Taxonomy

Life began 4.2 Ga with the prokaryotes, which do not have a nucleus. Prokaryotes include bacteria and archaea.

Nutritional groups

• Energy source: phototrophs and chemotrophs. Both gain energy from oxidation of electron donors.
• Electron donor source: organotrophs and lithotrophs.
• Carbon source: autotrophs use carbon dioxide, while heterotrophs need organic compounds.

Growth medium

• An agar plate contains growth medium solidified with agar
• Lysogeny broth is a rich medium of milk, B vitamins, trace elements, and minerals
• Minimal medium contains a glucose or succinate carbon source, salts for protein and nucleic acid synthesis, and water. It can be supplemented with an amino acid or sugar for specific auxotrophs.
• Selective media requires a gene that confers antibiotic resistance or ability to synthesize a metabolite.
  • MacConkey agar selects for Gram-negative bacteria and has a pH indicator that turns red for lactose fermenters.
  • Eosin methylene blue selects for Gram-negative bacteria and turns green or black for lactose fermenters.
  • Mannitol salt agar selects for gram-positive bacteria.
• Cell cultures usually require serum hormones or growth factors.
• Chromogenic agar can distinguish different fungi.

Eukaryotes formed 2.1 Ga from the endosymbiosis of an aerobic bacterium inside an anaerobic Asgard archaea. They have a cell nucleus and usually a mitochondrion with double membrane and aerobic respiration. They consist mainly of the SAR supergroup, amoebozoa, plant, fungus, and animal.

• The protist kingdom is polyphyletic and deprecated. It included all eukaryotes except for plants, animals, and fungi. Protozoa (“first animals”) is also deprecated. It included unicellar eukaryotes.
• Amoeboids or amoebas are a polyphyletic grouping of single-celled organisms that can move and feed using finger-like projections called pseudopods. Amoeba also refers to a monophyletic genus. Slime molds are a polyphyletic grouping of amobeoids that form spore-producing fruiting bodies.
• Marine niches include plankton (“wanderer”) that cannot swim against a current, nekton which can swim against a current, neuston that float on the water’s surface, and benthos which live on the sea floor. Phytoplankton are autotrophic plankton which can photosynthesize and live in photic zones, while zooplankton are heterotrophic. Many ocean organisms undergo diel vertical migration, sinking to 1,000’ the day and rising near the surface at night, causing the deep scattering layer.

Eukaryote phylogeny

• Ancyromonadida are most basal and have two flagella.
• Bikonts (“two flagella”) are basal. The genes for thymidylate synthase (TS) and dihydrofolate reductase (DHFR) are fused to encode a single protein with two functions.
  • Metamonada: anaerobic
    • Giardia causes giardiasis in the small intestine, with diarrhea.
    • Trichomonas vaginalis is an STD.
  • Discoba or JEH
    • Euglenozoa have flagella.
      • Euglena are green ovoids with chloroplasts.
      • Trypanosoma causes trypanosomiasis and Chagas disease.
      • Leishmania causes leishmaniasis.
    • Percolozoa alternate between biflagellate and trophozoite or amoeboid forms.
      • Naegleria fowleri is a brain-eating amoeba, causing primary amoebic meningoencephalitis. Freshwater and thermophilic.
  • Diaphoretickes.
    • Haptista > haptophyte algae
      • Prymnesium parvum produces prymnesin-2, a hemolytic toxin
    • TSAR supergroup: Telonemia and the SAR supergroup.
    • Archaeplastida including plants
• CRuMs: Collodictyonidae, Rigifilida, and the basal Mantamonadida.
• Amorphea
  • Amoebozoa contains many clades including Amoeba genus, Chaos which is multinucleated, and Pelomyxa which can grow up to 5 mm.
    • Entamoeba causes amoebiasis, killing 50,000 people per year.
    • Acanthamoeba causes encephalitis and corneal infection or keratitis from contact lens.
  • Obazoa
    • Basal Breviatea
    • Apusomonadida
    • Opisthokonta
      • Fungi
      • Animals

SAR supergroup

• The SAR ancestor captured a unicellular photosynthetic red alga, so many members have chloroplasts surrounded by four membranes and tubular mitochondrial cristae. SAR are common marine and soil species.
• Rhizaria can produce complex pseudopodial networks in 1 meter-long cyclindrical colonies and intricate mineral skeletal structures of opal (SiO2), celestite (SrSO4) or calcite (CaCO3).
  • Cercozoa
  • Retaria
    • Foraminifera (“hole bearers”) or forams have a streaming granular ectoplasm for catching food and often an external shell.
    • Radiolaria
      • Acantharea are microplankton with strontium sulfate skeletons.
• Halvaria
  • A stramenopile or heterokont has tripartite hairs consisting of a flexible basal membrane insert, a long stiff tube, and a tip section with delicate hairs.
    • Gyrista phylum > Ochrophyta
      • Chrysista
        • Brown algae (class Phaeophyceae): contains many seaweeds with a holdfast, stipe, and lamina. Produces alginate used as a thickening agent and gelling agent.
          • Kelp (order Laminariales): bull kelp (Nereocystis)
          • Fucales: Sargassum, Ascophyllum, Fucus, southern bull kelp (Durvillaea)
        • Golden algae (Chrysophyceae) has an active flagellum.
      • Diatoms (Bacillariophyceae) have a silica cell wall called a frustule. Mostly pennate diatoms with bilateral symmetry.
        • Pseudo-nitzschia accounts for 4% of all pennate diatoms. Some species produce domoic acid neurotoxin, which excite the ionotropic glutamate AMPA and kainate receptors and causes amnesic shellfish poisoning.
        • Coscinodiscophyceae: centric diatoms have radial symmetry.
    • Bigyra phylum > Blastocystis infection causes diarrhea.
    • potato blight (Phytophthora infestans)
  • Alveolata have cortical alveoli.
    • Ciliate (Ciliophora phylum)
      • Paramecium
      • Tetrahymena was used to discover telomerase by Elizabeth Blackburn and Carol Greider.
      • Ichthyophthirius multifiliis can infect most freshwater fish, causing white spots and death.
    • Dinoflagellata are phytoplankton. Many produce defensive phycotoxins.
      • Alexandrium produces saxitoxin, a voltage-gated sodium channel blocker that causes paralytic shellfish poisoning.
      • Karenia brevis causes red tides in the Gulf of Mexico and produces brevetoxin, neurotoxins that bind to voltage-gated sodium channels.
      • Dinophysis produces okadaic acid, a serine/threonine phosphatase inhibitor which causes Diarrhetic Shellfish Poisoning (DSP). It potentially also produces halichondrin, a microtubule inhibitor which led to the cancer drug eribulin.
      • Azadinium produces azaspiracid toxin, which inhibits hERG voltage-gated potassium channels.
      • Gambierdiscus produces several toxins. The lethal nerve agent maitotoxin activates calcium channels. Ciguatoxin and gambierol lowers the threshold of voltage-gated sodium channels and causes ciguatera.
      • Gonyaulax and Lingulodinium produce yessotoxin, which activates ion channels.
      • Zooxanthellae symbiotic with coral and other sea creatures e.g. Symbiodinium
      • Durinskia contains an intact diatom endosymbiont without its cell wall.
    • Apicomplexa have apicoplasts: toxoplasmosis (Toxoplasma), malaria (Plasmodium), tick-borne Babesia.

The taxonomic ranks are domain, kingdom, phylum, class, order, family, genus, species.

Viruses are not alive because they cannot reproduce independently. They reproduce in a lysogenic cycle which incorporates their DNA into the host genome, and a lytic cycle which destroys the cell to release the virus. There are six viral realms:

• Duplodnaviria contains all dsDNA viruses that encode the HK97-fold major capsid protein.
  • Herpes simplex virus HSV. Majority of people have HSV-1.
  • Varicella zoster virus causes chickenpox (varicella) in children and shingles (herpes zoster) in adults.
  • Crick used Bacteriophage T4 to study DNA transcription.
• Monodnaviria contains all ssDNA DNA viruses that encode a HUH superfamily endonuclease.
  • Parvovirus family causes disease in cats and dogs.
• Riboviria contain RNA viruses, which are a major source of horizontal gene transfer.
  • Orthornavirae encode an RNA-dependent RNA polymerase (RdRp).
    • Negarnaviricota phylum use (-)DNA.
      • influenza virus
      • measles virus
      • mumps virus
      • rabies virus
      • ebolavirus
      • Phlebovirus causes Pappataci fever around the Mediterranean to northern India.
    • Pisuviricota are mostly (+)ssRNA.
      • rhinovirus (Enterovirus) is the most common virus in humans.
      • coronavirus
    • Kitrinoviricota are (+)ssRNA.
      • Rubella virus
      • Hepatitis C virus (HCV)
      • Orthoflavivirus
        • yellow fever virus results in jaundice and is spread by mosquitos.
        • Arboviruses are tick-borne: West Nile virus, tick-borne encephalitis virus, Zika virus.
          • Dengue virus can cause hemorrhagic fever. It has antibody-dependent enhancement. Non-neutralizing antibodies bind the virus, which helps the virus enter and infect white blood cells.
      • Venezuelan equine encephalitis virus (VEE) is spread by mosquitos.
      • tobacco mosaic virus is the first discovered virus.
  • Retrovirus family is the sole member of the kingdom Pararnavirae. It encodes a reverse transcriptase.
    • ssRNA-RT (Baltimore group VI).
      • HIV (Lentivirus) derives from simian immunodeficiency virus.
    • dsDNA-RT (Baltimore Group VII) includes hepatitis B virus (HBV).
• Varidnaviria contains all dsDNA viruses that encode a vertical jelly roll major capsid protein.
  • Bamfordvirae kingdom
    • Preplasmiviricota phylum > Tectiliviricetes class
      • Adenovirus family > Mastadenovirus is a nucleocapsid causing mild colds.
    • Nucleocytoviricota phylum > Pokkesviricetes class > Chitovirales order
      • poxvirus (Poxviridae family) > Chordopoxvirinae subfamily
        • smallpox or variola (Orthopoxvirus) causes dimpled bumps all over the skin. vaccinia is a strain used for the smallpox vaccine.
        • cowpox virus causes painful skin blisters and resistance to smallpox.
        • monkeypox virus causes mpox disease. Transmissible from rodents and monkeys.
        • Molluscipoxvirus causes water warts or Molluscum contagiosum causing pearly dimpled bumps on the skin.
• Adnaviria contains archaeal filamentous viruses with A-form double-stranded (ds) DNA genomes encoding a unique alpha-helical major capsid protein.
• Ribozyviria have circular (-)ssRNA genomes.
• Naldaviricetes are dsDNA viruses that infect arthropods.
  • Baculovirus can transfect DNA into mammalian cells (BacMam). Infected host cells eventually lyse.

Transmissible spongiform encephalopathy or prion disease

• PRNP gene encodes the major prion protein (PrP).
• Creutzfeldt–Jakob disease (CJD)
  • mad cow disease
  • variant CJD can be transmitted by infected beef
  • kuru was caused by cannibalism and no longer exists.
• Fatal familial insomnia

Bacteria kingdom

• Gracilicutes are gram-negative
  • PVC superphylum
  • Pseudomonadota
    • alphaproteobacteria
    • betaproteobacteria
    • gammaproteobacteria
• Terrabacteria are gram-positive
  • Actinomycetota
  • Bacillota or Firmicutes
  • Cyanobacteria
  • Archaea and Eukaryotes

Gracilicutes or Hydrobacteria or Negibacteria are diderms (gram-negative).

• Aquificota includes Aquifex
• Thermodesulfobacteriota
• Myxococcota
• Campylobacterota
  • Sulfurimonas live in hydrothermal vents and can reduce nitrate and oxidize sulfur and hydrogen.
  • Helicobacter pylori causes gastric ulcers.
• Sphingobacteria or FCB superphylum
  • Bacteroidota phylum: Bacteroides is 30% of human gut bacteria. Prevotella also a common human gut bacteria.
  • green sulfur bacteria (Chlorobiota phylum)
• Deinococcota > Deinococci class are extremophile diderms that stain gram-positive due to a thick cell wall.
  • Thermus is the source of Taq polymerase used for polymerase chain reaction (PCR).
  • Deinococcus can survive 5,000 Gy radiation.
• Fusobacteria
• PVC superphylum
  • Planctomycetota are important in the carbon and nitrogen cycles. Many are capable of anaerobic ammonium oxidation (anammox).
  • Chlamydiota are very small pathogens that infect eukaryotic cells.
    • Chlamydia trachomatis is the most common sexually transmitted bacterium.
    • Chlamydia psittaci causes psittacosis, a bird-transmitted atypical pneumonia.
• Acidobacteriota e.g. Acidobacterium are acidophiles
• Nitrospirota phylum > Nitrospiria have complete ammonia oxidation (commamox).
• Phylum Pseudomonadota are the predominant phylum. They are gram-negative.
  • Alphaproteobacteria class is basal.
    • Acetobacteraceae family > Acetic acid bacteria ferments ethanol to acetic acid
      • Acetobacter can oxidize lactate and acetate into carbon dioxide and water.
    • Anaplasma causes the tick-borne anaplasmosis.
    • Rickettsia cause typhus and spotted fever rickettsiosis, which includes Pacific Coast tick fever and Rocky Mountain spotted fever.
    • Nitrobacter oxidizes nitrite into nitrate.
  • Betaproteobacteria class.
    • Bordetella pertussis or whooping cough
    • Neisseria gonorrhoeae causes gonorrhea
    • N. meningitidis causes meningitis
  • Gammaproteobacteria class.
    • Pseudomonadales order
      • Pseudomonas is highly drug resistant and glows yellow-green under Wood’s lamp. Source of mupirocin antibiotic.
        • P. syringae is a common plant pathogen which produces a protein that is a nucleating center for frost damage.
      • Moraxella catarrhalis causes pneumonia.
      • Acinetobacter baumannii is a common highly resistant nosocomial infection.
    • Azotobacter is a nitrogen-fixing soil microbe. It is also used to produce alginic acid.
    • Aeromonas causes gastroenteritis and necrotizing fasciitis.
    • Haemophilus influenzae was the first organism to have its whole genome sequenced, in 1995. Causes pneumonia.
    • Legionellales order
      • Legionella pneumophila causes Legionnaires’ disease (a pneumonia) and Pontiac fever (a respiratory tract infection). Facultative intracellular bacteria.
      • Coxiella burnetii causes Q fever, an atypical pneumonia.
    • Thiotrichales order > Francisella tularensis causes tularemia, an atypical pneumonia.
    • Pasteurella causes pasteurellosis, a zoonotic skin infection.
  • Enterobacterales order: rod-shaped bacteria > Enterobacteriaceae family
    • Enterobacter
    • Escherichia coli or E. coli.
    • Shigella is a leading cause of dysentery (bloody diarrhea). Africa and South Asia. Caused by shiga toxin.
    • Salmonella is the most common cause of food poisoning. Can also cause typhoid fever.
    • Vibrio cholerae
    • Yersinia pestis (bubonic plague)
    • Legionella causes Legionnaires’ disease, an atypical pneumonia.
    • Proteus mirabilis causes UTIs.
    • Klebsiella pneumoniae can produce carbapenemase.
    • Serratia forms reddish biofilm in damp places due to prodigiosin.
  • Hyphomicrobiales order contains several phyla of rhizobia, which fix nitrogen in plant roots, such as Rhizobium.
    • Bartonella causes cat-scratch disease.
    • Agrobacterium is a genetic vector used to bioengineer plants.
  • Thiomargarita is the largest known bacterium at 2 cm.
  • spirochete
    • Treponema causes treponematosis or syphilis.
    • Borrelia causes Lyme disease.

Terrabacteria adapted to live on land 3 Ga. They are monoderms with just one peptidoglycan cell wall, which stains gram-positive.

• Mycoplasmatota phylum > Mollicutes class is gram negative
  • Mycoplasma causes sexually transmitted genital infections and atypical pneumonia.
• Chloroflexota phylum are monoderms that stain gram-negative.
  • Chloroflexia class contain filamentous anoxygenic phototrophic bacteria.
  • Thermomicrobia class > Sphaerobacter thermophilus.
• Actinomycetota aka Actinobacteria have high GC content.
  • Actinomyces: common soil and human flora, form branched networks of hyphae
    • Arthrobacter is used to produce L-glutamate
    • Brevibacterium is used to produce cheese. It also causes foot odor from thioesters.
  • Micrococcus: spherical cells
  • Mycobacterium: tuberculosis and leprosy
  • Corynebacterium is usually not pathogenic but can cause diphtheria. Glows coral red under Wood’s lamp.
  • Cutibacterium acnes glows orange under Wood’s lamp.
  • Amycolatopsis orientalis produces vancomycin.
  • Streptomyces: spore-producing soil bacteria that produces geosmin. Complex secondary metabolism including streptomycin, neomycin, doxycyclin, thienamycin, bottromycin, etc.
  • Bifidobacterium: common human gut flora
• Bacillota or Firmicutes phylum are have low GC content. 30% of human gut bacteria. Some species can grow dormant in tough endospores.
  • Bacilli class
    • Bacillales order
      • Bacillus are aerobic. Rod-shaped, can form endospores
        • B. subtilis: widely studied and used for enzyme production
        • anthrax (B. anthracis)
        • B. cereus produces enterotoxin, cytotoxin K, and hemolysin BL which cause food poisoning
        • B. atrophaeus or B. globigii is a black-colored non-pathogenic model for anthrax.
        • B. thuringiensis is the most common biological pesticide. The spores form crystal proteins of pore-forming insecticidal delta endotoxin.
      • Listeria is foodborne
      • Staphylococcus form in grape-like clusters. Produce Emmentaler or Swiss cheese. Cause strep throat, pneumonia, endocarditis.
        • Methicillin-resistant Staphylococcus aureus (MRSA) can cause necrotizing fasciitis. Treat with vancomycin.
        • S. aureus causes food poisoning via enterotoxin type B. It is coagulase-positive, producing an enzyme to convert fibrinogen to fibrin.
        • S. epidermidis and S. haemolyticus are the most common skin isolates.
    • Lactic acid bacteria (Lactobacillales order)
      • Lactobacillus ferments wine, yogurt, cheese, sourdough, pickles, beer, cider, kimchi, cocoa, and kefir.
      • Lactococcus lactis ferments brie, camembert, Cheddar, Colby, Gruyère, Parmesan, and Roquefort.
      • Oenococcus oeni is the main baceteria for malolactic fermentation, converting tart grape must into softer lactic acid for red wine and Chardonnay.
      • Pediococcus and Leuconostoc ferment sauerkraut, kombucha, kefir.
      • Streptococcus also used to ferment cheese.
        • Group A streptococcal infection by S. pyogenes can cause skin infections and toxic shock syndrome via M protein and hemolysins.
        • S. pneumoniae was the main cause of pneumonia.
        • S. mutans and S. sobrinus causes cavities by metabolizing sucrose to lactic acid.
      • Enterococcus faecalis is highly antibiotic resistant.
        • Vancomycin-resistant Enterococcus (VRE) is treated with linezolid.
  • Clostridia class are anaerobic
    • Faecalibacterium prausnitzii is the most abundant human gut species at 5%.
    • Clostridium botulinum has botox, which causes botulism, severe flaccid paralysis. It grows in anaerobic, low-acid environments such as oil. It is the most potent toxin by LD50. Also has tetanus toxin.
    • Clostridium difficile (C. diff) spread by spores in feces.
    • Desulforudis is found in groundwater 2 mi deep.
• Cyanobacteria (blue-green algae) can photosynthesize
  • Microcystis aeruginosa causes harmful algal blooms in freshwater and produce microcystin hepatoxins that bond to protein phosphatase.
  • Moorea produces lyngbyatoxin, a protein kinase C agonist and blister agent.
  • Chroococcidiopsis can survive in arid environments.
• Candidate phyla radiation (CPR group) are uncultivated ultra-small bacteria proposed in 2015. They lack many biosynthetic pathways and often have self-splicing introns within their rRNA genes.

Archaea kingdom

Archaea formed 3.7 Ga and are characterized by a cell membrane containing ether lipids like archaeols. Closer to eukaryotes. Contain many extremophiles.

• DPANN are ultra-small nanoarchaea.
• Proteoarchaeota
  • TACK group includes Nitrososphaerota, Korarchaeota phyla.
    • Thermoproteota phylum is the most abundant marine archaea.
  • Asgard superphylum might be the parent of eukaryotes.
• Euryarchaeota
  • Sulfolobus grows in volcanic springs at 2 pH and 80°C. It oxidizes sulfur for energy.
  • Halobacterium lives in very salty water.
  • Haloquadratum has square cells.
  • Thiomargarita lives in hydrothermal vents and prefers 100 °C.
  • Thermococcus is the most radiation resistant organism, tolerating 5,000 Gy. It prefers 100 °C.
  • Picrophilus is the most acidophilic organism, growing at pH 0.5.

Plant kingdom

Plants formed from the endosymbiosis of a cyanobacterium inside an aerobic eukaryote, leading to chloroplasts surrounded by two membranes.

Phenotypes

• Can be deciduous or evergreen.
• Monoecious (both male and female flowers on the same plant) or not.
• Annual (grow and die within one year).
• Perennial (enduring).
  • Trees which have a stem or trunk. Hardwoods from dicot trees, and softwoods from monocots. https://news.ycombinator.com/item?id=35081277
  • Shrubs or bushes are short with multiple stems.
• Herbaceous plants are not woody and tend to be low-growing and annual. They include ferns, graminoids, and forbs (broad-leafed herbs).
• Woody plants are trees, shrubs, or woody vines (lianas) where stems and larger roots contain cellulose fibers in a matrix of lignin. These tend to be perennial.

Structure

• Leaf
  • stomata are pores for gas exchange.
  • attaches to the stem at the axil, which can have axillary buds, which are a site for shoot growth.
• Stems
  • Epidermis
    • Can be replaced by periderm: Cork (phellem), cork cambium, phelloderm.
    • Lenticel is porous tissue for gas exchange on bark, fruit, potato tubers.
  • Cortex: outer layer below the epidermis but outside the vascular bundles
  • Phloem transports sugar.
  • vascular cambium produces secondary xylem inwards, towards the pith, and secondary phloem outwards
  • xylem (central lignified tissue): heartwood (duramen) is more durable, and sapwood is softer
  • pith: soft, spongy parenchyma cells.
  • Terminal bud on the end.

Plant hormones

• Auxins promote cell elongation and division.
  • Cells in sunlight produce less auxin, making the tip point towards the sun.
  • Apical dominance: shoot apical meristem produces auxin to inhibit lateral buds. The meristem contains plant stem cells.
• Cytokinins promote cell division and differentiation.
• Gibberellins promote cell division and seed germination.
• Abscisic acid is a stress hormone that promotes dormancy over growth.
• Ethylene ripens fruit and causes leaf abscission (dropping).

Diploidization: a newly polyploid genome reduce gene dosage by losing chunks of duplicated DNA.

Pigments

• Anthocyanins are purple water-soluble flavonoids in acai, berries, black rice, black beans, red cabbage.
• betalains (beets).

Archaeplastida

• glaucophyte
• red algae (Rhodophyta) are photoautotrophic. Gracilaria and Gelidiaceae produce agar, a mixture of agarose and agaropectin.
• green algae (Viridiplantae) contain chlorophyll a and chlorophyll b and store food as starch in their plasmids. Has a dominant gametophyte phase which produces gametes and is haploid.
  • Chlorophyta
    • Chlorella
    • Dunaliella is used to produce β-carotene.
  • Streptophyta or Charophyta
    • order Desmidiales: asymmetrical single-celled green algae.
    • land plants (embryophytes) emerged within the green algae.
      • non-vascular plants (bryophytes)
        • hornwort is most basal
        • liverwort
        • moss (Bryophyta)
      • vascular plants (tracheophytes) have a dominant sporophyte phase (produces spores, diploid). They are the only extant polysporangiophytes, plants with branching stems or axes bearing sporangia. They produce plant lipid transfer proteins, a conserved panallergen and class 1 food allergen.
        • lycophytes > clubmoss (400 mya) have microphylls, leaves with only one vein. Includes Lycopodium and Diphasiastrum.
        • ferns (Polypodiopsida class)
          • horsetail (Equisetum)
          • cinnamon fern (Osmundastrum)
          • bracken fern (Pteridium)
        • seed plants (spermatophytes)
          • conifers (gymnosperms)
          • flowering plants (angiosperms)

Conifers (gymnosperms) have naked ovules which are seeds when fertilized. They contain pinene, the most common terpenoid, an insect repellant, and an acetylcholinesterase inhibitor.

• Order Cupressales (cyprus) includes redwood (Sequoia), yew (Taxaceae), Japanese cedar (Cryptomeria)
  • juniper (Juniperus) berry is a seed cone used to flavor gin.
• Order Pinales
  • Family Pinaceae
    • Pine (Pinus) resin distills into turpentine, a solvent and varnish. It contains carene with an earthy pine scent and camphene with a pungent smell.
    • Cedar (Cedrus)
    • Douglas fir (Pseudotsuga)
    • Firs (Abies)
    • Larches (Larix)
    • Spruce (Picea)
    • Hemlock (Tsuga)
• Order Ginkgoales: ginkgo has fan-shaped leaves
• Order Ephedrales: Ephedra máhuáng 麻黄 contains the stimulant ephedrine

Flowering plants

Basal flowering plants have two embryonic leaves or cotyledons and 1-pore (monosulcate) pollen. Pollen profilins are major respiratory allergens causing allergic rhinitis or hay fever.

• Basal angiosperms: star anise (Illicium), water lily (Nymphaea)
• Magnoliids
• Monocots (131 mya) have one cotyledon and evolved from dicots.
• Eudicots have 3-pore (tricolpate) pollen
  • Proteales are basal: lotus (Nelumbo), Platanus is sycamore. Very tolerant of pollution.
    • London planetree: often pollarded or pruned, creating large stubs at the top. Featured at SF city hall and Berkeley.
  • Order Ranunculales are basal: buttercup (Ranunculus), poppy (Papaver) codeine and morphine, California poppy (Eschscholzia), columbine flower (Aquilegia), larkspur (Delphinium) spike of purple flowers
    • camphor laurel (Camphora) produces white crystalline camphor, a decongestant, itch reliever, and insecticide.
    • aconite (Aconitum) contains toxic pseudaconitine which inhibits acetylcholinesterase. Monkshood fùzǐ 附子 (A. carmichaelii).
    • hellebore root has cardiac glycosides, and leaves have ranunculin and protoanemonin.
    • Sassafras was ground to make gumbo filé, a thickener. But it contains safrole is a possible liver carcinogen and covalently bonds with DNA.
    • goldthread 黄连 (Coptis) is contains fluorescent yellow berberine dye. Fundamental herb.
  • superrosids
    • Order Saxifragales: witch hazel (Hamamelis), peony báisháo 白芍 (Paeonia) large pink flowers blooming in late spring, root used in herbal medicine.
      • blackcurrant or gooseberry (Ribes) is an edible sour red or black berry.
    • rosids
      • Order Vitales: grape (Vitis). Grape flavor includes methyl anthranilate.
      • eurosids
        • fabids: Fabales, Rosales, Fagales, Cucurbitales, Malpighiales, etc
        • malvids: Myrtales, Malvales, Brassicales, Sapindales, etc
  • superasterids

Flowers

• Nonreproductive perianth consists of calyx (sepals) and corolla (petals)
• Stamen is the male reproductive organ: filament topped with anther and microsporangium.
• Pistil is the female reproductive organ. The stigma receives pollen, which travels down the style tube and to the ovary containing ovules. An ovule contains a female egg cell in a protective carpel, which can have a visible line of suture or seam.
• A fertilizated ovary matures into a fruit or pericarp containing seeds.
  • Simple fruits from a single flower. A berry is an indehiscent simple fruit.
  • Multiple fruits, collective fruits, or syncarpous fruits develop from gynoecium fused from multiple carpels (flowers): pineapple.
  • Aggregate fruit forms from merging ovaries in a single flower: blackberry, strawberry, etc.
  • Stone fruits or drupes have a hard, lignified endocarp pit with a seed inside.
  • A nut is a fruit with a woody pericarp developing from a syncarpous gynoecium.

https://en.wikipedia.org/wiki/APG_IV_system
National Garden Bureau https://ngb.org

https://en.wikipedia.org/wiki/Cover_crop
Forage
Grain

Botanical Reddit post viewed 4/16/17 4 pm https://www.reddit.com/r/mildlyinteresting/comments/65prjf/this_plant_made_a_leaf_instead_of_a_branch_then/
The immediate thing to see is that this is a bipinnately compound leaf: http://www.life.illinois.edu/help/digitalflowers/Vegetative/47.htm
A leaf is distinguished by an axillary bud: http://www.meritnation.com/ask-answer/question/what-is-meant-by-axillary-buds-please-explain-with-a-diagr/morphology-of-flowering-plants/9278125
More broad intro to plant anatomy: http://www.tfhmagazine.com/details/articles/botany-an-introduction-to-plant-biology-part-2-anatomy-of-a-plant.htm
Structured cell division occurs at shoot apical meristem: http://wiki.plantontology.org/images/9/99/MAG_Leaf-morph_B.pdf

Magnoliids

• Order Magnoliales produces lignan derivative Honokiol with anticancer effects. ylang-ylang (Cananga) floral scent is “queen of perfumes”. Champak has fragrant flowers.
  • Magnolia or champaca has fragrant flowers.
  • Nutmeg (Myristica fragrans). The butter is mostly trimyristin, the triglyceride of myristic acid. The essential oil contains terpenes, terpineol (lilac smell), borneol, and myristicin, which is cytotoxic and psychoactive.
  • Annona squamosa or sugar apple fan4li4zhi1 番荔枝 or shi4jia1 释迦. Custard taste, soft eith some pear-like grit, knobby segments each with a large seed. Native to American tropics, and brought to Asia by Spanish traders.
  • cherimoya or custard apple (Annona cherimola). “the most delicious fruit known” -Mark Twain.
• Order Piperales
  • pepper (Piper) contain piperine: black pepper unripe and white pepper ripe
  • Peperomia: round cupped leaves
  • Kava root contains kavalactone, a GABA agonist and anxiolytic. makes a drink
• Order Laurales: avocado (Persea)
  • cinnamon 桂枝 (Cinnamomum) bark is a popular spice. C. cassia is most common in America.
  • laurel (Laurus) produces bay leaf which contains eucalyptol.
  • boldo (Peumus boldus) contains the antioxidant boldine and toxic ascaridole.

Monocots

Monocots (Lilidae) have seeds with one embryonic leaf or cotyledon. Culm is the above ground stem of a grass or sedge.

• Alismatales are basal
  • frogbit (Hydrocharis)
• Dioscoreales order: yam and ube (Dioscorea)
• Pandanales order
  • karuka nut (Pandanus): New Guinea food crop.
  • toquilla palm (Carludovica) used to weave Panama hats.
  • Stemona 百部 contains the pesticide stemofoline, an ACh agonist.
• Liliales
  • lilies (Lilium) and tulips (Tulipa) grow from bulbs
  • sarsaparilla (Smilax) is a perennial vine with prickly stems, used to make a root beer-like drink.
  • lílú 藜蘆 (Veratrum) contains veratridine, a sodium channel agonist and potent neurotoxin. Less toxic during winter. Used topically in herbal medicine.
• .
  • Asparagales
  • commelinids
    • Arecales are most basal
    • graminoids (Poales) are basal
    • Zingiberales
• Acorales order > sweet flag (Acorus calamus)

Order Alismatales: seagrasses, the only marine flowering plants

• arum (Araceae family): tropical plants
  • taro (Colocasia) has large, heart-shaped leaves.
  • Anthurium: bright red, heart-shaped flower with a yellow spike inflorescence
  • Philodendron has yellow or pink variegation
  • Monstera: fenestrated leaves with slits and holes
  • Zamioculcas zamiifolia (zz): rhizomes store water, striking black or green alternating leaves
  • Alocasia: broad, wrinkly, pointy oval leaves
  • bànxià 半夏 (Pinellia ternata) used in 小柴胡湯.
• Zostera: marine eelgrass

Order Asparagales: daffodil (Narcissus), Vanilla, Amaryllis, asphodel (Asphodelus), Aloe, onion/garlic/scallion (Allium), snowdrop (Galanthus).

• asparagus family: Asparagus
  • bluebell/hyacinth (Hyacinthus) spike or raceme of purple flowers
  • Yucca has sharp leaves with panicles of white flowers incl. Joshua Tree.
  • snake plant (Dracaena) is a houseplant which survives with little water or sun.
  • spider plant (Chlorophytum): resilient houseplant. Fluoride in tap water gives burnt tips.
  • Cordyline rhizome is a Maori food crop.
• lily of the valley sensitive (Convallaria). Produces the cardenolide convallatoxin.
• Orchids (Orchidaceae family) is diverse, with 28,000 species. Includes Orchis, Cattleya, and Vanilla planifolia.
  • moth orchids (Phalaenopsis) are epiphytes with long-lasting flowers. They like warm temperatures, indirect light, humidity, and often die from overwatering.
• Iris is associated with wisdom. Orris oil derives from its orris root, a yellow-white wax containing myristic acid.
• Crocus is the source of saffron. Saffron color comes from crocin.
• dragon tree (Dracaena) produces red dragon’s blood resin.
• Agave sap is fermented to produce tequila and mezcals. Tuberose (Agave amica) has an overpowering floral scent.

Order Arecales: date palm (Phoenix), açaí palm (Euterpe)

• coconut (Cocos) has a fibrous mesocarp husk, hard endocarp shell, a thin brown testa seed coat layer, and endosperm flesh and liquid. Three carpels fuse at three ridges. There are three eyes or pores at the peduncle end between the ridges, including one soft germ pore where the embryonic shoot will emerge.
• oil palms (Elaeis) produce palm oil, which is high in saturated fat and often refined at high heat which produces carcinogenic glycidyl fatty acid esters. African E. guineensis is the main source and American E. oleifera is used locally.
• rattan (Calamoideae subfamily) are climbing palms. Calamus draco produces dragon’s blood.

Graminoids (Order Poales)

• Poaceae (grass family) have a hollow culm or stalk which is plugged at the nodes. Narrow alternate leaves attach at the nodes. The leaf contains a lower sheath hugging the stem, a blade, and a ligule membrane at the junction to prevent water from entering the sheath. Leaves can contain rigid silica phytolith to discourage grazing. Flowers are arranged in spikelets, each with one or more florets.
  • BOP clade
    • Oryzoideae is basal
      • rice (Oryza)
      • wild rice (Zizania latifolia) stem 高笋 is crisp when stir-fried.
    • bamboo
      • Bambusa vulgaris and Phyllostachys edulis have edible shoots.
      • Dendrocalamus sinicus reaches 150 ft tall.
    • Pooideae: oat (Avena), wheat (Triticum), barley (Hordeum), rye (Secale), fescue (Festuca), bluegrass or meadowgrass (Poa)
      • sweet grass (Hierochloe odorata) and sweet vernal grass (Anthoxanthum odoratum) produce coumarin.
  • PACMAD clade. The only group of grasses with C4 photosynthesis (“warm-season” grasses), which arose independently many times.
    • Panicoideae subfamily
      • corn or maize (Zea). Corn oil contains 50% linoleic acid, a polyunsaturated, omega-6 fatty acid.
      • millet (Cenchrus)
      • Sugarcane (Saccharum)
      • Sorghum
      • lemongrass (Cymbopogon) produces citronella oil containing geraniol (rose scent) and citronellol.
      • vetiver (Chrysopogon zizanioides) essential oil is used as a fixative in 90% of perfumes. It has a woody, earthy, amber scent.
    • reed (Phragmites) used for thatching
    • air plants (Tillandsia)
• Sedge (Cyperaceae family): sawgrass (Cladium), bogrush (Schoenus)
  • papyrus (Cyperus papyrus) is the earliest paper at 2560 BC.
• Rush (Juncaceae family)
• Bromeliads incl. pineapple (Ananas)
• cattail (Typhaceae family): bur-reed (Sparganium)

Order Zingiberales: ginger jiāng 姜 (Zingiber), banana (Musa), bird of paradise flower (Strelitzia)

• green cardamom (Elettaria) and black cardamom (Amomum) contains terpineol and myrcene
• Calathea has large variegated leaves which fold at night

Fabids

Order Fabales contains nitrogen-fixing bacteria (Rhizobia) in root nodules > legume (Fabaceae family)

• Faboideae subfamily usually has papilionaceous flowers (“butterfly-shaped”).
  • ADA clade
    • Amburaneae tribe > Myroxylon balsamum resin is used to make tolu balsam, which has a warm, mellow, slightly spicy scent. Toluene is the paint thinner smell and was isolated from tolu balsam.
    • Dipterygeae tribe > Tonka bean (Dipteryx odorata) produces coumarin.
  • Meso-Papilionoideae
    • Old World clade > Non-protein amino acid-accumulating (NPAAA) clade
      • inverted repeat-lacking clade (IRLC)
        • Fabeae
          • Lathyrus: green peas (formerly Pisum), snow peas, and snap peas
          • lentils (Lens)
          • vetch (Vicia)
        • milk-vetch huángqí 黄耆 (Astragalus) is the largest plant genus, with 3,000 species.
        • chickpeas aka garbanzo beans (Cicer)
        • Wisterieae > Wisteria 紫藤 vine with purple flowers in hanging racemes.
        • Trifolieae tribe
          • alfalfa (Medicago): important forage crop
          • clover (Trifolium)
          • sweet clover (Melilotus) contains coumarin, a glycoside toxin that inhibits vitamin K synthesis and is used in perfume as a sweet vanilla scent.
          • fenugreek (Trigonella)
        • licorice gāncǎo 甘草 (Glycyrrhiza)
        • fava beans (Vicia)
        • sweetvetch (Hedysarum)
        • goat’s rue (Galega officinalis) contains galegine and guanidine, the inspiration for metformin.
        • Tephrosia contains rotenone, which kills dopaminergic neurons.
      • Phaseoleae tribe
        • soybean (Glycine)
        • genus Phaseolus: need to soak and cook to break down toxic phytohemagglutinin. Lima bean (P. lunatus).
          • green bean/kidney bean/pinto bean/black bean (P. vulgaris).
        • cowpea including black-eyed pea (Vigna)
      • Indigofereae tribe
        • guar bean (Cyamopsis) used for guar gum
        • Indigofera tinctoria is a source of indigo dye.
      • Robinioid clade
        • Loteae tribe > Lotus japonicus is a model legume.
        • Robinieae tribe > black locust (Robinia) is a medium-sized deciduous hardwood.
    • Genistoid
      • Genisteae tribe
        • Lupin bean or bluebonnet (Lupinus) was an Egyptian food source since 2100 BC.
        • Genista tinctoria produces a yellow dye.
      • Crotalarieae tribe > rooibos (Aspalathus linearis) herbal tea from fynbos shrubland in the Cape Floral Region of South Africa.
    • Dalbergioid clade > Dalbergieae tribe
      • peanut (Arachis)
      • Dalbergia: rosewood and kingwood, the most expensive wood, very hard.
      • sola (Aeschynomene aspera) used for pith helmets.
• Caesalpinioideae subfamily
  • carob (Ceratonia)
  • mesquite (Prosopis)
  • Acacia or wattle. The yellow flowers are known as mimosa.
  • Senna is a laxative.
  • zào jiá 皂荚 (Gleditsia sinensis) is a fundamental herb.
  • touch-me-not (Mimosa pudica) folds its leaves. Mimosa tenuiflora bark has DMT and is brewed in ayahuasca. DMT is a serotonin agonist and indole alkaloid derived from tryptophan.
  • Desmanthus bark has a DMT analog and toxic gramine.
• Detarioideae subfamily
  • tamarind (Tamarindus)
  • Uganda ironwood (Cynometra alexandri) is sturdy. Chimpanzees prefer to nest in these.
• soap bark (Quillaja) produces a glycoside saponin used as a foaming agent in beverages and as a humectant in foods. milkwort or 远志 (Polygala) root is used as an exporant in Chinese medicine.

Order Rosales

• Rosaceae family produces pome, an accessory fruit composed of fused carpels in a tough endocarp membrane surrounded by edible mesocarp and exocarp tissue.
  • rose (Rosa): rose oil contains citronellol, geraniol, and nonadecane
  • strawberry (Fragaria), hawthorn (Crataegus), meadowsweet (Filipendula) contains salicylic acid.
  • bramble fruits (Rubus): blackberry, raspberry, cloudberry have thorny stems.
  • apple (Malus) has five carpels. The flavor contains ethyl butyrate and ethyl acetate, a fruity flavor also used as a solvent including for decaffeination.
    • Gala, Fuji, Granny Smith, Red Delicious.
  • Prunus: almond, apricot, cherry, plum.
    • Peaches are fuzzy to block water and insects. Nectarines are not fuzzy.
  • Pear (Pyrus) may russet, forming microcracks in the cuticle cutin and forming a brownish rough suberin layer that may reduce shelf life.
    • Callery pear is common ornamental tree with small white flowers, five petals, 1 inch. In the spring, they produce volatile amines, trimethylamine and dimethylamine, which smell like ammonia or rotting fish to help attract flies. They have tiny inedible fruit with seeds that contain cyanide. It starts out with neat, dense growth, but is prone to splitting at forks in its branches and typically only lasts 15 years.
  • Dryas is an Arctic-alpine flower with eight petals which flourishes in cold temperature. It is used as an geological indicator for the Younger Dryas.
• Hemp (Cannabaceae family)
  • hops (Humulus)
  • Cannabis or hemp contains cannabidiol (CBD), psychoactive tetrahydrocannabinol (THC), and cannabinol (CBN). The hashish resin has been used since 1123.
  • qing tan 青檀 (Pteroceltis tatarinowii) for Xuan paper.
• Moraceae family: fig incl. banyan (Ficus), mulberry (Morus)
  • jackfruit (Artocarpus) is the largest tree fruit, reaching 120 pounds.
  • breadfruit (Artocarpus) is a tropical staple.
  • Osage orange (Maclura) is a bumpy yellow-green multiple fruit native to America.
  • paper mulberry (Broussonetia) used to make barkcloth and Japanese paper or washi.
  • Panama rubber tree (Castilla) native to the New World.
• Nettle (Urticaceae family) has trichome stinging hairs.
  • nettle (Urtica)
  • gympie-gympie (Dendrocnide moroides) in Australia produces painful gympietides.
  • giant stinging tree (Dendrocnide excelsa).
  • Pilea includes the Chinese money plant, which has pleasingly round leaves
• Elm (Ulmaceae family) > elm (Ulmus)
• buckthorn (Rhamnaceae family)
  • jujube 枣 (Ziziphus)

Order Fagales produces potent allergens.

• Family Fagaceae: beeches (Fagus), chestnuts (Castanea)
• Family Betulaceae (birch), alder (Alnus).
  • Oaks (Quercus) produce acorns.
  • Hazel (Corylus) produce hazelnuts.
  • birch (Betula) produces Bet v I allergen, the main cause of type I allergies, affecting 20% of Americans. The tar has a leather and tobacco scent and is used since the stone age as an adhesive, a waterproofing agent, an antiseptic, and a slug repellant.
• Family Juglandaceae: walnut (Juglans), hickory/pecan (Carya)

Gourds: Cucurbitales order > Cucurbitaceae family

• Squash or gourd (Cucurbita): summer squash (zucchini) harvested while immature, while winter squash (pumpkin, butternut squash) is late-growing
• watermelon (Citrullus)
• cucumber, orange cantaloupe, green honeydew, Hami melon 哈密瓜, Canary melon (Cucumis)
• bitter melon (Momordica)
• winter melon 冬瓜 aka wax gourd (Benincasa)
• monkfruit 罗汉果 (Siraitia grosvenorii) contains the glycoside mogroside, which is 250 times sweeter than sucrose.

Order Malpighiales (100 Mya): willow (Salix) contains salicin, violet modesty and pansy 三色堇 (Viola), poinsettia, manchineel, coca plant, cassava (Manihot), Erythroxylum contains cocaine

• St. John’s wort (Hypericum) contains hyperforin, a monoamine reuptake inhibitor that increases drug metabolism.
• Populus: poplar, aspen, and cottonwood.
• Euphorbiaceae
  • Spurges (Euphorbia): Poinsettia
  • castor bean (Ricinus) contains castor oil, which contains ricinoleic acid, a hydroxy acid used as a laxative, mold inhibitor, moisturizer, and chemical precusor. The seed contains ricin, a potent toxalbumin with a human lethal dose of 1 mg/kg. Toxalbumins are a ribosome-inactivating protein.
  • Croton tiglium 巴豆 seeds are laxatives containing phorbol, which promotes inflammation, cell proliferation, and tumors.
  • candlenut (Aleurites moluccanus) oil is used in moisturizers.
  • rubber tree (Hevea). Proteins can cause allergies.
• Passiflora edulis is passionfruit. P. incarnata or maypop is a calming sedative. Contains neuroactive β-Carboline alkaloids such as harmine.
• Banisteriopsis contains harmala alkaloids, monoamine oxidase inhibitors (MAOI) used in ayahuasca.
• stinking corpse lily (rafflesia) has the largest flower in the world. It smells like rotting flesh to attract fly pollinators. It is a vine parasite.

Order Celastrales incl. khat (Catha) which contains the monoamine stimulant cathinone

Order Zygophyllales: chaparral or creosote bush (Larrea tridentata) is an evergreen shrub that can form large clonal colonies. It has bitter, dark green leaves and yellow flowers with five petals.

Order Oxalidales: wood sorrel (Oxalis)

Malvids

Order Myrtales: pomegranate (Punica), guava (Psidium), Fuchsia, Eucalyptus, clove (Syzygium) eugenol analgesic, bloodwood (Corymbia), evening primrose (Oenothera)

• tea tree (Melaleuca) produces tea tree oil containing terpineol, terpinene, and eucalyptol. Cajeput oil is a subtype used in Tiger Balm.

Order Geraniales: Geranium sincerity

Order Malvales: mallow (Malva), linden tree (Tilia), baobab (Adansonia)

• cacao/cocoa (Theobroma). Cocoa bean is fermented, roasted, and husked to produce cocoa nibs, which are ground to cocoa mass and pressed to separate out cocoa butter from the other solids, which contain caffeine and theobromine.
• cotton (Gossypium) also makes cottonseed oil.
• roselle 洛神花 (Hibiscus sabdariffa)
• rockrose (Cistus) leaves are coated in labdanum resin, which is the main amber scent, which is sweet and woody.
• gurjan (Dipterocarpus) produces plywood and gurjan oil, a Chinese medicine.
• yuán huā 芫花 (Daphne genkwa) is a fundamental herb.
• durian (Durio) has a strong, sweet, fetid odor from ethanethiol.

Order Brassicales produce mustard oil (glucosinolate)

• Genus Brassica
  • B. oleracea: broccoli, cauliflower, red cabbage
    • gailan or jièlán 芥兰 has a thick stem and is slightly more bitter.
  • B. rapa: turnip/napa cabbage/bok choy, produces rapeseed or canola oil
  • B. nigra: black mustard
  • B. mustard: brown mustard used in mustard greens
• Arabidopsis is main model plant, and the first plant sequenced due to its small 150 Mbp genome.
• watercress (Nasturtium), radish (Raphanus), wasabi (Eutrema)
  • horseradish (Armoracia): blend and add acid, which stops further spiciness.
• Papaya (Carica)
• meadowfoam (Limnanthaceae family)
• woad or Isatis tinctoria has leaves containing woad, an important blue dye.
• yellow weld (Reseda luteola) is the source of weld, an important yellow dye containing the flavonoid luteolin

Order Sapindales

• Genus Citrus: pomelo, mandarin orange, orange (pomelo-mandarin hybrid), lime. The skin contains limonene, a cyclic monoterpene fragrance also used as a solvent and cleanser. The oldest Italian perfume, Eau de Cologne (179), is a citrus scent.
  • grapefruit (pomelo-orange hybrid) contains the furanocoumarin bergamottin which inhibit CYP450.
  • lemon
  • Bergamot oil is a common citrus scent. It is a primary scent in Shalimar (1921), Guerlain’s second most popular fragrance.
  • Bitter orange hybrid: orange blossom. Petitgrain essential oil is extracted from leaves and twigs with a greenish woody orange scent and has a high citral concentration. Neroli essential oil is sweet and honeyed, containing farnesol (floral).
• Burseraceae family > myrrh 没药 (Commiphora) produces the myrrh resin, also known as the balm of Mecca or opopanax, with an earthy, incense, and sweet fragrance. Boswellia produces frankincense resin 乳香. The resin contains anti-inflammatory boswellic acids not included in the essential oil.
• Cashew family (Anacardiaceae) can produce the irritant urushiol. Includes mango (Mangifera), cashew nut (Anacardium) and pistachio (Pistacia)
• soapberry (Sapindaceae family)
  • rambutan (Nephelium lappaceum) is a Southeast Asian fruit covered in soft red spinterns with translucent aril flesh.
  • lychee 荔枝 (Litchi chinensis): aromatic brown or red fruit with leathery skin and broad tubercles or prickles or bumps. Harvest in summer.
  • longan 龙眼 (Dimocarpus longan)
  • Maple (Acer)
  • Horse chestnut (Aesculus)
  • Mahoe (Alectryon) native to Hawaii
• Rutaceae family > Sichuan pepper huājiāo 花椒 (Zanthoxylum)
• Poison ivy and poison oak (Toxicodendron)
• Sumac (Rhus)
• Rue flower (Ruta)
• Pistacia lentiscus produces mastic resin, used as a chewing gum since biblical times.

Superasterids

• Santalales order: sandalwood (Santalum) has α-santalol used in perfumes
• Caryophyllales
• asterids
  • Cornales are basal: hortensia (Hydrangea): lovely balls of flowers that are pink-blue soil pH indicators
  • Ericales
  • euasterids
    • Campanulids clade
      • Asterales
      • Apiales: celery (Apium), carrot (Daucus), parsnip (Pastinaca), parsley (Petroselinum), fennel (Foeniculum), ginseng rénshēn 人参 (Panax), anise (Pimpinella), cumin, New Zealand kaikomako (Pennantia)
        • chaíhú 柴胡 (Bupleurum chinense) used in 小柴胡湯 for liver health.
        • dāngguī 当归 (Angelica sinensis) is an anticoagulant.
        • chuānxiōng 川芎 (Ligusticum striatum) contains 3,8-dihydrodiligustilide, a progesterone agonist. Fundamental herb.
      • Dipsacales order: Valerian sedative, elderberry (Sambucus), Viburnum, teasel (Dipsacus).
        • Japanese honeysuckle rěndōngténg 忍冬藤 (Lonicera japonica) used in 双黄连.
    • lamiids
      • Order Solanales (nightshades) contain alkaloids: sweet potato and morning glory (Ipomoea), tomato/potato/eggplant (Solanum), goji berry or wolfberry gǒuqǐzǐ 枸杞子 (Lycium), Petunia.
        • Capsicum: bell pepper, paprika, and chili pepper contains capsaicin
        • tobacco (Nicotiana).
        • deadly nightshade (Atropa belladonna)
        • jimsonweed or thornapple (Datura stramonium) is an antimuscarinic deliriant.
        • henbane (Hyoscyamus) has hyoscyamine (daturine) or L-atropine.
      • Lamiales
      • Gentianales
      • Boraginales: forget-me-not (Myosotis), bluebell (Mertensia), California bluebell (Phacelia), lungwort (Pulmonaria), borage or starflower (Borago)

Order Caryophyllales: carnations (Dianthus), amaranth (Amaranthus) incl. Quinoa (Chenopodium), ice plant (Aizoaceae family), beet (Beta), rhubarb (Rheum), buckwheat (Fagopyrum), many carnivorous plants, many succulents, chickweed (Stellaria)

• Cactus (Cactaceae family) incl. prickly pear (Opuntia), dragon fruit (Selenicereus) or pitaya (Stenocereus), saguaro (Carnegiea), giant barrel cactus in Mexico (Echinocactus), Ferocactus barrel-shaped
  • San Pedro cactus (Echinopsis) which produces mescaline seratonin agonist which excites neurons in the prefrontal cortex
  • peyote (Lophophora williamsii) contains mescaline.
• purslane and moss rose (Portulaca): succulent with bright ruffled flowers, native to South America
• Family Montiaceae: redmaid/purslane flower (Calandrinia) have 3/4" magenta flowers with five petals
• four o’clock (Mirabilis jalapa) shows incomplete dominance.
• soapwort (Saponaria) produces saponins.
• Jesuit’s tea (Dysphania ambrosioides) contains ascaridole, a toxic organic peroxide and antihelmintic.

Order Ericales

• Tea (Camellia): C. sinensis produces green tea, oolong (semi-oxidized in the sun), black tea (fully oxidized), fermented tea like pu’er and kombucha
  • Tieguanyin 铁观音: Anxi oolong
  • Longjing tea 龙井茶 from Hangzhou, Zhejiang province.
  • Da Hong Pao 大紅袍 from Fujian province.
  • Lushan Cloud tea 庐山云雾 green tea
  • Contains phenols: catechins, theaflavins, tannins, and flavonoids.
• Blueberry and cranberry (Vaccinium).
• Kiwi 猕猴桃 (Actinidia) is a woody vine with white flowers with gold and fuzzy species.
• Wintergreen (Gaultheria procumbens) makes minty methyl salicylate.
• Brazil nut (Bertholletia)
• Rhododendron strength.
• Diospyros: persimmon and ebony hardwood.
• lingonberry (Vaccinium) is an evergreen shrub with smooth red berries.
• Primrose (Primula)
• Heather (Calluna) solitude
• Strawberry tree or madrone (Arbutus) has a rough, bumpy lychee-like exterior. The coat of arms of Madrid features the bear and the strawberry tree.
• Phlox
• touch-me-not (Impatiens) has seed capsules with explosive dehiscence.
• Manilkara used for chicle chewing gum by Maya and Aztecs.

Order Asterales > sunflower (Asteraceae family). Flower heads or composite flowers with hundreds of disk florets surrounded by “petals” of colorful ray flowers. Largest plant family, with 32,000 species. Chrysanthemum happy yellow flowers, Dahlia, safflower (Carthamus).

• Aster purple star-shaped flower. zǐwǎn 紫菀 (A. tataricus) is a fundamental herb.
• báizhú 白术 (Atractylodes macrocephala) root is traditional medicine.
• Cichorieae tribe have milky latex.
  • Lactuca sativa: lettuce and Celtuce or stem lettuce or wosun 莴笋
  • dandelion (Taraxacum).
  • chicory (Cichorium) root contains the fructan inulin, which is 10% as sweet as sucrose.
• sunflower (Helianthus): sunflower seeds come in linoleic (most common), high oleic, and sunflower oil varieties.
• chamomile (Matricaria and Chamaemelum) contains GABA agonist apigenin and may reduce anxiety.
• Stevia leaf extract contains steviol glycosides like stevioside and rebaudioside which are 30 times sweeter than sucrose. They cannot be metabolized by humans, so they have no calories or glycemic response.
• ragweed (Ambrosia) causes half of pollen-related allergies.
• daisy (Bellis) represents attachment.
• marigold (Calendula) has an intense orange disk.
• wormwood/tarragon and mugwort (Artemisia) contains artemisinin which treats malaria. Wormwood used in absinthe. àicǎo 艾草 (A. argyi).
• thistle (Cardueae tribe): Carduus, Cirsium.
  • milk thistle (Silybum). The silymarin seed shell extract contains the antioxidant flavonolignan silibinin. It helps with liver disease and poisoning via competitive inhibition of toxins.
• Campanulaceae family: dǎngshēn 党参 (Codonopsis pilosula) used in 小柴胡湯

Order Lamiales

• Lamiaceae family: psyllium (Plantago), mint (Mentha), thyme (Thymus), basil (Ocimum), snapdragon (Antirrhinum), teak (Tectona), lemon balm (Melissa), oregano (Origanum), catnip (Nepeta) sedative, savory (Satureja).
  • jasmine faithfulness (Jasminum). The main ingredient of Joy (1929), the second-best selling perfume.
  • lavender 薰衣草 (Lavandula) is a scruffy shrub with spikes of purple flowers on stalks and narrow bluish green leaves with fine hairs. It contains linalyl acetate and linalool, which are fruity scents.
  • Salvia: sage, rosemary, chia. Sage has broad herbaceous leaves and spikes of purple flowers on stalks. Clary sage essential oil contains sclareol, a balsamic scent.
  • Patchouli oil has a heavy, woody, earthy scent. It contains patchoulol, a sesquiterpene alcohol, and norpatchoulenol.
  • ironwort (Sideritis) is used in herbal tea. It contains diterpenes, which are anti-inflammatory.
  • Family Oleacaea: olive (Olea), sesame (Sesamum), lilac 紫丁香 (Syringa), ash (Fraxinus)
  • Chinese skullcap huangqin 黄芩 (Scutellaria baicalensis) stem is a traditional Chinese medicine. Contains flavones baicalin and wogonin, with calming and antitumor effects. Used in shuanghuanglian 双黄连.
  • Paulownia or kiri is a fast-growing Asian hardwood with very high strength-to-weight ratio
  • foxglove (Digitalis) contains cardiac glycosides digoxin and digitoxin, as well as digitalin. It also contains the detergent digitonin.
• Bignoniaceae family
  • Jacaranda has tubular purple flowers.
  • Indian trumpet (Oroxylum indicum) used in traditional medicine.
• Oleaceae family: liánqiáo 连翘 (Forsythia suspensa) is a fundamental herb.
• Orobanchaceae family: dìhuáng 地黄 (Rehmannia) used in 四物汤.

Order Gentianales

• Rubiaceae
  • Coffee nut contains caffeine, an adenosine receptor antagonist and stimulant promotes acetylcholine release.
  • Gardenia produces crocetin, a saffron color.
  • sweet woodruff (Galium odoratum) produces coumarin.
  • Psychotria contains DMT and is used in ayahuasca.
  • Rubia: madder or garance (R. tinctorum) root contains red alizarin dye used in India since 2000 BC.
• Cynanchum acidum is used in the ritual Hindi drink soma.
• dogbane (Apocynaceae family)
  • milkweed (Asclepias) produces latex containing toxic cardenolide when damaged.
  • rubber vine (Cryptostegia) native to Madagascar.
  • dogbane (Apocynum) produces the cardiac glycoside cymarin.
  • frangipani (Plumeria) associated with Maya life deities and Aztec nobility.
• Cinchona has quinine which treats malaria.
• Gentiana large blue trumpet flower
• Kratom (Mitragyna) opioid agonist
• Wax plant (Hoya): thick waxy leaves, round balls of five-lobed flowers

Fungi kingdom

Fungi include yeasts, molds, mushrooms. They are closely related to animals and cannot photosynthesize. They consist of parasites, mutualistic symbionts, and saprotrophs or decomposers which play a vital role in nutrient cycling. Mycorrhiza are a symbiosis where fungi grow in plant roots, giving water and minerals in exchange for carbohydrates. Wood-decay fungi: white rot fungi can decompose lignin; brown rot fungi can only decompose cellulose; and soft rot fungi secrete cellulase and can survive a wider range of temperatures.

• Ascomycota or sac fungi form spores enclosed in a sac-like ascus. Includes truffles (Tuber), morels (Morchella), and filamentous fungi.
  • Saccharomycetales order.
    • Candida causes thrush, the most common fungal infection. C. albicans present in most gut flora, usually benign.
    • Saccharomyces cerevisiae: brewer’s yeast/nutritional yeast. Key component of the Symbiotic culture of bacteria and yeast (SCOBY).
      • S. boulardii and S. bayanus are also used.
      • It is a killer yeast that produces pore proteins.
    • Komagataella or pichia uses methanol for carbon and energy. Model organism and bioreactor.
    • Debaryomyces is common in cheese and barrel-aged beer.
    • Geotrichum is used in Camembert and caco fermentation.
    • Pichia kudriavzevii helps ferment cacao beans to remove the bitter taste.
  • Eurotiales order
    Penicillium: blue, Camembert, Brie, and Roquefort cheeses. Helps produce many enzymes
    • Aspergillus: helps produce citric acid, glucose oxidase, lysozyme, lactase, anthraquinone. Causes opportunistic infection in immunocompromised people.
  • Ergot (Claviceps): rye fungus that can cause ergotism
  • Eurotiomycetes class
    • Onygenales order can cause dermatophytosis or tinea skin infection, including ringworm, athlete’s foot, jock itch.
      • Trichophyton
      • Microsporum
      • Epidermophyton
  • Botrytis: gray mold or noble rot in drier conditions.
  • Sordariomycetes class
    • black mold (Stachybotrys chartarum) produces the hemolysin stachylysin which may cause sick building syndrome.
    • Trichoderma includes house mold and soil fungi that protect against root disease.
    • Acremonium is the source of cephalosporin.
    • Myceliophthora thermophila is thermostable, digests cellulose, and low viscosity. Used to produce protein and biofuel.
      • Laccase is a multicopper oxidase that oxidizes phenols. It can crosslink proteins, polysaccharides, and lignin or degrade lignin as a lignin-modifying enzyme. It can degrade aromatic contaminants such as azo dyes and bisphenol A.
    • Neurospora crassa is a haploid red bread mold and an easy-to-grow model organism.
    • Fusidium coccineum is the source of fusidic acid.
  • Pneumocystidales order
    • Pneumocystis jirovecii causes pneumonia in immunocompromised people.
• Basidiomycota
  • Agaricomycotina division
    • Agaricomycetes class
      • Agaricales order
        • Agaricaceae family includes the button mushroom Agaricus bisporus and the field mushroom Agaricus campestris, the dominant cultivated mushrooms in America.
        • Pleurotaceae family > oyster mushroom (Pleurotus ostreatus)
        • Omphalotaceae family > shiitake (Lentinula edodes).
        • Physalacriaceae family > honey fungus (Armillaria mellea) edible, bioluminescent, tree parasite.
        • Lycoperdaceae family > puffball (Bovista) is edible.
        • Hymenogastraceae family > Psilocybe contains psychoactive psilocybin, a DMT analog.
      • Boletales order
        • porcini mushroom (Boletus edulis)
        • brown rot or dry rot (Serpula lacrymans) causes the most wood damage in temperate regions.
      • Auriculariales order
        • black wood ear 黑木耳 (Auricularia heimuer) is slippery.
        • cloud ear 毛木耳 (Auricularia cornea) is coarser and crunchier.
      • Polyporales order
        • fúlíng 茯苓 (Wolfiporia extensa) contains pachymic acid with antiviral, antitumor, and antivenom activity.
        • hen-of-the-woods (Grifola frondosa) is highly edible.
        • sulfur shelf (Laetiporus sulphureus) is edible. Golden yellow.
    • Tremellomycetes class > Tremellales order
      • 银耳 (Tremella fuciformis) is a tasteless gelatinous fungus.
      • Cryptococcus neoformans causes meningitis in people with AIDS
  • Rhodotorula is the most common hospital fungus. It is orange on Sabouraud’s dextrose agar (SDA). Variants can degrade polycyclic aromatic hydrocarbons (PAH) for bioremediation.
  • Moesziomyces antarcticus lipase is used in acylation for food coloring.
  • Amanita. Some species have amatoxin, a potent and thermostable RNA polymerase inhibitor with a lethal dose of two mushrooms or 0.2 mg/kg.
    • Caesar’s mushroom (Amanita caesarea) was a favorite in antiquity. It has an orange cap with yellow gills and stipe (stalk).
    • Amanita velosa is edible.
    • death cap (Amanita phalloides) contains amatoxin and phallotoxins like phalloidin, which destroys liver cells by binding filamentous actin and is used to visualize F-actin.
    • destroying angel (Amanita ocreata) is a poisonous white mushroom.
    • fly agaric (Amanita muscaria) contains the psychoactive GABA agonist muscimol. It is a red mushroom with white spots and white gills.
  • Malassezia is the main cause of dandruff, seborrhoeic dermatitis, and tinea versicolor. It requires skin oils to grow.

Animal kingdom

Animals arise around 700 mya in the Ediacaran period, as stationary filter feeders with bilateral symmetry, and radiate in the Cambrian explosion 538 mya.

• Sponges (Porifera phylum) are the most basal clade. They circulate water through their body.
• Comb jellies (Ctenophora) are a basal clade. They use their cilia (combs) to move.
• Cnidaria, 700 mya
• Bilateria
  • protostomes typically form a mouth before the anus. Includes many helminths which cause helminthiasis.
    • Spiralia
      • Gnathifera is very basal and abundant. It has chitin mouthparts.
        • Rotifers are freshwater filter feeders.
        • Chaetognaths are marine plankton.
      • flatworm (platyhelminths) is basal
        • tapeworm (cestode)
          • dwarf tapeworm (Hymenolepis)
          • beef tapeworm (Taenia)
        • fluke (trematode)
          • blood fluke (Schistosoma) causes schistosomiasis, the second-most devastating parasitic disease.
          • Trichobilharzia causes swimmer’s itch when it dies on the skin.
          • Canadian liver fluke (Metorchis) causes fever from raw fish.
      • lophotorochozoa
        • annelid: ringed or segmented worm
          • giant tube worm (Riftia) lives near hydrothermal vents.
          • Pompeii worm (Alvinella) are the second most heat-tolerant animal, surviving up to 80°C.
        • mollusc, 550 mya
    • molting animals (Ecdysozoa)
      • roundworm or nematode
        • Pinworm (Enterobius) is the most common worm infection in America and Europe.
        • Ancylostoma and Necator are the most common hookworm parasite, common in warm, moist, tropical climates.
        • Caenorhabditis elegans has 302 neurons and can be frozen.
        • Ascaris causes ascariasis. More common in tropical areas.
        • Trichuris causes trichuriasis.
        • anguillula (Strongyloides) is a tropical intestinal parasite.
        • Halicephalobus is the deepest-living organism, found in groundwater 2 mi below the earth.
      • tardigrade or water bear is the most resilient animal.
      • arthropod, 550 mya
  • deuterostomes
    • echinoderms have radial symmetry
      • common starfish (Asterias)
      • brittle star (Ophiura) and basket star (Astroboa)
      • sea urchin (Echinoidea class) incl. sand dollar
      • sea cucumber hǎishēn 海參 (Holothuroidea class): slippery texture.
    • chordates have a notochord, dorsal hollow nerve cord, endostyle or thyroid, pharyngeal slits, and a post-anal tail.
      • Lancelet (Branchiostoma) is most basal
      • Tunicates are sea squirts (Ascidiacea) and salps (Thaliacea)
        • Ciona 160 Mbp was sequenced in 2002.
      • Vertebrates are fish.
        • Tetrapods evolved within fish.

Cnidaria: radially symmetric aquatic animals with mouths surrounded by tentacles with stinging cnidocytes. Swimming medusa and sessile polyp stages.

• Anthozoa subphylum
  • Octocorallia class: colonial polyps with 8 arms
    • blue coral
    • Alcyonacea: soft corals and sea fans
  • Hexacorallia class: colonial polyps with six-fold symmetry
    • Sea anemone order e.g. Heteractis
    • Acropora: Elkhorn coral with flat branches and staghorn coral are fast growing
  • Coral class: brain coral (Diploria), sea fingers (Alcyonium), etc
• Medusozoa subphylum
  • Hydrozoa class
    • Hydra don’t age
    • Immortal jellyfish (Turritopsis) can revert to a polyp
    • Siphonophore order are colonies of medusoid and polypoid zooids. Portuguese man o’ war or bluebottle (Physalia) have a gas pneumatophore float. Erenna can emit red light.
  • box jellyfish (Cubozoa class) have tentacles with stinging cnidocytes. The venom includes pore proteins causing hyperkalemia.
• Jellyfish: moon jelly (Aurelia), lion’s mane jellyfish (Cyanea), Nomura’s jellyfish (Nemopilema)

Mollusca phylum: 260 mya, often produces mother-of-pearl
https://en.wikipedia.org/wiki/Template:Edible_molluscs

• Slugs and snails (Gastropoda)
  • true limpet (Patellogastropoda subclass): aquatic snail with a conical shell. clings strongly to rocks with their muscular foot.
  • Roman snail (Helix)
  • Cone snail (Conidae family) like Conus and Californiconus produce conotoxin, short peptides.
  • Eremina desertorum is native to Middle East desert can hibernate without water for a decade.
  • Moon snail (Natica)
  • Abalone (Haliotis)
  • apple snail (Ampullariidae family) are freshwater snails with a gill and a lung.
  • Sacoglossa superorder eat algae and use their chloroplasts to photosynthesize for several months.
  • murex snails or rock snails (Muricidae family) secrete mucus containing Tyrian purple dye used by Phoenicians from 1200 BC. Bolinus brandaris, Hexaplex trunculus, Stramonita haemastoma.
• Cephalopod class: siphon for jet propulsion, beaked mouth, chromatophores for camouflage and signaling, ink cloud to defense
  • Indo-Pacific nautilus
  • squid (Decapodiformes superorder) has ten arms: two tentacles and eight short arms. Rod-like gladius skeleton made of chitin, an amide glucose polymer
    • Cuttlefish have a W-shaped pupil and a cuttlebone shell
    • Humboldt squid (Dosidicus)
  • octopus order
    • Octopus genus grows to 20 lb and lives up to 2 years. It hunts at dusk.
    • giant octopus (Enteroctopus) is the largest, growing to 100 lb and 20 ft armspan. It is found down to 2,000 m. It has longitudinal folds dorsal on its mantle.
    • Blue-ringed octopus (Hapalochlaena) has tetrodotoxin.
• Bivalve class
  • Blue mussel (Mytilus)
  • Surf clam (Spisula)
  • Scallop (Placopecten, Pecten)
  • Oysters: Ostrea, Pacific oyster (Magallana)
  • venerid family or Venus clams are mostly edible. They have a posterior ligament.
    • hard clam or quahog (Mercenaria)
    • butter clam or Washington clam (Saxidomus)

Arthropoda phylum has an open respiratory system which transports gas via spiracles, tracheae, and tracheoles. Diatomaceous earth is a clay-based soil that cuts up arthropods.

• Chelicerae subphylum have pincer-like mouthparts
  • Arachnida class: eight legs. Book lungs are folds in an open ventral abdominal, air-filled cavity (atrium) which allow hemolymph to exchange oxygen.
    • Spider (Araneae order): 50,000 species
      • Araneomorphae infraorder comprises 93% of living spiders. They die after a year and their fangs are angled toward each other.
        • cobweb spider (Theridiidae family) is the most common arthropod in human houses. 3,000 species.
          • American house spider (Parasteatoda)
          • Hawaiian happy-face spider (Theridion) is used to study color morphism.
          • widow spiders (Latrodectus) have painful nonfatal venom containing latrotoxin. Includes the black widow, brown widow, and the redback spider found in Australia.
        • brown recluse (Loxosceles) has a painful venom containing sphingomyelinase D.
        • jumping spider (Salticidae family) has excellent vision. 6,000 species.
        • daddy long-legs (Pholcus) are harmless and prey on other spiders.
        • funnel weaver (Agelenidae family)
        • huntsman spider (Sparassidae family) has the largest legspan at 10".
      • Mygalomorphae infraorder can live for 40 years. Fangs points straight down.
        • tarantula family (Theraphosidae)
          • Goliath birdeater is the largest spider at 175 g.
        • Australian funnel-web spiders (Atracidae family) contain deadly atracotoxin venom.
    • harvestman or daddy longlegs (Opiliones order)
    • scorpion order
      • Deathstalker (Leiurus) produces many neurotoxins. Chlorotoxin can help target cancer cells.
    • mite: Acariformes superorder and Parasitiformes superorder, including tick
  • Horseshoe crab (Limulidae family). Blood used to make Limulus amebocyte lysate.
• Mandibulata
  • Myriapod: centipedes have one pair of legs per segment. They are carnivorous and inject venom through forcipules or toxicognaths, which are modified legs. Millipedes have two pairs of legs on most segments. Harmless slow-moving detritivores.
    • Scolopendra gigantea: largest centipede, native to South America.
  • Crustacea
    • Multicrustacea
      • barnacle (Cirripedia subclass)
        • Acorn barnacle (Balanus)
      • copepod
        • Cyclops, a freshwater copepod
        • Sea lice (Caligus)
      • Malacostraca
        • mantis shrimp (Stomatopoda)
        • Decapoda order
          • prawn (Dendrobranchiata order) > Penaeidae family: Tiger shrimp (Penaeus), whiteleg shrimp (Litopenaeus)
          • true shrimp (Caridea infraorder): brown shrimp (Crangon), pink shrimp (Farfantepenaeus), cold-water prawn (Pandalus)
          • Reptantia suborder
            • Lobster (Homarus)
            • Crayfish (Procambarus)
          • hermit crab (Paguroidea superfamily)
            • king crab (Lithodidae family)
        • krill (Euphausia)
        • Amphipoda
        • isopod
          • giant isopod (Bathynomus)
          • Woodlice 100 mya incl. Porcellio, rock lice (Ligia), pill bug or roly poly (Armadillidium)
        • Brown crab (Cancer), Asian crab (Portunus), Dungeness crab (Metacarcinus), blue crab (Callinectes)
        • Mantis shrimp (Oratosquilla)
    • Allotriocarida > Branchiopoda
      • Daphnia is a transparent filter feeder around 1 mm.
    • Hexapod
      • Springtails eat dead plants and are sensitive to soil pollution.
      • Insects have external mouthparts.

Insects have a thorax with three pairs of legs. 1 million species. Pyrethrin kills adult insects.

• jumping bristletail (Archaeognatha order) is most basal, and the remainder are Dicondylia.
• Zygentoma is basal and includes silverfish (Lepisma), a nocturnal pest that produces cellulase. The rest are winged insects (Pterygota subclass).
• mayfly
• dragonfly (Odonata)
• Neoptera infraclass can flex their wings over their abdomens. They lay eggs using an ovipositor.
  • Polyneoptera
    • earwig (Dermaptera order)
    • Orthoptera order
      • Ensifera suborder: house cricket (Acheta), field cricket (Gryllus), tree cricket (Oecanthus), katydid or bush cricket (Tettigonia)
      • grasshopper (Caelifera suborder) has shorter antenna. Swarm as locusts.
    • stick insect
    • Dictyoptera
      • mantis (Mantodea)
      • Blattodea
        • cockroach
        • termite
          • Macrotermitinae subfamily are fungus-growing termites.
  • Eumetabola
    • Paraneoptera
      • true bug (Hemiptera order): cicada (Cicadidae), aphid, bed bug (Cimex)
        • lac bug (Kerria lacca) produces shellac resin used for confectioner’s glaze, French polish for wood, ballet pointe shoe stiffener, art coating, and phonograph records. It contains aleuritic acid, jalaric acid, and shellolic acid. Lac bugs also produce a crimson anthraquinone lac dye.
        • Shield bug includes the brown marmorated stink bug (Halyomorpha)
        • Grape phylloxera devastates European grapevines.
      • louse or lice (Phthiraptera clade)
    • Holometabola go through complete metamorphism with distinctive larval, pupal, and adult stages.
      • Hymenoptera order is basal.
        • sawfly is most basal.
        • parasitoid wasp is second basal.
          • Samurai wasp (Trissolcus), a parasitoid wasp used for pest control.
        • Apocrita is basal and has a wasp waist.
        • chalcid wasp (Chalcidoidea superfamily) include several phyla of fig wasps and Encarsia used to control whitefly.
        • Aculeata (ovipositor stinger)
          • Vespidae
            • hornet (Vespa)
            • yellowjacket (Vespula)
          • ant (Formicidae family): weaver ants (Oecophylla), army ant (Eciton)
            • Myrmicinae subfamily > Attini tribe: fungus-growing ants. Leafcutter ants Atta and Acromyrmex carry leaves to their fungus colony, usually Lepiotaceae fungus.
            • Fire ant (Solenopsis) has peperine venom.
            • Bullet ant (Paraponera) has Poneratoxin which prevents inactivation of voltage gated sodium channels.
          • bee (Anthophila clade): bumblebee (Bombus), honey bee (Apis).
            • Beekeepers use a bee smoker to calm the bees.
      • Neuropteroidea
        • lacewing (Neuroptera order)
        • beetles (Coleoptera order) > Polyphaga suborder can fold their wings under elytra forewings. Originated in the Carboniferous period and contains 400,000 species, a quarter of animal species. A quarter of beetles are plant-eating, evolving pectinase and speciating with the speciation of flowering plants.
          • firefly
          • Cucujiformia infraorder
            • weevils (Curculionoidea superfamily): 97,000 species, many crop pests
              • bark beetle (Scolytinae subfamily). Includes ambrosia beetles, which bore through trees and grow gardens of ambrosia fungi, which extract nutrients from xylem.
            • Chrysomeloidea superfamily
              • leaf beetle (Chrysomelidae family): 40,000 speicies.
                • tortoise beetle (Cassidinae subfamily)
              • longhorn beetle (Cerambycidae family): 35,000 species.
                • Titan beetle (Titanus) is one of the largest, at 7". It lives in the Amazon.
            • Darkling beetle (Tenebrionidae superfamily): 20,000 species.
              • Flour beetle is a grain pest
                • Tenebrio: mealworm larval form is a common food in Asia.
            • Coccinelloidea superfamily > ladybug (Coccinellidae family): 10,000 species.
              • seven-spotted ladybug (Coccinella)
              • Harmonia is native to Asia and invasive in America and Europe. It can bite and reflex bleed a foul methoxypyrazine odor.
          • scarab infraorder: 35,000 species
            • Dung beetles feed on feces
          • Elateriformia infraorder
            • jewel beetle (Buprestidae family): 15,000 species
      • Panorpida loses the ovipostor.
        • Lepidoptera: caterpillars are the larval stage.
          • butterfly (Rhopalocera suborder)
            • brush-footed butterflies (Nymphalidae family). 6,000 species.
              • milkweed butterflies (Danainae subfamily) lay their eggs on milkweed
                • monarch butterfly migrates to Mexico and Florida in the fall.
          • moth (Saturniidae family)
            • silkworm (Bombyx).
            • gem moth (Orthonama).
        • true fly (Diptera family)
          • fruit fly (Drosophila).
          • black soldier fly (Hermetia)
          • housefly (Musca): regurgitation and defecation transmits disease.
          • blow fly or carrion fly (Calliphoridae family) is polyphyletic
          • bot fly (Oestridae family). Larvae are parasites of mammals.
          • screw-worm fly (Cochliomyia) in New World tropics.
          • sandfly (Lutzomyia) spreads leishmaniasis.
          • crane fly or mosquito hawk (Tipuloidea superfamily)
        • flea (Siphonaptera order)
          • rat flea (Xenopsylla) spreads bubonic plague and typhus.
        • The puss caterpillar (Megalopyge) has venomous spines. It is American and becomes a flannel moth.

Fish

Oily fish include forage fish like sardines, herring and anchovies, and pelagic fish such as salmon, trout, tuna, swordfish and mackerel.

Salmon are anadromous (migrating to fresh water) semelparous (die after spawning) predatory fish with natal homing. Eggs contain larvae. Eggs hatch into sac fry which stays in the gravel feeding on its yolk sac. After a few days, it becomes a fry without a sac, and moves to feed on plankton. A fingerling gets scales and fins and a carnivorous diet, and develops into a parr, which has spots and bars for camouflage, and remain for up to three years. A smolt adjusts to brackish water in estuaries and grows silver scales with countershading. 6" long post-smolts spend a year in schools and up to four more years as an adult.

https://en.wikipedia.org/wiki/Lists_of_aquarium_life

Vertebrata

• Jawless fish: mostly saltwater, 530 Ma.
  • Hagfish (Myxini): scavenger that produces slime as a defense.
  • lamprey (Petromyzon): parasitic carnivore up to 3 ft.
• Gnathostomata infraphylum: jawed vertebrates, 420 Ma.
  • cartilaginous fish (Chondrichthyes class), 380 Ma.
    • Holocephali subclass > Chimaeriformes order: chimaera or ratfish
    • Elasmobranchii subclass
      • sharks (Selachii superorder)
        • Galeomorphii
          • bullhead shark (Heterodontus)
          • carpet shark (Orectolobiformes order)
            • whale shark (Rhincodon) largest, filter-feeder
            • Nurse shark (Ginglymostoma) use buccal pumping
          • mackerel shark (Lamniformes)
            • great white shark (Carcharodon)
            • basking shark (Cetorhinus) second-largest, filter-feeder
            • mako shark (Isurus)
            • thresher shark (Alopias)
            • goblin shark (Mitsukurina) is a deep-sea carnivore with pointed snout and protruding jaws.
          • ground shark (Carcharhiniformes)
            • hammerhead shark (Sphyrna)
            • tiger shark (Galeocerdo)
            • requiem shark (Carcharhinidae family)
              • bull shark (Carcharhinus) in Africa
              • blue shark (Prionace)
        • Squalomorphii
          • Squaliformes
            • cookiecutter shark (Isistius) gouges animals like a lamprey. It undergoes diel vertical migration.
          • Squatiniformes
            • dogfish shark (Squalidae family)
            • sawshark (Pristiophoriformes)
      • rays (Batoidea superorder)
        • electric ray (Torpedo), from Latin torpere, to be paralyzed.
        • skates generate long (200 ms) electric discharges from tail muscles.
        • short-tail stingray (Bathytoshia) very southern
        • round ribbontail ray (Taeniurops)
        • diamond stingray (Dasyatis)
        • sawfish (Pristis)
  • Euteleostomi or Osteichthyes superclass: bony fish, 425 Ma.
    • Sarcopterygii class: lobe-finned fish, 418 Ma.
      • Actinistia class: coelacanths (Latimeria)
      • Rhipidistia
        • Dipnoi class: lungfish 380 Ma. Oldest fish is 90 years old.
        • Tetrapod
    • Ray-finned fish (Actinopterygii class), 400 Ma

Ray-finned fish (Actinopterygii class)

• Cladistia subclass: bichirs and relatives
• Actinopteri subclass
  • Chondrostei subclass: sturgeon and paddlefish
  • Neopterygii subclass
    • Holostei subclass: bowfin (Amiiformes) and gar (Lepisosteiformes)
    • Teleostei subclass: 96% of living fish species
      • Elopomorpha megacohort
        • Elopiformes order: tarpon, tenpounder, ladyfish
        • .
          • Albuliformes order: bonefish
          • Notacanthiformes order (deep-sea) and eel (Anguilliformes order)
            • eel (Anguilla), pelican eel (Eurypharynx)
      • Osteoglossocephalai megacohort
        • Osteoglossomorpha
          • Osteoglossiformes: bony-tongued African fishes. Highly intelligent with a large cerebellum to process electrical signals.
            • freshwater Elephantfish
            • Peters’s elephantnose fish: freshwater African fish is weakly electric, using a large brain for sensing worms and invertebrates.
          • Hiodontiformes: mooneye and goldeye
        • Clupeocephala supercohort
          • Otomorpha cohort
          • Euteleosteomorpha cohort

Otomorpha cohort

• Clupeiformes order: prey fish
  • Clupeidae family: mostly feed on plankton
    • Clupea: Pacific herring and Atlantic herring. The Pacific herring fishery collapsed in 1993.
    • European pilchard (Sardina)
    • sprat (Sprattus)
  • Dorosomatidae family: Sardinella and white sardine (Escualosa)
  • anchovy (Engraulidae family)
  • shad (Alosidae family)
  • Menhaden (Brevoortia)
  • rainbow sardines (Dussumieria) and round herrings (Etrumeus)
• Alepocephaliformes order: deep-sea
• Ostariophysi superorder: 70% of freshwater species
  • Gonorynchiformes: milkfish
  • Otophysa
    • Cypriniformes
      • Cyprinidae family
        • Four Domesticated Fish in China: most fished
          • silver carp (Hypophthalmichthys)
          • bighead carp (Hypophthalmichthys)
          • grass carp (Ctenopharyngodon)
          • black carp (Mylopharyngodon)
        • carp and koi (Cyprinus)
        • minnow
        • loach
        • goldfish (Carassius)
        • zebrafish (Danio) has a large transparent embryo useful for developmental genomics.
      • sucker (Catostomidae family)
        • Bigmouth buffalo (Ictiobus): longest-lived freshwater fish, 120+ yrs, American
    • .
      • Characiformes: piranha, tetras, pencilfish, dorado (Salminus)
      • .
        • Gymnotiformes
          • Electric eel (Electrophorus) generates 600 V.
          • Knifefish: South American, weak electric fish
        • Siluriformes: catfish
          • Electric catfish in Africa generates 350 V from outer body muscles.

Euteleosteomorpha cohort

• Salamanderfish (Lepidogalaxias) is basal
• Protacanthopterygii subcohort, Argentiniformes is basal
  • Salmonidae family: freshwater whitefishes (Coregoninae subfamily) are basal
    • Salmoninae subfamily
    • Salmonini tribe
      • salmon (Salmo)
      • char aka lake trout (Salvelinus), including brook trout.
    • Pacific salmon and Pacific steelhead or rainbow trout (Oncorhynchus)
  • Esociformes: pike
• .
  • Stomiatii
    • Osmeriformes order: smelt
    • Stomiiformes: deep-sea dragonfish, bristlemouths, hatchetfishes. Bioluminescent photopores. Can emit red light.
  • Neoteleostei: basal Ateleopodidae (jellynoses)
    • Eurypterygia: basal Aulopiformes (lizardfish)
      • Ctenosquamata
        • basal lanternfish (Myctophidae family) use bioluminescence. They are the majority of deep-sea fish by mass, reaching 1 Gton.
        • Acanthomorpha have spiny fin rays
          • Lampriformes order: giant oarfish (Regalecus), opah, ribbonfish
          • Paracanthopterygii superorder
            • trout-perch (Percopsis)
            • dories (Zeiformes order)
            • Stylephorus, deep-sea
            • whitefish or true cods (Gadidae family): finned dermersal fish
              • Atlantic cod, Pacific cod, Alaska pollock (Gadus)
              • haddock (Melanogrammus)
              • pollock (Pollachius)
              • whiting (Merlangius)
          • Acanthopterygii
            • Holocentriformes: squirrelfish; soldier fishes
            • Percomorpha clade

Percomorpha clade: taxonomy is in flux between Fishes of the World, Deepfin, and Fish Tree of Life.

• Perciformes order: very diverse. Traditionally contains most Percomorpha, but is being broken up.
  • Serranidae family: sea bass, grouper, and anthia (Anthias).
  • cod icefish (Nototheniidae family): carnivorous antarctic fish with antifreeze proteins. Benthic without a gas bladder.
    • toothfish or Chilean sea bass (Dissostichus)
  • Percoidei suborder: freshwater fish.
    • Percidae family: true perch (Perca) and walleye. Freshwater, around 1 ft.
    • Centrarchidae family: American, colorful, up to 1 ft.
      • sunfish (Lepomis).
      • black bass (Micropterus). Largemouth bass grows to 29" and 25 lb.
    • grunt (Haemulidae family) produces sound by grinding teeth.
    • mojarra (Gerreidae family): food fish up to 1 ft.
  • snapper (Lutjanidae family)
• Anabantaria
  • labryinth fish (Anabantiformes order): air-breathing freshwater
  • swamp eel (Synbranchiformes)
• Syngnathiformes order: seahorse (Hippocampus), seadragon
• Scombriformes order: large pelagic fish.
  • Scombridae family: carnivorous fish in warm oceans. two dorsal fins, a series of dorsal finlets, a divided caudal fin (tail). The first dorsal fin and the pelvic fins are retractable for speed.
    • tuna (Thunnus) grows up to 1,500 pounds, can migrate long distances, and can warm its muscles and brain slightly. Includes albacore, yellowfin, and bluefin tuna.
    • mackerel
    • bonito
• Istiophoriformes order: predatory fish
  • barracuda (Sphyraena): tubular fish
  • billfish
    • marlin (Istiophoridae family): spear-like snout
    • swordfish (Xiphias)
• flatfish (Pleuronectiformes order): demersal
  • sole (Soleidae family)
  • righteye flounder (Pleuronectidae)
    • European plaice (Pleuronectes)
    • Atlantic halibut (Hippoglossus)
    • common dab (Limanda)
    • Pacific Dover sole (Microstomus)
    • summer flounder (Paralichthys)
  • lefteye flounder (Bothidae family)
  • tonguefish (Cynoglossidae family)
  • American sole (Achiridae family)
  • brill (Scophthalmidae family)
    • turbot (Scophthalmus)
    • megrim (Lepidorhombus)
  • sand flounder (Paralichthyidae family)
    • sanddab (Citharichthys)
• Gobiaria: benthic without a gas bladder, mostly ocean.
  • goby and dartfish (Gobiiformes order). The dwarf pygmy goby is the smallest fish at 1 cm.
  • Kurtiformes: nurseryfish, cardinalfish
• Carangaria
  • Carangidae family: pompano (Trachinotus), trevally, and runner
    • jack mackerel: warm ocean carnivores up to 6 ft
  • moonfish (Menidae)
  • remora (Echeneidae)
  • dolphinfish and mahi-mahi or dorado (Coryphaena)
• Eupercaria
  • stargazer (Uranoscopidae family). Electric fish with venom and eyes on top of their heads. The 5 V electric organ is derived from eye and ear muscles.
  • temperate bass (Morone)
  • Labriformes (wrasses, cales, parrotfish)
  • Acanthuriformes order
    • tang and surgeonfish (Acanthuridae family): tropical
    • freshwater drum (Aplodinotus): repetitive grunting noise
  • snapper (Lutjaniformes order)
  • sea bream (Spariformes order)
  • anglerfish (Lophiiformes order)
    • Bufoceratias
    • Photocorynus
    • Handfish is benthic without a swim bladder. Instead, it just walks around on the bottom of the ocean. Only found in Tasmania.
  • Tetraodontiformes have symbiotic bacteria to produce tetrodotoxin, a sodium channel blocker. Includes pufferfish, triggerfish (Balistidae), and ocean sunfish (Mola).
• Ovalentaria
  • cichlids (Cichliformes order)
    • tilapia (Oreochromis)
  • mullet (Mugilidae family)
  • blenny (Blenniiformes family)
  • Cyprinodontiformes
    • freshwater guppy aka rainbow fish (Poecilia)
  • Pomacentridae family
    • clownfish (Amphiprion) lives in sea anemone
    • damselfish

Tetrapods

Tetrapods evolved within fish: amphibians and amniotes. Many tetrapods have a cloaca, a common digestive, reproductive, and urinary orifice at the rear.

Amphibians (250 mya): cold-blooded with four-limbs. Needs water to breed. Generally undergoes metamorphosis from a larva with gills to an air-breathing adult. Breathes using buccal pumping, breathing with the floor of the mouth.

• Frogs (Anura order)
  • clawed frog (Xenopus) embryos are a model organism for vertebrate development.
  • poison dart frogs (Phyllobates) contain batrachotoxin, which opens sodium channels in nerve cells. The toxin comes from their diet so captive frogs are nontoxic. They are brightly colored.
• Salamanders and newts (Urodela order)
  • Pacific newts (Taricha) have tetrodotoxin
• caecilians (Gymnophiona order)
  • Siphonops annulatus. Young eat the mother’s skin and drink milk from her cloaca.

Amniotes (300 mya) are true land animals, with impermeable keratinized skin, costal respiration by expanding the ribs, and fetal membranes.

• Sauropsids
  • Reptiles (Lepidosauria)
  • Archelosauria
    • turtles (Testudines order) have a keratin carapace and plastron belly which forms from the ribs.
      • leatherback sea turtle (Dermochelys coriacea) is the largest at 1,000 lb. It does not have a bony shell.
      • loggerhead sea turtle (Caretta) grows to 1,000 lb.
      • box turtle (Terrapene) has a hinged shell.
      • tortoise (Testudinidae family) are slow and land-dwelling.
        • Galapagos tortoise is the largest tortoise at 900 lb and lives to 175 years.
    • Archosaur clade
      • Crocodilia: crocodiles, and alligators and caimans.
      • Avemetatarsalia > Ornithodira clade
        • pterosaurs
        • dinosaurs: all extinct except for birds
          • Ornithischia
            • Triceratops
          • Saurischia
            • sauropods: very long necks, long tails, four thick legs, and relatively small heads. Includes Brontosaurus, Apatosaurus, Diplodocus
              • Titanosaurs grew to 120 ft and 70 tons and survived to the Cretaceous extinction.
            • theropods
              • Tyrannosaurus, Giganotosaurus
              • Birds
• Mammals (synapsids)

Reptiles: Lepidosauria superorder includes the tuatara (Sphenodon) and lizards (order Squamata).
Lizards have scaly skin that molts and movable upper jaws. They form the second-largest order of vertebrates, after the perciform fish. Most can lose their tails in self-defense.

• geckos are most basal. They have very grippy toe pads and are the only lizards to chirp, click, or hiss.
• Skinks are basal and have tiny legs.
• monitor lizards (Varanus) have long necks and powerful claws. They are native to Africa, Asia, and Oceania. The Komodo dragon is the largest lizard, reaching 10 ft and 150 lb.
• Iguania suborder.
  • Iguanas are American herbivores with elongated spiny scales on their back.
    • Galapagos land iguana (Conolophus) is large.
  • Chameleons can change color. They have laterally compressed bodies and projectile tongues, and are native to the Old World.
  • Anoles (Dactyloidae family) such as Anolis can also change color and eat grasses and insects.
  • Bearded dragons (Pogona) inflate their throat when threatened or mating.
  • Horned lizard or horny toad (Phrynosoma) has a round body with spines to prevent water loss.
• worm lizards (Amphisbaenia clade) are small and legless.
• Anguimorpha suborder
  • slowworms (Anguis) are legless lizards.
  • Bearded lizards and Gila monsters (Heloderma) are venomous, fat, and slow. They are the largest lizards native to North America.
• Snakes evolved from lizards, losing front limbs, eyelids, and ear openings. They have forked tongues.
  • basal python family is a non-venomous constrictor. The reticulated python is the longest snake, reaching 20 ft and endemic to southeast Asia. The Burmese python is the second-heaviest. The ball python is African and curls up when threatened.
  • basal boa family
    • The green anaconda is the heaviest snake, endemic to South America.
  • colubrid family is the largest snake family. Many clades evolved short, grooved rear fangs, a precursor to front fangs.
    • hognose (Heterodon) plays dead when threatened (thanatosis)
    • the boomslang is highly venomous, injecting a slow-acting hemotoxin that causes tiny blood clots and hemorrhaging.
    • grass snake (Natrix) is Eurasian.
  • viper family are Old World snakes with venomous, long, hinged fangs.
    • pit vipers (Crotalinae subfamily) have a heat-sensing pit organ and are the only subfamily in the Americas.
      • Crotalidae polyvalent immune Fab contains four sheep antibodies.
      • The rattlesnake is the leading cause of snakebites. Includes the diamondback rattlesnake (Crotalus).
      • Moccasins, copperhead, and cottonmouths (Agkistrodon).
    • horned viper (Cerastes) is found in the North African desert to Persia.
    • adder (Vipera) is the only venomous snake native to Britain.
  • elapid family has permanently erect fangs. It is usually venomous and rears upwards and spreads out its neck flap when threatened.
    • True cobras (Naja) includes the Egyptian cobra or asp (Naja haje)
    • The king cobra (Ophiophagus) is venomous, injecting dangerous three-finger toxins and snake venom metalloproteinases.
    • mamba (Dendroaspis) has dendrotoxins, alpha-neurotoxins, cardiotoxins, and fasciculins.
    • taipan is venomous and native to Oceania.

Birds

A pennaceous feather has a stalk or quill. It has a hollow calamus base and a solid rachis (shaft). The rachis has vanes or vaxillum spreading to either side. Each vane has many flattened barbs that criss-cross with barbules.

Flight feathers are long, stiff, asymmetric pennaceous feathers.

• Wing remiges and tail rectrices.
• 9-16 primaries attach to the manus (carpometacarpus and phalanges). They are longest, narrowest, and can individually rotate.
• Secondaries connect to the ulna. Ligaments can form raised quill knobs (ulnar papillae) along the ulna.
• The alula is a freely moving digit on the wing with three to five flight feathers. It moves forward at low speeds to act as a slat or vortex generator.

Down feathers have few barbs. Powder down disintegrates into fine keratin particles which can cause allergies.

Aves class

• Palaeognathae (“old jaw”): ratites
  • ostrich (Struthio)
  • Casuariidae family: emu (Dromaius) and cassowary (Casuarius)
  • kiwi (Apterygiformes order)
  • tinamou (Tinamidae family)
• Neognathae
  • Fowl (Galloanserae superorder)
    • waterfowl: Anseriformes order
      • Anatidae family: water birds incl. duck/mallard (Anas), geese (Anser), swans (Cygnus)
    • landfowl: Galliformes order
      • chicken (Gallus)
      • basal Cracidae family: tropical and subtropical chachalaca, guan, and curassow in Central and Southern America
  • Neoaves
    • Mirandornithes superorder
      • Flamingo (Phoenicopteriformes order)
      • Grebe (Podiceps)
    • Columbimorphae superorder
      • Columbidae family: doves and pigeons, including mourning dove (Zenaida)
      • mesite (Mesitornithidae family)
      • Sandgrouse (Pteroclidae family)
      • Passerea

Passerea clade

• Bustard (Otididae family) and cuckoo (Cuculidae family)
• Crane (Gruiformes order)
• Shorebirds (Charadriiformes order):
  • Gulls (Laridae family) dive for fish: seabirds incl. gull (Larus), tern 35M (Onychoprion), kittiwake 15M (Rissa)
    • Arctic tern (Sterna paradisaea) has the longest migration at 40,000 miles a year. It breeds in the Arctic and winters in the Antarctic. It mates for life and lives up to thirty years.
  • Waders (Charadrii suborder) feed in coastal and freshwater mud
    • lapwing or tuit 20M (Vanellus)
    • plover (Charadriidae family): Pluvialis and Charadrius. Killdeer is a plover.
  • Scolopaci suborder
    • snipe 20M (Gallinago)
    • sandpiper: woodcock 10M (Scolopax)
  • Lari suborder: auks nest on sea cliffs and appear to swim underwater
    • auklet 20M (Aethia)
    • puffin 12M (Fratercula)
    • murre 40M (Uria)
    • little auk 20M (Alle)
• nightbirds (Strisores superorder)
  • Nightjar or nighthawk (Caprimulgidae family)
  • Apodiformes: swift (Apodidae) and hummingbird (Trochilidae)
• Phaethoquornithes clade
  • Eurypygimorphae superorder
    • Tropicbirds (Phaethontidae family)
    • Eurypygiformes order: sunbittern and kagu
  • waterbirds (Aequornithes superorder)
    • basal loon (Gavia)
    • Austrodyptornithes clade
      • Penguin order: Emperor penguin (Aptenodytes), gentoo penguin (Pygoscelis)
      • Procellariiformes order: albatross (Diomedea) and petrel
    • .
      • basal stork (Ciconiidae family)
      • Suliformes order: booby (Sula) and cormorant
        • Frigatebird (Fregatidae)
        • .
          • Sulidae family: booby (Sula) and gannet (Morus)
          • darter (Anhinga), great cormorant (Phalacrocorax), European shag (Gulosus)
      • Pelecaniformes order: pelican, heron or egret, ibis
• Landbirds: Telluraves superorder

Landbirds

• Accipitrimorphae order
  • Accipitriformes order: golden eagle (Aquila), bald eagle (Haliaeetus), harrier (Falco), goshawk (Accipiter), osprey (Pandion), harpy eagle (Harpia).
    • hawk and buzzard (Buteo) includes the red-tailed hawk which produces a rasping scream.
  • New World vultures (Cathartidae family): California condor (Gymnogyps), black vulture (Coragyps), turkey vulture (Cathartes)
• Owls (Strigiformes order) have night vision and excellent hearing and are mostly nocturnal.
  • Barn-owl (Tytonidae family) includes barn owl (Tyto), the most common owl.
  • True owls (Strigidae family): Burrowing owl (Athene) are often active during the day. Pygmy owl (Glaucidium).
• Cavitaves is mostly Picocoraciae
  • hornbill (Bucerotiformes order)
  • Picodynastornithes clade
    • rollers and kingfishers (Coraciiformes order)
    • woodpeckers and toucans (Piciformes order)
• Eufalconimorphae clade: falcon and caracara (Falconidae family) basal. Rest in Psittacopasseres clade:
  • Parrot (Psittaciformes order)
    • macaw (Arini tribe)
    • Amazon parrot: green parrot native to the Americas.
  • Passerine (Passeriformes): perching birds. Many have tendon locking to sleep without falling off. Basal suboscine (Tyranni suborder) includes hornero or ovenbird, which builds mud nests. Rest are songbird or oscine (Passeri suborder):
    • Corvides infraorder
      • Corvoidea superfamily: fantail (Rhipiduridae)
        • Corvid family: ravens/crows/rooks (Corvus), nutcracker (Nucifraga), blue jay (Cyanocitta)
      • Orioloidea superfamily: Old World oriole (Oriolus)
    • Passerida https://en.wikipedia.org/wiki/Passerida
      • Muscicapoidea superfamily
        • Old World flycatcher and chat (Muscicapidae) incl. waxwing (Bombycilla)
        • starling (Sturnidae family)
        • oxpecker (Buphagus)
        • mockingbird, thrasher, and catbird (Mimidae family)
        • thrush (Turdidae family)
          • bluebird (Sialia)
      • Certhioidea superfamily: wren (Troglodytidae family) and nuthatch (Sitta).
      • Passeroidea superfamily
        • Estrildidae family
          • Zebra finch (Taeniopygia): seed-eater in Australia and Indonesia. A model organism with a fully sequenced genome.
        • Old World sparrow (Passeridae family)
          • house sparrow (Passer)
        • Nine-primaried oscines
          • true finch (Fringillidae family)
            • domestic canary (Serinus)
            • cardueline finch subfamily
              • Hawaiian honeycreeper
              • grosbeak
          • Emberizoidea superfamily: new world
            • New World warbler (Parulidae family)
              • Setophaga e.g. Townsend’s Warbler
            • cardinal family
            • bunting (Emberiza)
            • New World sparrow (Passerellidae family)
            • yellow-breasted chat (Icteria)
            • New World blackbird (Icteridae family)
              • New World oriole (Icterus)
              • cowbird (Molothrus)
              • Meadowlark (Sturnella): North America, yellow-breasted

Mammals

Mammalia class: monotremes are basal. Other extant mammals are in Theriimorpha > Theriiformes > Trechnotheria > Cladotheria > Theria, which divides into Eutheria > Placentalia and Metatheria > Marsupials.

• Monotreme order (220 Ma) is basal.
  • platypus (Ornithorhynchus): egg-laying venomous mammal which secretes milk from its skin. It eats 20% of its weight a day and has electroreceptors. Duck bill, beaver tail, 10 sex chromosomes, fluorescent under UV light.
  • echidna (Tachyglossus)
• Marsupials have a pouch: opossums, Tasmanian devils, kangaroos, koalas, wombats, wallabies, bandicoots, sugar gliders (Petaurus).
• Placental mammals (Placentalia infraclass)
  • Atlantogenata magnorder.
    • Xenarthra superorder: American.
      • Pilosa order
        • anteater (Vermilingua suborder): giant anteater (Myrmecophaga)
        • Sloth (Folivora suborder): three-toed sloth (Bradypus) and two-toed sloth (Choloepus)
      • armadillo (Cingulata order)
    • Afrotheria superorder
      • Tethytheria
        • sea cow (Sirenia): manatee and dugong
        • Proboscidea
          • African bush elephant (Loxodonta) is the largest living land animal. Jumbo (“hello” in Swahili) lived at London Zoo in 1865, and was sold to P. T. Barnum in 1882.
          • Asian elephant (Elephas)
      • Afroinsectiphilia: aardvark, elephant shrew, tenrec
  • Boreoeutheria magnorder
    • Laurasiatheria superorder
    • Euarchontoglires superorder

Laurasiatheria magnorder

• Eulipotyphla order: hedgehogs, gymnures, shrews, moles, and solenodons
  • pygmy shrew (Sorex) is the smallest mammal at 1.8 g. It has a fast metabolism and eats twice its body weight every day.
• Bats (Chiroptera order) typically hunt at night.
  • Mexican free-tailed bat (Tadarida) can reach 100 mph and 10,000 ft. The Congress Avenue Bridge in Austin is home to the largest urban bat colony of 1 million bats. Female bats form maternity colonies in moist, warm places to raise their young. Each bat gives birth to one pup in June.
  • ghost-faced bat (Mormoops) has a flat nose and large ears.
  • fruit bats (Pteropodidae family)
  • bumblebee bat (Craseonycteris) is the shortest mammal at 3 cm and 2 g.
• Euungulata
  • Odd-toed ungulates (Perissodactyla order): horse/zebra/ass/donkey (Equus), Rhinoceros and black rhinoceros (Diceros), South American tapir (Tapirus)
  • Even-toed ungulates (Artiodactyla order)
    • Camelidae family: camel (Camelus) and llama (Lama)
    • boar/pig (Sus)
    • Moose (Alces)
    • Ruminants use foregut fermentation: antelope, gazelle goat (Capra), deer/elk (Cervus), giraffe (Giraffa)
      • sheep (Ovis) includes bighorn.
      • Bos: bovine cattle. Male bulls, female cows, castrated male steers, young female heifers, young male oxen or bullocks.
      • Bison: includes American buffalo.
      • buffalo (Bubalus) including water buffalo.
      • Musk deer (Moschus) has a musk gland producing muscone, a fixative which binds to the OR5AN1 smell receptor.
    • Hippopotamus
    • Cetaceans
      • Baleen whale filters krill
        • blue whale and rorqual (Balaenopteridae)
        • right whale (Eubalaena)
        • gray whale (Eschrichtius)
      • Toothed whale (Odontoceti parvorder): has a melon for echolocation.
        • Sperm whale (Physeter) has a spermaceti organ for echolocation. Its bile duct secretes ambergris, a perfume fixative which ages to a sweet, earthy scent. It contains the terpenoid ambroxide.
        • Giant beaked whale (Berardius)
        • river dolphin (Platanistidae)
        • Delphinoidea
          • oceanic dolphin (Delphinidae): second-highest encephalization in mammals
            • orca or killer whale (Orcinus): black-and-white
            • right whale dolphin (Lissodelphis):
            • bottlenose dolphin (Tursiops)
          • porpoise (Phocoena)
          • Monodontidae: Arctic
            • beluga whale (Delphinapterus): swims under ice and lacks a dorsal fin
            • narwhal (Monodon): has a long tusk
  • Ferae: Carnivora. Also pangolin, which has 114 chromosomes.

Carnivora order: African wild dog (Lycaon), wolverine (Gulo)

• Caniformia suborder
  • Canidae is most basal: wolves, coyotes, golden jackals (Canis), fox (Vulpes)
    • Dog. Young puppies.
    • Eastern wolf or timber wolf is Canis lycaon.
    • gray wolf, red wolf
    • Japanese raccoon dog or tanuki 狸 (Nyctereutes).
  • Arctoidea
    • bear (Ursidae) is very basal.
      • bear (Ursus): brown bear has a prominent shoulder hump. Polar bear can interbreed with the brown bear. Black bear is the smallest and climbs trees.
      • giant panda (Ailuropoda melanoleuca)
    • Pinniped clade is basal.
      • Walrus (Odobenus)
      • Eared seals (Otariidae family): common harbor seal (Phoca), northern fur seal (Callorhinus) and sea lions (Zalophus).
      • Earless seals (Phocidae family): elephant seal (Mirounga) and ~1000 Hawaiian monk seals (Neomonachus).
    • Musteloidea superfamily
      • red panda (Ailurus)
      • skunk
      • Mustelid family: weasel/ferret/polecat (Mustela), otter (Lontra), American mink (Neogale), wolverine (Gulo), Honey badger (Mellivora), American badger (Taxidea), Eurasian badger (Meles), snow forest marten (Martes), skunks (Mephitis and Conepatus)
        • sea otter (Enhydra) has the densest fur with 150,000 hairs per cm^2.
      • Procyonidae family: New World
        • raccoon (Procyon)
        • kinkajou (Potos).
        • coatimundi (Nasua).
        • ringtail (Bassariscus astutus)
• Feliformia suborder
  • Felidae family
    • Panthera: tiger, lion, jaguar, leopard, snow leopard. Bengal tiger is the national animal of India.
      • Siberian tiger subspecies reached a low of 250 adults in 2005 due to deforestation and poaching and has increased slightly since.
    • clouded leopard (Neofelis)
    • Small cats (Felinae subfamily) have a bony hyoid.
      • Caracal and serval (Leptailurus) are most basal. Native to Africa.
      • ocelot (Leopardus) is very basal.
      • Lynx is basal.
      • mountain lion or cougar (Puma)
      • cheetah (Acinonyx).
      • Cat (Felis). Young kittens.
  • Hyena
  • Mongoose (Herpestidae family)
  • Viverridae family are civets, nocturnal mammals which secrete civet oil containing civetone, which has a strong musky odor.

Euarchontoglires superorder

• Glires grandorder
  • Rodent order: mouse, rat, vole, dormouse (Glis), guinea pig (Cavia).
    • Hystricognathi infraorder
      • Phiomorpha parvorder is African
        • naked mole-rat (Heterocephalus) is the only eusocial mammal.
        • blesmol or mole-rat (Bathyergidae family)
      • Caviomorpha parvorder is New World.
        • capybara (Hydrochoerus) is the largest at 100 lb.
        • chinchilla is colonial, crepuscular, and native to the Andes mountains. It has the densest fur of all land mammals, with 20,000 hairs per cm^2.
        • New World porcupine (Erethizon)
        • guinea pig
        • tuco-tuco (Ctenomys) is subterranean.
        • Octodontoidea superfamily
          • plains viscacha rat (Tympanoctomys barrerae) is tetraploid.
          • Bolivian bamboo rat (Dactylomys boliviensis) reported to have chromosome number 118.
    • Anomaluromorpha suborder
    • Castorimorpha suborder
      • beaver (Castor). Beaver castor sacs produce castoreum to mark their territory. It is used as a leather scent.
      • kangaroo rat (Dipodomys) is native to western American desert.
    • Sciuromorpha suborder
      • squirrel (Sciuridae family) hoards many caches of food, especially nuts.
        • Tree squirrels: Eastern gray squirrel (Sciurus)
        • Ground squirrels (Marmotini tribe): marmots weigh around 18 lb. Chipmunks have a striped back. Prairie dogs are a keystone species. They form colonies and bark as a warning call. They make mounds that renew the soil and serve as bird nests.
        • Flying squirrel (Pteromyini tribe)
      • dormouse (Gliridae family) hibernates most of the year.
    • Myomorpha suborder
      • Muroidea superfamily
        • Spalacidae family: African mole-rat (Tachyoryctes), blind mole-rat (Spalacinae subfamily)
      • Muridae family: Gerbillus, true mouse (Mus)
      • Cricetidae family: hamster (Cricetinae subfamily), vole (Arvicolinae subfamily), lemming (Arvicolinae subfamily), muskrat (Ondatra), New World rats and mice (Cricetidae subfamily)
  • Lagomorpha order: hare and jackrabbit (Lepus), domestic rabit (Oryctolagus), cottontail rabbit (Sylvilagus), pika (Ochotona)
• Primate order 70 mya
  • Madagascar Lemur, African bush babies (Galago), Asian Loris have wet noses
  • Tarsiers (Tarsius) in Asia
  • simian (Simiiformes infraorder): monkeys and apes
    • New World monkeys Platyrrhini > Ceboidea superfamily.
      • Atelidae family
        • spider monkey (Ateles) is the most intelligent New World monkey. It has a long prehensile tail.
        • howler monkey (Alouatta) is most widespread in south America.
      • Cebidae family
        • Capuchin monkey (Cebus) or street organ monkey.
        • squirrel monkey (Saimiri)
    • Old world monkeys: baboon (Papio), macaque (Macaca), African vervet (Chlorocebus), African langur (Colobus)
      • Apes (Hominoidea superfamily)
        • Great apes (Hominidae family)
          • Orangutan (Pongo)
          • Homininae
            • Gorilla
            • Hominini
              • Chimpanzee/bonobo (Pan). Use stones to crack nuts and various sticks to fish for ants.
              • Human (Homo)

Traditional Chinese medicine

• Ginseng
• Goji berry
• chaíhú 柴胡
• Angelica
• Astragalus
• Forsythia
• Atractylodes
• Wolfiporia

https://en.wikipedia.org/wiki/Chinese_herbology#50_fundamental_herbs
https://en.wikipedia.org/wiki/Pharmacopoeia_of_the_People%27s_Republic_of_China
https://en.wikipedia.org/wiki/Monofloral_honey
https://en.wikipedia.org/wiki/Fragrance_wheel
https://en.wikipedia.org/wiki/List_of_Great_British_Trees
https://en.wikipedia.org/wiki/Phytochorion
https://en.wikipedia.org/wiki/The_Jepson_Manual
https://en.wikipedia.org/wiki/IUCN_Red_List