. **Protracted Speciation events happened in the meta-community:** Shows number of protrated species in the community.
3. **Point-mutations:** Shows number of point mutations.
4. **Total number of deaths in the local community:** Shows total number of deaths in the local community. Equals to number of ticks in netlogo.
5. **Meta-community species richness at time _t_ = 0:** Shows initial species richness in the meta-community.
6. **Meta-community species richness at time _t_ = t:** Shows the current species richness in the meta-community.
7. **Number of species appeared in the meta-community _t_ = 0 to _t_ = t:** Total number of new species appeared in the meta-community.
8. **Effective-meta-community size:** See Etienne and Alonso (2007).
9. **JL:** Current local community size.
10. **JM:** Current meta-community size.
11. **Number of temporal extinct species in the meta-community:** Number of species temporally extinct from local community. Temporal extinction happens only if immigration rate is non-zero. Otherwise it is shows number permenant extinct species.
12. **Shade-tolerant-species:** Number of shade tolerant species presents in the community.
13. **Shade-intolerant-species:** Number of shade intolerant species presents in the community.
14. **Conspecifics density:** Proportion of conspecifics within a crowd-radius.

### Plots:
1. **Total speciation events happen in the meta-community:** Cumulative function of speciations over time.
2. **Meta-community species richness:** Number of meta-community species presents over time.
3. **Local community species richness:** Number of local community species presents over time.
4. **Incipient species in the meta-community:** "During the transition period of a lineage undergoing protracted speciation, the individuals of this lineage are interpreted as an incipient species (Rosindell et al., 2010)"
5. **Generic-tree meta-community:** Similar to meta-community pylogenetic tree that also includes extinct lineages.
6. **Generic-tree local community:** Similar to local-community pylogenetic tree that also includes extinct lineages.
7. **Species Abundance Distribution meta-community:** Meta-community species abundance fluctuations.
8. **Species Abundance Distribution local community:** Local-community species abundance fluctuations.
9. **Number of extinct species from local-community:** Cumulative distribution of temporaly extinct species from local-community.
10. **Relative Species Abundance Meta Community:** Species abundance (_J_) / Meta-community size (_J__M).
11. **Species Abundance Distribution of Meta-Community:** Number of individuals from each species in the meta-community sorted.
12. **Number of extinct species from meta-community:** Cumulative distribution of permenantly extinct species from meta-community.
13. **Relative Species Abundance Local Community:** Species abundance (_J_) / Local-community size (_J__L).
14. **Species Abundance Distribution of Local-Community:** Number of individuals from each species in the local community sorted.

## THINGS TO TRY

* Move sliders w1 and w2 to change the meta and local community size.
* Move sliders theta and theta2 to change the fundamental Biodiversity number for meta and local community.
* Move slider immigration-rate to change the immigration rate (0-1).
* speciation-initiation-rate is determine by one of the swithces (Moran, Hubbell-2001-Wright-Fisher, Etienne-Alonso-Hubbell) usually. Off three swiches to change the speciation-initiation-rate user defines values.
* Off the switches dispersal-limitation, light-sensitivity, intra-specific competition then the model becomes a fully neutral model (_i.e._ Hubbell's 2001 model)

## EXTENDING THE MODEL

Model can in corperate many othe non-random processes (e.g. inter-specific competition, Forest fires, Pathegons and herbivores effects, seed dispersal syndrome, habitat association of species) to increase the complexity of the model.

## NETLOGO FEATURES

## RELATED MODELS

Gause, G. F. (1932). "Experimental studies on the struggle for existence: 1. Mixed population of two species of yeast". _Journal of Experimental Biology_, **9**: 389–402.

Moran, P. A. P. (1958). Random processes in genetics. _Proceedings of the Cambridge Philosophical Society_, **54**: 28 60-71.

Ewens, W. J. (1972). The sampling theory of selectively neutral alleles. _Theoretical Population Biology_, **3**: 87-112.

Connell, J. H. (1978). "Diversity in Tropical Rain Forests and Coral Reefs". _Science_, **199**(4335): 1302–10.

Kimura, M. (1983). _The Neutral Theory of Molecular Evolution_. Cambridge, UK: Cambridge University Press.

Hubbell, S. P. (1979). Tree Dispersion, Abundance, and Diversity in a Tropical Dry Forest: That tropical trees are clumped, not spaced, alters conceptions of the organization and dynamics. _Science_, **203**(4387), 1299–1309.

Hubbell, S. P. (1997). A unified theory of biogeography and relative species abundance and its application to tropical rain forests and coral reefs. _Coral Reefs_ **16**:S9–S21.

Hubbell, S. P. (2001). _The Unified Neutral Theory of Biodiversity and Biogeography_. Princeton, NJ: Princeton University Press.

Wright, J. S. (2002). Plant diversity in tropical forests: A review of mechanisms of species coexistence. _Oecologia_, **130**(1), 1–14.

Etienne, R. S., & Alonso, D. (2007). Neutral Community Theory: How Stochasticity and Dispersal-Limitation Can Explain Species Coexistence. _Journal of Statistical Physics_, **128**(1–2), 485–510.

Comita, L. S., & Hubbell, S. P. (2009). Local neighborhood and species’ shade tolerance influence survival in a diverse seedling bank. _Ecology_, *90*(2), 328–334.

Rosindell, J., Cornell, S. J., Hubbell, S. P., & Etienne, R. S. (2010). Protracted speciation revitalizes the neutral theory of biodiversity. _Ecology Letters_, **13**(6), 716-727.

Bagchi, R., Henrys, P. A., Brown, P. E., Burslem, D. F. R. P., Diggle, P. J., Gunatilleke, C. V. S., Gunatilleke, I. A. U. N., Kassim, A. R., Law, R., Noor, S., & Valencia, R. L. (2011). Spatial patterns reveal negative density dependence and habitat associations in tropical trees. _Ecology_, **92**(9), 1723–1729.

## CREDITS AND REFERENCES

For the model itself:

* Punchi-Manage, R. (2023b). NetLogo Unified Neutral Non-Neutral Model. http://netlogo/models/Unified-Neutral-Non-Neutral-Model.

Please cite the NetLogo software as:

* Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.