Understanding Taxonomy

• Taxonomy is the science of classifying and organizing living things
• Classification aims to provide a practical way to organize and communicate information about organisms
• Classification reduces confusion, provides clues about structures and indicates lines of descent
• Classifying helps monitor ecosystem health, changes and inspires new technologies

History of Classification

• Aristotle, a Greek philosopher (322 B.C.), divided organisms into plants and animals and further divided animals by their movement (walking, flying, swimming)
• The Aristotelian system was used until the 1600s
• Carolus Linnaeus classified organisms by similarities in form, with closer relations indicating more common features
• Linnaeus designed a system assigning each organism a 2-part scientific (Latin) name, known as binomial nomenclature
• The "Genus" is always capitalized with the species uncapitalized
• Scientific names are written in italics or underlined

Levels of Classification

• Rank is the term for categories used to classify organisms
• Eight ranks distinguish degrees of similarity
• Organisms are classified according to 6 kingdoms within 3 domains
• Taxon is the named rank for each organism
• The number of members in each taxon decreases as you proceed down the ranks

Human Taxonomy

• Domain: Eukarya, eukaryotic cells (animals, plants, fungi, protista)
• Kingdom: Animalia, heterotrophs, sexual reproduction, move, multicellular
• Phylum: Chordata, have a vertebrate (dorsal nerve cord)
• Class: Mammalia, give live birth, warm-blooded, have hair, produce milk
• Order: Primate, have thumbs
• Family: Hominidae, bipedal, walk on 2 legs, stand at 4–7 million
• Genus: Homo, large cranial capacity, use tools - 2.75 million
• Species: sapiens (sapiens), appear around 300,000 years ago

Species

• The most used definition of a species is the biological species concept which focuses on organisms that interbreed freely and produce viable, fertile offspring.
• The morphological species concept classifies organisms via similarities in anatomy
• The phylogenetic species concept focuses on evolutionary relationships

Charles Darwin

• Darwin spurred a new era of taxonomy with "The Origin of Species" (1859)
• He identified natural selection as a driving force behind evolution, focusing on groups descended from a common ancestor
• Attempts were made to find "missing links" between higher taxa, exemplified by Archaeopteryx, the fossil between reptiles and birds

Modern Taxonomy

• Advances in molecular biology impacted taxonomy, now biologists clone and sequence organism DNA
• DNA sequence comparisons are used to estimate relationships and construct classification systems

Determining Relatedness in Species

• A goal of taxonomy is determining the evolutionary history of groups
• This is done by comparing current species to species throughout history, using several forms of evidence:

Anatomy/Morphology

• Evolutionary history can be determined by studying living organisms or fossils.
• Features with a common evolutionary origin are homologous, such as the bones in a human arm, cat's leg, bat's wing or whale's flipper
• All of the above appendages perform different jobs but have the same bone arrangement
• Homologous structures differ from analogous structures which perform the same/similar functions via a similar mechanism but evolved separately (ex: bird vs insect wings)

Development

• Comparing early developmental stages can reveal relationships unseen by only comparing adult organisms
• Some parts appear and disappear (gills, tail), while others lose function (vestigial)

Biochemistry

• Scientists compare molecules from organisms
• Comparisons of macromolecules like proteins indicate genetic similarities/differences

DNA

• Study of DNA can determine percentage of genes in common for species, ex: humans/chimpanzees DNA share 98%
• DNA analysis determines time since two species diverged from a common ancestor
• Divergence is predicted by studying mitochondrial DNA (passed from mother to offspring), it mutates at a predictable rate

Phylogeny

• Classifying presents a hypothesis about the evolutionary history (phylogeny)
• Phylogeny information is organized in a phylogenetic tree (cladistics)
• The base of the tree represents the oldest ancestral species
• The upper branches are present-day descendants
• Forks indicate species splitting off into two new species
• New features from a primitive ancestor are called derived characteristics

Kingdom Fungi

• Fungi cannot photosynthesize, are eukaryotic, heterotrophic (saprotrophs/decomposers) which feed on organic matter
• They release digestive enzymes externally, then absorb the nutrients (external digestion)
• Fungi can be unicellular (yeasts), but are usually multicellular (molds, mildew, mushrooms)
• Fungal cells have cell walls made of chitin

Reproduction

• Fungi reproduce sexually and asexually but produce spores
• Spores are the main means of reproduction and may be asexual (mitosis) or sexual (meiosis)
• Spores have a protective outer coating that prevents drying out, and are produced in trillions that spread by wind, water, or animals
• If a spore lands in a suitable environment, it can grow into a new organism
• A germinating fungal spore produces hyphae, a network of microscopic filaments found underground
• Hyphae are also referred to as mycelium
• A hyphae piece breaking off will grow into a new mycelia, a type of asexual reproduction known as fragmentation

Helpful Fungi

• Fungi are a significant food source (mushrooms, soy sauce)

Saccharomyces Cerevisiae

• Well studied eukaryotic organism used in baking, winemaking and brewing (alcohol fermentation)
• Fungi are decomposers and are essential in ecosystems
• Many produce antibiotics (penicillin, cyclosporin)

Fungi Mutualistic Relationships

• Plant Roots for mycorrhizae: Fungal hyphae help plants absorb nutrients (increase surface area), and plants share carbohydrates/amino acids
• Cyanobacteria or Green Algae for lichens: Fungal mycelia provide structural support and carbon dioxide/water, the autotrophic partner shares carbohydrates, and serves as an important composite organism for primary succession

Harmful Fungi

• Fungi cause disease in humans, plants, and animals, some produce fatal toxins Examples:
• Athlete's foot is a fungal infection of the skin characterized by itchy red skin. It is spread through contact with skin scales or fungi in dampness.
• Aspergillosis is fungal and comes from breathing in outside mold spores. Symptoms include wheezing, shortness of breath, and cough.
• Candidiasis is a fungal infection caused by a yeast called Candida, which grows in moist location i.e. the mouth, throat, gut, and vagina. An infection can occur if Candidia grows out of control or enters into another area of the body.

"Magic Mushrooms"

• These mushrooms contain hallucinogens (psilocybin, psilocin) and can cause hallucinations, anxiety, fear, nausea, and muscle twitches accompanied by increased heart rate and blood pressure

Death Cap Mushrooms

• This mushroom causes most fatal poisonings and contains toxins that damage the liver and kidney
• Cooking cannot inactivate the toxin
• Symptoms occur 8-12 hours after ingestion as cramping, abdominal pain, vomiting, watery diarrhea, dehydration
• Symptoms can resurface within 72 hours of consumption and cause severe illness (low blood pressure, jaundice, liver/kidney failure, seizures, delirium, convulsions, coma)
• Organ transplants may be required

Cordyceps

• Grows in humid temperate or tropical areas throughout Asia, and is parasitic to arthropods
• It replaces tissues with spore-bearing structures which then burst out for reproduction
• Cordyceps can cause altered and erratic behaviour in arthropods

Classifying Fungi

• Zygospore Fungi (Zygomycotes): Includes bread molds, they form zygosporesafter the mating of two opposite hyphae strains (+ and -). Some produce stolons (horizontal) and rhizoids (downward).
• Club Fungi (Basidiomycotes): Includes the mushrooms that grow on lawns They have short-lived reproductive structures called basidiocarps (fruiting bodies) that form basidiospores on basidia
• Sac Fungi (Ascomycotes): Largest group of fungi, includes mildew and single-celled yeasts Sac fungi form small finger-like sacs (asci) during sexual reproduction to contain spores (ascispores)
• Imperfect Fungi (Deuteromycotes): Do not appear to have a sexual phase, developing asexually from spores called conidia with some producing antibiotics or are used in the production of foods

Kingdom Animalia

• Eukaryotic, multicellular heterotrophs that reproduce sexually. They are capable of movement.
• The kingdom is divided into two broad groups:
  • Invertebrates (majority) which do not have a backbone (leeches, clams, insects)
  • Vertebrates: Have a notochord (rod-shaped structure extending the length of the body which replaces the spine.) (fish, amphibians, birds, reptiles, mammals)
• Major characteristics used to classify animals:
  • Body organization: cells organized into tissues, organs, organ systems etc
  • Body layers: three types: ectoderm (outer, skin, nervous system), endoderm (inner, lining of body cavity) and mesoderm (middle layer, circulatory system)
  • Symmetry: radial, bilateral and asymmetrical
  • Digestive tract/gut: one opening (closed, hydra) or two openings (open, earthworm)
  • Coelom: fluid-filled body cavity which allows for development of more complex organ systems

A Quick Look at Animals

• Sponges (Porifera) are live permanently attached to one surface
• Cells are organized simply with one opening and two layers of cells with no tissue or organs
• Jellyfish, Corals and Anemones (Cnidaria): Two cell layers and a single opening with simple nervous/muscle tissue
• It can then swim and capture prey, use digestive enzymes, and does not have special excretory or respiratory systems
• Flatworms (Platyhelminthes): Parasitic tapeworms/flukes as well as free living planarians
• The digestive system is a closed pouch with one opening and a simple excretory and nervous system
• Segmented Worms (Annelida) - Earthworms and leeches
• Their bodies are divided into ringed segments for excretion/circulation/nerve control. Segmentation marks an evolution of more complex animals
• Mollusca: Squid, Snails, mussels which has soft bodies and a hard outer shell

Joint-Legged Animals (Arthropoda)

• Arthropods resemble annelids with similar larval stages
• As arthropods evolved they developed distinct differences from annelids with fewer body segments and a hard external cuticle for an exoskeleton
• Legs are divided into moveable segments connected by joints. Separate muscles are arranged into groups for specific movements.
• Has strongly developed jaws and better developed nervous systems and sense organs

Starfish or Sea Star (Echinodermata)

• All are marine
• Include starfish, sea urchins, sea cucumbers and sand dollars
• Adults are radially symmetrical, larvae are bilateral and contain a coelom

Chordates (Chordata) At some stage of life all chordates have

• A dorsal nerve cord from which other nerves branch
• A notochord, or rod of cartilage, which runs along the dorsal length of the body
• The notochord only occurs in the embryo
• A backbone of cartilage or replacement of the notochord by bone
• Gill slits in the pharynx, or throat which appear in terrestrial vertebrates

Kingdom Archea

• Archaea are single celled (unicellular) prokaryotes that live in very extreme environments (extremophiles)
• Thrive in cold/hot water and land masses (-4°C, 95°C), acidic/basic waters (ph 2, ph 12), and salty waters (25%)
• Some are anaerobic and obtain energy from inorganic molecules (chemotrophs), others are aerobic and obtain energy from organic molecules (heterotrophs) or light (phototrophs)
• Bacteria and Archaea look similar but biochemically and genetically they are very different
• Genes, RNA, cell membranes and the cell wall differ but contain lipids and pseudopeptidoglycan (protein) that allow them to survive in extreme conditions
• Archaea is unique and scientists exploit their ability to do this when conducting experiments that require harsh processing, PCR (polymerase chain reaction)
• Major Phyla:
  • Euarchaeota: Contains three groups of Archaea including
    • Methanogens (methane producing) live in oxygen free environments and produces methane as a waste product, utilizing inorganic molecules (CO2, N gas or H sulfide) and are found below swamps and sewage disposal plants
• Ex: Methanococcus jannischii isolated from a "white smoker" hydrothermal vent some 2600 m deep on the bottom of the Pacific Ocean - Halophiles (salt loving) that live in extremely saline environments (up to 25% where seawater is 3.5% for example), as well as other hypersaline water bodies
• Ex: Halobacterium salinarium lives in the Great Salt Lake - Thermophiles (heat loving) that live in extremely hot water or landmasses such as hot coals or rocks below the earth’s surface
  • Crenarchaeota: Most organisms are
    • Thermoacidophiles (heat and acid loving) found in a very acidic hot water environments growing to 80°C and using CO2 or sulfur from hot sulfur springs
• Found in hot springs, volcanoes, and deep hydrothermal sea vents

Archea

• Some are found in broad range of habitats (soils, oceans, marshlands) and are numerous in oceans and plankton (most abundant)
• It plays a major role in both the carbon and nitrogen cycle
• Some have recently been found on human skin and appears to be part of the microbiome
• No clear examples of archaea pathogens have been identified

Kingdom Bacteria

• All are prokaryotes and live as single cells (unicellular)
• Some exist in colonies
• They reproduce mainly asexually by binary fission but have sexual reproductive stage ( conjugation
• They are heterotrophs performing photosynthesis

Importance of Bacteria

Advantages:

• 1. Industry: Used in the production of cheese, vinegar and yogurt
• 2. Agriculture: Used as natural pesticides or added to enrich nitrogen content (nitrogen fixation – conversion of atmospheric nitrogen to nitrates)
• 3. Decomposers: Recycle organic material with some bacteria in the intestines which aids in the digestion process.
• 4. Genetic Engineering/Biotechnology/Recombinant DNA: Can be used to study cell metabolism with bacteria, engineered to produce insulin/antibiotics/hormones
• 5. Fighting Disease: Produces substances (antibiotics) to inhibit the harmful organisms, ie. stretomycin and erythromycin) which prevents us from being affected.
• 6. Bioremediation: Destroys, transforms or immobilize contaminants, ie pseudomas is used for wastewater sewage, or Flavobacterium used for toxic wood preservative

Bacteria

• A symbiotic relationship is a relationship between two organisms where In cases in which both partners benefit the interaction it is referred to as mutualism. Disadvantages:
• Spoilage of Food which can cause food to spoil/harmful: Clostridium botulinum (Botulism), Salmonella, E. coli
• Disease: Pathogens which is termed parasites which benefits and harms bacteria/host producing toxins and It is not harmful to the organism itself but only to other organisms. Toxin Examples:
  • Endotoxins: Released when certain bacteria split which causes fever/vomiting/diarrhea, rash - Seldom fatal and an Ex: Salmonella
  • Exotoxins: Released by living bacteria multiplying that travels which can be Often fatal/highly toxic and a Ex: Botulism which can kill a million with 1 gram.

Classification of Bacteria

• Shape (three types): Coccus/cocci (round), Bacillus/bacilli (rod), Spirillus/spirillum (spiral)
• Shape patterns (aggregate): Singles(mono), doubles (diplo), chains (strepto) and clusters (staphylo)
• Metabolic Needs: Either Heterotrophs or Autotrophs and if it needs oxygen whether Aerobic or Anerobic, Special food sources like carbon / Nitrogen.

Aerobic Examples

• Aerobic Needs oxygen and Obligate anerobe die when exposed and Facultative anerobe can survive with and without
• Phototroph’s Use light for energy and Chemotroph Use inorganic compounds, Heterotroph/Saprotroph needs dead organisms
• Thermophile’s will grow above 50C and Psychrophiles best at 15C and Mesophiles will best best at temperature

Describes The Appearance of a Colony in a Petri Dish

• Elevation
• Form
• Colour
• Margin

Bacteria Reaction

• Gram/Retain + crystal violet stain (purple) layer contains thick protein (peptidoglycan) in cell wall
• Gram Doesn’t retain + crystal violet stain (pink) - layer contains cell wall/ thin protein (peptidoglycan)
• Presence or Absence - Used for movementFlagellum
• Capsules: Used for cell protection + usually has a carbohydrate layer
• Spore Formation: Used as a dormant form of many Bacteria that is highly resistant

Kingdom Plantae

• Plants are multicellular, eukaryotic, and autotrophic, producing their own food through photosynthesis. Plant cells have cellulose cell walls, which humans cannot digest.
• Plants alternate two forms (alternation of generations) with a:
  • Haploid Form called a gametophyte which produces gametes as reproductive cells as well as,
  • Diploid Form called a sporophyte which results in the union of two gametes.
• Major Divisions for seed and non-seed plants

Vascular and Nonvascular Plants

• Most plants consist of roots, stems and leaves where Roots penetrate the soil and reach a water source, leaves create a greater surface for photosynthesis and Stems supply tissues that support the leaves
• Plants also carries out a constant stream of water and nutrients + consist of cells from vascular tissue to conduct tissue throughout the plants.
• Xylem transports water and minerals, while Phloem transports sugars
• Evolution of vascular tissue has increased the size plants

Non Vascular Plants (Mosses and their Relatives), Mosses

• Lack of vascular tissue and developed roots where diverse habitats are covered like bugs, exposed rocks, deep shade in which remains in small size by transferring from movement of diffusion concentrated by water

Seedless Vascular Plants ((Ferns and Their Relatives)

• .They Developed vascular tissue that allowed them to grow
• Sporophyte generation (fronds) is in its dominant stage and Produces spores located at Fronds.
• The Gametophyte generation is where new spores develop into plants

Vascular Plants (disperse by seeds)

• New development of plants without the need of water when dispersed with seeds
• Seeds providing food and protection against harsh conditions
• Two seed Producing Plant Groups: Gymnosperms (aka overgreens): the “naked seeds” which consists of pollen trapped by the female cone and undergoes in the development
• Angiosperms: Encodes seeds protects the seeds inside as developed offspring.

Prokaryotes and Eukaryotes Kingdoms

• The arrangement of cell division is both singular and multiple where Single chromosome and membrane or single division but no cell bound on replication
• Has a cell division in binary fission or mitosis which causes one division and replication sexually

Oxygen Needs

• Prokaryotes: Anaerobic (no oxygen) where aggregate / colony that creates a true multicellular and specialized ecosystem
• Eukaryotes - Aerobic needed: (Oxygen) for an Unicellular where creates an advanced Colony

General

• Protista are Eukaryotic, Microscopic (unicellular) and multicellular when creates in wet environment with the kingdoms divided into 3 with plants, animals, fungus as nutrients, The difficulty of its protists is they don’t fit inside normal guidelines + known to cause disease
• Protists: Plant-Like Protist (Algae) : They are autotrophs that contains sunlight with Chloroplast which will only produce water only. A unicellular ecosystem which is why only 80% Global Oxygen
• Protist: Animal:Heterotroph which is how the move around to require nutrients: pseudopods, Absorbed Nutrients which has no movement, where they for spores or reproduce

Fungi

• They’re are unicellular that contains cool and shady, moist surface conditions and has slime molds/ water molds/Saprophytes

Reproduction in Bacteria

• The reproduction of Bacteria is known as asexually- Binary fission or replication or sexual conjugation Fission is a replication to a small degree like dividing a cell, genetic code but does require some time
• The two cell strand will then begin developing through a midsection of the Prokaryote and when it becomes separate a individual strand

Cell Reproduction (conjunction)

• Used in organism where genes/receptors will form new connections that is made when altered where then it can move when necessary where it becomes the cell will be the offspring when then transfers and duplicates, It allows for the survival of variation on traits in organism.