Zoology

name: zoology

description: > Expert zoology assistant for academic researchers. Use this skill whenever the user needs: taxonomic classification or species identification, literature review or synthesis of animal biology research, scientific writing (papers, field notes, reports, grant sections), wildlife conservation analysis, ethological or behavioral study design, phylogenetic interpretation, ecological analysis, or any rigorous academic treatment of animal biology. Trigger for any zoology, wildlife, or animal biology question where academic depth, correct nomenclature, and scientific rigor are expected — even if the user doesn’t explicitly say “zoology”. license: MIT compatibility: opencode metadata: audience: researchers category: biology

Zoology — Academic Research Assistant

Covers: Taxonomy & Nomenclature · Literature Review · Scientific Writing · Behavioral Research · Conservation Analysis · Phylogenetics · Field Methods

Taxonomic Classification & Nomenclature

Binomial Nomenclature Rules (ICZN)

• Genus capitalized, species epithet lowercase: Panthera leo
• Always italicize in print; underline in handwriting
• Authority and year on first use in formal writing: Panthera leo (Linnaeus, 1758)
• Subspecies as trinomial: Panthera leo leo (Linnaeus, 1758)
• After first use, abbreviate genus: P. leo
• Common names are not regulated — always provide the scientific name in academic work

Taxonomic Hierarchy

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species
                                                     ↓
                             Intermediate ranks: Suborder, Infraorder,
                             Superfamily, Subfamily, Tribe, Subtribe

Current Authoritative Sources by Taxon

Always verify current accepted names — taxonomy changes frequently with molecular revisions. Note synonymies when relevant.

Handling Taxonomic Uncertainty

• Incertae sedis: position uncertain within a higher group — use the phrase explicitly
• cf.: cf. Ursus arctos — the specimen is comparable to but not confirmed as the species
• aff.: aff. Ursus arctos — the specimen has affinity to but is distinct from the species
• sp. nov.: new species not yet formally described
• Note when a taxon is paraphyletic or polyphyletic in modern molecular treatments

Literature Review

Search Strategy by Resource

Primary databases (peer-reviewed):

• Web of Science — best for citation tracking, impact metrics
• Scopus — broad coverage, good for systematic reviews
• Google Scholar — broadest coverage; include grey literature, theses
• PubMed — essential for physiology, neurobiology, parasitology
• Zoological Record (Clarivate) — taxonomy-focused, comprehensive back to 1864

Specialist resources:

• BioOne — ecology, conservation, field biology journals
• JSTOR — historical literature, essential for pre-1990 taxonomy
• biodiversitylibrary.org — historical natural history literature, free
• IUCN Red List — species accounts, population data, conservation status
• GBIF / iNaturalist — occurrence records, range data

Search Term Construction

("Panthera leo" OR "African lion" OR "lion*")
AND (behav* OR etholog* OR territorial*)
AND (savanna OR grassland OR "sub-Saharan")
NOT captiv*

# Use MeSH terms in PubMed for physiology/parasitology topics
# Use quotation marks for phrases; truncation (*) for word variants
# Filter: Article type = Original Research; exclude reviews for primary evidence

Literature Synthesis Standards

• Distinguish primary literature (original research) from reviews and grey literature
• Note sample sizes and geographic scope — small or regional studies may not generalize
• Flag when findings come from captive animals being applied to wild populations
• Track taxonomic changes: a species cited as X in 1990 may now be Y — check synonymies
• For behavioral claims, note whether data are observational or experimental
• Preferred citation format in zoology: author-date (Harvard) or journal-specific; never use footnote style

Scientific Writing

Paper Structure and Conventions

Abstract: Structured or unstructured depending on journal. Include: study question, methods summary, key quantitative findings, and significance. Never cite references in an abstract.

Introduction: Funnel from broad context → specific gap → study objectives. End with explicit aim/hypothesis statements. Cite the primary literature establishing the gap, not textbooks.

Methods:

• Specify study site with coordinates and habitat description
• Give sample sizes, sex ratios, age classes where relevant
• Provide ethical approval statement (IACUC number or equivalent)
• Include statistical software, version, and package names
• Describe how animals were identified to individual (marks, tags, genetics)

Results: Report statistics fully — test statistic, df, p-value, effect size, CI:

Males were significantly heavier than females
(t₄₂ = 4.31, p < 0.001, d = 1.32, 95% CI [8.2, 23.4 kg]).

Never interpret in Results — save interpretation for Discussion.

Discussion: Lead with your main finding restated plainly. Compare with prior work, explain discrepancies. Address limitations honestly. End with implications and future directions — not a summary of your own results.

Field Notes — Standard Format

Date: 2024-03-15
Time: 06:42 local (UTC+3)
Location: [Site name], [GPS coordinates — WGS84 decimal degrees]
Observer(s): [Initials]
Weather: 18°C, partly cloudy, wind NW ~10 km/h, visibility excellent
Species: Lycaon pictus (African wild dog)
Individual ID: Pack "Ruaha North", alpha female (ear tag #R-07)

Observation:
Alpha female initiated hunt at 06:42. Pack of 8 individuals (4 adults,
4 sub-adults) moved NE at ~8 km/h. Target prey: Thomson's gazelle
(Eudorcas thomsonii), single adult female. Hunt lasted 4 min 22 sec.
Outcome: unsuccessful — prey escaped into dense bush at 06:47.

Behavioral notes:
[Ethogram codes if applicable]

Voucher/media:
Photos: DSC_4421–4438
GPS track: ruaha_20240315_0642.gpx

Conservation Reports

Structure for IUCN-style or agency reports:

1. Species Account: taxonomy, distribution, population size/trend
2. Threats Assessment: use IUCN threat classification scheme (1.1–11.4)
3. Conservation Actions: existing (in-place) vs. needed
4. Data Gaps: explicit statement of what is unknown
5. Recommendations: specific, actionable, prioritized
6. Red List Criteria: state which criterion (A–E) applies and why

Behavioral Research & Ethology

Sampling Methods (after Altmann 1974)

Key rule: state your sampling method explicitly in Methods. Mixing methods without justification is a common reviewer complaint.

Ethogram Construction

• Define behaviors mutually exclusively and exhaustively (MEE)
• Use operational definitions: observable, not inferred (“approaches within 1 m” not “shows interest”)
• Distinguish states (duration matters: resting, foraging) from events (instantaneous: vocalization, attack)
• Establish inter-observer reliability before data collection: Cohen’s κ > 0.80 is standard

Statistical Considerations for Behavioral Data

• Behavioral data are rarely normally distributed — test before assuming
• Repeated observations of the same individual are not independent: use mixed models with individual as random effect
• Circular statistics for temporal/directional data (e.g., activity rhythms, orientation)
• Correct for multiple comparisons (Bonferroni, FDR) when testing multiple behaviors
• Report effect sizes, not just p-values; behavioral ecology increasingly requires this

Phylogenetics & Systematics

Reading a Phylogeny

• Branch lengths = evolutionary distance (in molecular trees) or are arbitrary (in cladograms)
• Node support: bootstrap values ≥ 70 or posterior probability ≥ 0.95 considered supported
• Polytomies (>2 branches from one node) indicate unresolved relationships, not simultaneous divergence
• Outgroup must be specified and justified
• Always note the gene(s) or genomic region used — mitochondrial vs. nuclear trees sometimes conflict

Reporting Molecular Systematics Results

• Specify substitution model (e.g., GTR+Γ) and how it was selected (AIC/BIC in ModelTest)
• Report both maximum likelihood and Bayesian analyses when possible
• Deposit sequences in GenBank; cite accession numbers
• Note if morphological and molecular evidence conflict — this is scientifically significant

Wildlife Conservation Analysis

IUCN Red List Criteria (Summary)

Population Viability Analysis (PVA)

• Software: VORTEX (most common), RAMAS, Insightmaker
• Required inputs: survival rates by age/sex, fecundity, carrying capacity, catastrophe probabilities
• Report: median time to extinction, probability of extinction at 50/100 years, minimum viable population (MVP)
• Sensitivity analysis is mandatory — show which parameters most affect outcomes
• PVA outputs are highly sensitive to input quality; be explicit about data limitations

Threat Classification

Use the IUCN-CMP Unified Classification of Direct Threats (v3.3) for consistency:

• 1. Residential & commercial development
• 1. Agriculture & aquaculture
• 1. Biological resource use (hunting, logging, fishing)
• 1. Invasive & problematic species
• 1. Climate change & severe weather

Always assign a threat scope (% of population affected), severity (% of population declining per decade), and timing (past/ongoing/future).

Common Errors to Avoid

• Using common names as primary identifiers — always anchor to binomial
• Citing a review paper for a specific finding — go to the primary source
• Applying captive animal data to wild population conclusions without caveat
• Reporting p < 0.05 without effect size — significance ≠ biological importance
• Describing a clade as “primitive” or “advanced” — use ancestral/derived (plesiomorphic/apomorphic)
• Anthropomorphizing — describe behavior in operational terms, not mental state terms, unless specifically studying cognition with validated methods
• Ignoring taxonomic synonymies in literature searches — a species may have 3–5 names across decades of literature