Functional group data preparation#
The concept of functional groups#
The animal communities in animal module are represented by functional groups (FGs) rather than individual species. Functional groups are defined by combinations of ecological traits and life-history strategies that influence how organisms interact with resources, predators, and their environment. Functional traits are measurable characteristics that influence organism growth, survival, and reproduction Violle et al. (2007). By focusing on traits rather than species, ecological patterns can be generalised across communities and ecosystems Funk et al. (2017), Lavorel and Garnier (2002). Therefore, functional groups represent ecologically similar organisms that perform comparable roles in ecosystems. For example, multiple canopy herbivorous insects may be represented by a single FG describing small arboreal herbivorous invertebrates. This approach captures ecological function without modelling every species individually.
Functional group definitions#
The functional group definitions for a simulation need to be stored in a CSV file: each functional group must have a unique name and each row then provides the functional traits for that group. A path to this CSV file must then be provided as part of the animal model configuration as shown below:
[animal]
functional_group_definitions_path = '../data/animal_functional_groups.csv'
The functional group file needs to include the following fields defining its name and values for all of the traits:
Field name |
Description |
Optional |
Examples |
|---|---|---|---|
name |
The name you would like to call your functional group |
No |
carnivorous_bird, herbivorous_bird, or even something more specific like dung_beetle. |
taxa |
The taxa of the functional group |
No |
mammal, bird, invertebrate, amphibian, reptile |
diet |
The diet of the functional group. Users are required to provide one or more diet types below with a lowercase underscore-separated string such as flowers_fruit_fish. |
No |
algae, detritus, flowers, foliage, fruit, seeds, nectar, wood, blood, invertebrates, fish, vertebrates, carcasses, waste, mushrooms, fungi, waste, POM, bacteria |
metabolic_type |
The metabolic types of the animals. Endotherms (e.g. birds and mammals) are warm blooded animals that generate their own heat to maintain a constant body temperature while ectotherms (e.g. reptiles, insects) are cold blooded animals whose body temperature and metabolic rate fluctuate with the environment. |
No |
endothermic, ectothermic |
reproductive_environment |
The environment where reproduction happens. |
No |
terrestrial, aquatic |
reproductive_type |
The reproductive strategy of the functional group. Semelparous describes cohorts that reproduce only once during their lifetime, after which death is inevitable. Iteroparous describes cohorts that reproduce multiple times throughout its lifetime, often able to produce offspring in successive reproductive cycles. Non-reproductive describes cohorts that are not involved, do not relate to, or are incapable of reproduction. |
No |
semelparous, iteroparous, nonreproductive |
development_type |
Is the transition from larval to adult stages direct or indirect? Indirect development cohorts have metamorphosis in their development stage from larvae to adult. Direct development cohorts have no metamorphosis and therefore direct transition from larvae to adult. |
No |
direct, indirect |
offspring_functional_group |
The offpspring type produced by this functional group in reproduction or metamorphosis. For functional groups without metamorphosis, the same functional group is recommended. For functional groups with metamorphosis such as the butterfly, the larval form, caterpillar is recommended. Note that this should be a functional group existing as a row. |
No |
[name of existing functional group] |
excretion_type |
Animals have evolved different strategies for excretion, the removal of waste from the body. Uricotelic cohorts like reptiles, birds and insects excrete uric acid waste while ureotelic cohorts like mammals and adult amphibians on land excrete urea as nitrogenous waste. |
No |
ureotelic, uricoletic |
migration_type |
This attribute determines whether the cohort is migratory. If seasonal, the cohort performs migration behaviour once a year. |
No |
none, seasonal |
vertical_occupancy |
This attributes determines which vertical structure the cohort occupies. The input is a similar parse string we see in diet. |
No |
soil, ground, canopy or a combination of any three structures using lowercase underscore-separated string such as ground_canopy, soil_ground_canopy |
birth_mass |
The mass of the functional group at birth in kilograms. |
No |
0.1 |
adult_mass |
The mass of the functional group at adulthood in kilograms. |
No |
1 |
density_individuals_m2 |
The density of individuals of functional group in meter square. If set as none, densities will be set following madingley or damuth equations |
Yes |
0.5 |
t_opt |
Optimal activity temperature for terrestrial ectotherms in degree celsius. If set as none, the value will be calculated using diurnal temperature range and mean and standard deviation annual temperature. |
Yes |
35 |
t_max_crit |
Upper critical temperature for terrestrial ectotherms in degree celsius. If set as none, the value will be calculated using diurnal temperature range and mean and standard deviation annual temperature. |
Yes |
42 |
t_min_crit |
Lower critical temperature for terrestrial ectotherms in degree celsius. If set as none, the value will be calculated using diurnal temperature range and mean and standard deviation annual temperature. |
Yes |
30 |
To compile this ecological trait information a large number of sources must be drawn from, including species-level ecological literature, trait databases (e.g., Elton Traits), regional field guides, species accounts, and relevant ecological syntheses. Key information typically includes body size metrics (such as adult body mass or birth mass), life-history traits (e.g., reproductive strategy and developmental type), physiological traits (e.g., metabolic and excretion type), population metrics and ecological traits (e.g., diet composition, habitat use, and vertical occupancy). However, trait data for many tropical taxa remain incomplete, and therefore trait estimation and ecological inference are often required.
For our preparation of site-specific simulations such as the Maliau simulation, we used commonly found species as representatives for each functional group to estimate parameters such as adult body mass. In the case where adult body mass is unavailable, particularly for taxa where body mass is rarely reported and body dimensions are more commonly used (e.g., shell height for molluscs or snout–vent length for amphibians and reptiles), body mass may be estimated from body length using published allometric relationships (e.g., Sohlström et al. (2018) for invertebrates). Another example where information is lacking, such as birth mass, which is rarely reported in ecological literature. In such cases, birth mass is estimated using proportional relationships relative to adult mass or taxonomic generalisations (e.g., Hendriks and Mulder (2008)), and then all body mass values are converted to kilograms to match the unit requirements of the model.
Metabolic type currently assigned based on taxonomic classification, with mammals and birds treated as endotherms and reptiles, amphibians, and most invertebrates treated as ectotherms. Diet descriptions from literature sources are translated into trophic categories compatible with the model, while habitat use and vertical occupancy are assigned based on ecological descriptions of species behaviour and typical habitat associations reported in the literature.
Note
Vertical occupancy is tricky to define, as some groups overlap between strata. When groups are assigned to multiple strata they are assumed to spend equal amounts of “active” time in each strata. In reality, some groups will move between strata depending on the time of year or their condition (e.g., canopy frogs may move down to the mid-canopy for breeding but otherwise stay in the upper canopy). This equal allocation of time between strata means that they must be chosen carefully for each functional group.
Population density information is often unavailable for many taxa included in ecosystem models. When empirical estimates are lacking, density may be approximated using macroecological scaling relationships such as body mass–density relationships (e.g., Damuth’s Law) or abundance scaling approaches used in ecosystem models such as Madingley. These provide approximate initialisation values when site-specific data are not available.
Optimal activity temperatures, upper critical temperature and lower critical temperature of functional group can be obtained from literature when available.
Limitations and Assumptions#
The process set out above relies on several simplifying assumptions. Ecological trait information for many tropical species remains incomplete, requiring the estimation of parameters such as birth mass or population density. Scaling relationships introduce additional uncertainty when empirical measurements are unavailable.
Functional group-based modelling also simplifies species diversity by representing groups of organisms with shared traits rather than modelling individual species. While this approach improves computational efficiency and captures major ecosystem processes, the decisions may overlook some ecological variability and species-specific interactions.
Example file#
The dropdown below shows the example version of the animal functional group definitions:
pft_definitions.csv
name,taxa,diet,metabolic_type,reproductive_environment,reproductive_type,development_type,development_status,offspring_functional_group,excretion_type,migration_type,vertical_occupancy,birth_mass,adult_mass,density_individuals_m2,t_opt,t_max_crit,t_min_crit
carnivorous_bird,bird,vertebrates_invertebrates_carcasses,endothermic,terrestrial,iteroparous,direct,adult,carnivorous_bird,uricotelic,none,ground_canopy,0.1,1.0,None,None,None,None
herbivorous_bird,bird,foliage_fruit,endothermic,terrestrial,iteroparous,direct,adult,herbivorous_bird,uricotelic,none,ground_canopy,0.05,0.5,None,None,None,None
carnivorous_mammal,mammal,vertebrates_invertebrates_carcasses,endothermic,terrestrial,iteroparous,direct,adult,carnivorous_mammal,ureotelic,none,ground,4.0,40.0,None,None,None,None
herbivorous_mammal,mammal,foliage_fruit_seeds,endothermic,terrestrial,iteroparous,direct,adult,herbivorous_mammal,ureotelic,none,ground,1.0,10.0,None,None,None,None
carnivorous_insect_iteroparous,invertebrate,invertebrates,ectothermic,terrestrial,iteroparous,direct,adult,carnivorous_insect_iteroparous,uricotelic,none,soil_ground_canopy,0.001,0.01,None,None,None,None
herbivorous_insect_iteroparous,invertebrate,foliage_fruit,ectothermic,terrestrial,iteroparous,direct,adult,herbivorous_insect_iteroparous,uricotelic,none,soil_ground_canopy,0.0005,0.005,None,None,None,None
carnivorous_insect_semelparous,invertebrate,invertebrates,ectothermic,terrestrial,semelparous,direct,adult,carnivorous_insect_semelparous,uricotelic,none,soil_ground_canopy,0.001,0.01,None,None,None,None
herbivorous_insect_semelparous,invertebrate,foliage_fruit,ectothermic,terrestrial,semelparous,direct,adult,herbivorous_insect_semelparous,uricotelic,none,soil_ground_canopy,0.0005,0.005,None,None,None,None
butterfly,invertebrate,foliage_fruit,ectothermic,terrestrial,semelparous,indirect,adult,caterpillar,uricotelic,none,ground_canopy,0.0005,0.005,None,None,None,None
caterpillar,invertebrate,foliage_fruit,ectothermic,terrestrial,nonreproductive,indirect,larval,butterfly,uricotelic,none,canopy,0.0005,0.005,None,None,None,None
frog,amphibian,vertebrates_invertebrates_carcasses,ectothermic,aquatic,iteroparous,direct,adult,frog,ureotelic,none,ground,0.005,0.5,None,None,None,None
swallow,bird,invertebrates,endothermic,terrestrial,iteroparous,direct,adult,swallow,uricotelic,seasonal,canopy,0.005,0.2,None,None,None,None
earthworm,invertebrate,detritus_fungi_pom_bacteria,ectothermic,terrestrial,iteroparous,direct,adult,earthworm,uricotelic,none,soil_ground,0.0005,0.005,None,None,None,None
dung_beetle,invertebrate,waste,ectothermic,terrestrial,iteroparous,direct,adult,dung_beetle,uricotelic,none,soil_ground,0.0003,0.003,None,None,None,None
scavenging_mammal,mammal,carcasses,endothermic,terrestrial,iteroparous,direct,adult,scavenging_mammal,ureotelic,none,ground,2.0,20.0,None,None,None,None
detritivorous_insect,invertebrate,detritus,ectothermic,terrestrial,iteroparous,direct,adult,detritivorous_insect,uricotelic,none,soil_ground,0.0004,0.004,None,None,None,None
fungivorous_mammal,mammal,mushrooms,endothermic,terrestrial,iteroparous,direct,adult,fungivorous_mammal,ureotelic,none,soil_ground,1.0,10.0,None,None,None,None
herbivorous_lizard,reptile,foliage_fruit,ectothermic,terrestrial,iteroparous,direct,adult,herbivorous_lizard,uricotelic,none,ground_canopy,0.01,0.5,None,None,None,None
carnivorous_snake,reptile,vertebrates_invertebrates_carcasses,ectothermic,terrestrial,iteroparous,direct,adult,carnivorous_snake,uricotelic,none,ground,0.02,1.0,None,None,None,None
thermophilic_lizard,reptile,foliage_fruit,ectothermic,terrestrial,iteroparous,direct,adult,thermophilic_lizard,uricotelic,none,ground,0.01,0.3,0.005,35.0,42.0,30.0