mims-harvard/tooluniverse-ecology-biodiversity

Ecology & Biodiversity Research

Reasoning Strategy

1. Species & Taxonomy Questions

When a question involves identifying or comparing species:

1. LOOK UP DON'T GUESS — Use GBIF_search_species to get taxonomy, WoRMS_search_species for marine organisms
2. If the question asks about invasive species impacts, consider: ecological niche overlap, reproductive rate, predator release, and ecosystem engineering effects
3. Use PubMed_search_articles or EuropePMC_search_articles to find studies on specific ecological impacts

2. Invasive Species Impact Assessment

Reasoning framework — when comparing invasive species impacts:

1. Identify the ecosystem: What habitat/biome is affected?
2. Assess impact mechanisms: Competition? Predation? Disease vector? Habitat modification? Hybridization?
3. Scale of impact: Local (single site) vs regional vs continental?
4. Trophic position: Invasives at higher trophic levels (predators) often cause more damage than lower (herbivores)
5. Ecosystem engineering: Species that modify habitats (beavers, earthworms, honeybees displacing native pollinators) cause outsized impacts
6. Look up specifics — don't rely on general knowledge. Search for "[species name] invasive impact [region]" in literature

3. Pollinator Ecology

Reasoning framework for pollination questions:

1. Foraging behavior: Distinguish investigation (approach/assessment) from actual feeding (proboscis insertion)
2. Interaction types: Mutualistic (pollination reward), parasitic (nectar robbing), commensal
3. Observation methods: Camera traps have resolution/FOV limitations — consider what's identifiable at given resolution
4. Statistical considerations: Observer agreement (inter-rater reliability), sampling effort, temporal patterns
5. Ethogram interpretation: Each behavior category has specific start/end criteria — follow them precisely

4. Population Dynamics

Reasoning framework for population ecology questions:

1. Growth models: Exponential (unlimited), logistic (K-limited), Allee effects (low-density problems)
2. Extinction analysis: Distinguish deterministic extinction (r < 0) from stochastic extinction (small population fluctuations)
3. Survival analysis: Time-to-event analysis needs appropriate statistical tests (log-rank, Cox regression, Kaplan-Meier)
4. Microbial ecology: For microbial stressor responses, use survival curve analysis with time-kill kinetics. To compare extinction points between populations, you need time-to-extinction data analyzed with survival statistics (not just endpoint comparisons)

5. Community Ecology & Food Webs

1. Trophic cascades: Removing top predators → mesopredator release → prey decline
2. Keystone species: Disproportionate impact relative to abundance
3. Island biogeography: Species-area relationship, distance-colonization tradeoff
4. Competitive exclusion: Two species cannot stably coexist on single limiting resource (Gause's principle)

6. Evolutionary Ecology

1. Aposematism: Warning coloration signals toxicity/unpalatability
2. Mimicry: Batesian (harmless mimics dangerous) vs Mullerian (dangerous mimics dangerous)
3. Life history tradeoffs: r-selected (many offspring, low investment) vs K-selected (few offspring, high investment)
4. Birth-death models: For phylogenetic questions, identifiability issues arise with time-varying rates. Strategies to resolve: constrain rate variation, add fossil data, use molecular data calibration, or restrict to specific functional forms

Available Tools

| Tool | Use For | |------|---------| | IUCN_get_conservation_status | Red List conservation status (CR/EN/VU/NT/LC) by scientific name — the authoritative extinction-risk source (needs a free IUCN_API_KEY) | | GBIF_search_species | Species taxonomy, occurrence data, distribution | | GBIF_search_occurrences | Where has a species been observed? | | GBIF_get_taxon_parents | Walk UP the GBIF Backbone tree — ranked ancestor lineage (kingdom→genus) for a taxonKey | | GBIF_get_taxon_children | Walk DOWN the tree — direct child taxa (e.g. species in a genus) for a taxonKey | | GBIF_get_taxon_synonyms | Alternative / historical scientific names for an accepted taxonKey | | GBIF_get_vernacular_names | Common names (with language code) for a taxonKey; optional language filter | | GBIF_parse_name | Parse messy/authored name strings into canonical name + genus/epithet/author/year | | iDigBio_search_records | Search 130M+ digitized museum/herbarium specimen records (Darwin Core) by genus/scientificname/locality — use to complement GBIF with physical-specimen provenance | | iDigBio_get_record | Full Darwin Core detail for one specimen by uuid (from iDigBio_search_records) | | WoRMS_search_species | Marine species taxonomy | | ensembl_get_taxonomy | Taxonomic classification | | NCBIDatasets_get_taxonomy | NCBI taxonomy lookup | | PubMed_search_articles | Literature on ecology topics | | EuropePMC_search_articles | European literature including ecology |

Navigating the GBIF taxonomic tree

Resolve a name to a GBIF usageKey once, then navigate the Backbone tree:

key = tu.run_tool("GBIF_match_name", {"name": "Panthera leo"})["data"]["usageKey"]  # 5219404
tu.run_tool("GBIF_get_taxon_parents", {"taxon_key": key})        # Animalia→...→Felidae→Panthera
tu.run_tool("GBIF_get_taxon_synonyms", {"taxon_key": key})       # Felis leo Linnaeus, 1758, ...
tu.run_tool("GBIF_get_vernacular_names", {"taxon_key": key, "language": "eng"})  # Lion, African Lion
# Walk down from a genus key (Panthera = 2435194) to its species:
tu.run_tool("GBIF_get_taxon_children", {"taxon_key": 2435194, "limit": 8})
# Normalize an authored name string without a key:
tu.run_tool("GBIF_parse_name", {"name": "Quercus robur L."})     # canonicalName 'Quercus robur'

All five tools hit the public GBIF API with no key. Get the starting taxon_key from GBIF_match_name or GBIF_search_species.

LOOK UP DON'T GUESS

Ecology questions often have counter-intuitive answers. For example:

• Honeybees (Apis mellifera) are invasive in the Americas and displace native pollinators — this surprises people who think of bees as "good"
• The most damaging invasive species are often not the most obvious ones
• Microbial extinction points require survival analysis, not simple t-tests

Always search the literature before answering ecology questions. Use PubMed_search_articles with specific terms like "[species] invasive impact [region]" or "[organism] [ecological process]".

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.