Phylogenetic Tree

This is a very complex version of a phylogenetic tree, but it doesn't need to be hard to understand or follow. The following blog breaks down the phylogenetic tree into five sections and six kingdoms: Archaebacteria, Eubacteria, Protista, Fungi, Plantae, and Animalia. Each post will contain brief but useful information regarding each kingdom, as well as characteristics and examples of each. This post will be the starting point. Starting with Archaebacteria and Eubacteria, each post afterward will be what the previous kingdom evolved into over time.

Archaebacteria & Eubacteria

Archaebacteria: the oldest living organisms on Earth
Three phyla - methanogens, extreme halophiles, thermoacidophiles

-Body plan – prokaryotic and unicellular
-Found in very harsh, extreme conditions (bottom of sea, volcanic vents)
            -the very beginning of evolution
            -only survivor of early Earth’s atmosphere that had little oxygen
            -no previous event led to the evolution of the kingdom
-Metabolism – mostly autotrophic
            -capable of self-nourishing by converting inorganic materials to nutrients
-Digestion – doesn't have a digestive system
-Circulation – no heart
-Respiration – obtain energy from carbon dioxide, oxygen, and sun
-Nervous – no brain
-Reproduction – asexual
            -binary fission – bacterial DNA replicates, pinches off at center, divides into two- each with a copy of the DNA
            -quick, some species divide once every 20 minutes

Phylum: Methanogen
-Live in environments without oxygen
            -swamps, deep-sea waters, sewage facilities, stomachs of cows (hence, why they produce methane as a waste product)
-Obtain energy from carbon dioxide and hydrogen gas
-Example: Methanosarcina barkeri

Phylum: Extreme halophiles
-“Salt loving”
-Live in areas with high salt concentration
            -Dead Sea, Great Salt Lake
-Cannot tolerate unsalty environments
-Bacteriorhodopsin – sunlight as a source of photosynthetic energy
Example: Halobacterium- Halococcus

Phylum: Extreme Thermoacidophiles
-“Heat and acid loving”
-Live in hot, acidic waters
            -sulfur springs or deep-sea thermal vents
            -temps of 160 degrees Fahrenheit or higher
            -pH levels of 1 or 2 (concentrated sulfuric acid)
-Example: Picrophilus torridus

Eubacteria: the common bacteria
More complex and common than Archaebacteria
Four phyla - cyanobacteria, spirochetes, proteobacteria, and gram-positive bacteria
-Found everywhere around us (body, food, etc.)
-Classification – gram staining

            -using 4 liquids: crystal violet, iodine, safranin, alcohol wash
            -purple (crystal violet): gram-positive – thick layer of peptidoglycan, but susceptible to antibiotics
            -pink (safranin): gram-negative – thick lipid bilayer makes it selectively permeable and not as susceptible to antibiotics
-3 general shapes: bacilli, cocci, and spirilla
            -bacilli – oblong and thick
            -cocci – round
            -spirilla - spiral

-Body Plan – prokaryotic, mostly unicellular
-Divergent event - when little amounts of oxygen started appearing in the Earth's atmosphere, eubacteria started evolving from the extreme archaebacteria
            -Some of these bacteria used the oxygen that the archaebacteria expelled as a waste product
-Metabolism – autotrophic and heterotrophic, lithotrophic (inorganic electron donors), organotrophic (organic compounds as electron donors), chemotrophic (energy conservation)
            -Example Autotroph: phototrophic cyanobacteria
            -Example Heterotroph: pseudomona
-Digestion – doesn’t have a digestive system
-Circulation – no heart
-Respiration – use oxygen and chemicals to obtain energy
-Nervous system – no brain
-Reproduction – asexual
            -binary fission, formation of identical bacterial cells

Phylum: Cyanobacteria
-Use sun’s energy to make food
-Give off oxygen as byproduct
            -allow aerobic organisms to survive
-Found in water, once thought to be blue-green algae
-Certain cyanobacteria grow in chains that sometimes form heterocysts
            -heterocyst - specialized cells that contain enzymes that fix atmospheric nitrogen
-Causes eutrophication - sudden increase of cyanobacteria due to a high availability of nutrients
-Example: Prochlorococcus

Phylum: Spirochetes
-Gram-negative, spiral-shaped, and heterotrophic
-Some live with oxygen (aerobic), others do not (anaerobic)
-Some are parasitic, some are free-living
-Treponema pallidum causes syphilis
-Example: Borrelia burgdorferi (causes Lyme Disease)

Phylum: Gram-Positive Bacteria
-Produces yogurt by growing and fermenting in milk (produces lactic acid)
-Produces antibiotics
-Found in oral cavity and intestinal tract where they retard the growth of disease-causing bacteria
-Lactobacilli releases acid to stop tooth decay
-Example: Streptococcus (causes Strep throat)

Phylum: Proteobacteria
-Largest phylum - divided into three groups
1. Enteric bacteria
            -gram-negative, heterotrophic bacteria found in the intestinal tracts of animals
            -aerobic or anaerobic
            -produces vitamins and enzymes that help break down food
Example: Escherichia coli - produces vitamin K and assists enzymes in breaking down food

2. Chemoautotrophs
            -gram-negative bacteria that extracts energy and breaks down minerals
3. Nitrogen-fixing bacteria
            -fix nitrogen, usually found in symbiotic relation with the roots of plants


Protista: "the very first"
Eukaryotic - have a nucleus

-Body Plan -mostly unicellular, some multicellular (algae)

-Divergent event -
-80 different groups have long, independent evolutionay histories that go back to more than 2 billion years ago
-Some show that they are derived from complex bacterial ancestors
-Many of the groups are not closely related to one another at all
-Start and foundation of kingdoms fungi, plantae, and animalia

-Metabolism- autotrophic and heterotrophic
-Heterotrophic – flagellates (animal-like, ingest food, mobile)
-Autotrophic – algae (green, red, brown, golden)

-Digestion- intracellular
-No consistent digestive tract
-Some protists like paramecium use cilia to move particles from its mouth pore and into its gullet
            -Food pinches off into vacuoles that move through the cytoplasm
            -Waste comes out through the anal pore
-Amoeba digest through endocytosis and produce waste through exocytosis
-Photosynthesis in algae

-Circulation- no heart

-Respiration- no lungs, but oxygen and materials are transported through protists through diffusion

-Nervous- no brain

-Reproduction – asexual, sometimes sexual
-Binary fission
-Conjugation, where the only diploid cell is the zygote
            -undergoes meiosis
-All other cells are formed by mitosis

-Plasmodium (causes malaria)

-Macrocystis (giant kelp)
            -one of most complex protists

Phylum: Ciliaphora
-Have tiny hair-like structures called cilia that beat back and forth
-Enables the protist to move through aquatic environment & capture food
-Ten pairs of microtubules
            -9+2 config, nine pairs form circle, tenth pair in circle
Example- Paramecium

Phylum: Euglenophyta
-Live in water
-Have two flagella for movement
-Chloroplasts for photosynthesis
            -Heterotrophs if kept in dark
-Eyespot for sensing light and dark
-Pellicle - like a cell wall, helps maintain shape
Example - Euglena

Phylum: Rhodophyta
-Red algae
-Presence of the pigment phycoerythrin, reflects red light and absorbs blue
-Different concentrations of the pigment
-Important in the formation of tropical reefs


Fungi: in air, in water, on land, in soil, and on plants and animals... everywhere!
-Determine the types of plants and eventually the types of animals in an area
-Some are microscopic, others are extremely large
-Million plus species of fungi, only identified 5% of all fungi

Body plan-
-Almost entirely multicellular (composed of filaments called hyphae), some have two nuclei (multinucleate)
-Rarely unicellular
Example multicellular: mushrooms
Example unicellular: yeast (Saccharomyces cerviseae)

Divergent event-
-1 billion years ago
-Fungal cell wall composed of glucans and chitin – the only organisms that combine these two molecules in their cell walls
-More complex than protists, but protists were the start of fungi development
-Most fungi share a common ancestor with kingdom Animalia, not Plantae (surprisingly)

-Heterotrophic – absorption
            -saprophytic – secrete enzymes to break down dead organic matter
            -parasitic – obtain nutrients from living hosts

-Extracellular – secrete enzymes and absorb nutrients provided

Circulation - no heart

-yeast requires anaerobic respiration
            -use glucose and oxygen to produce carbon dioxide, water, and energy

Nervous - no brain

-sexual or asexual (spores, budding, binary fission)
            -zygote is the only diploid cell, two nuclei do not fuse – they coexist (dikaryoitic stage, unique to fungi)


-Rhizopus (mold on breads, fruits and vegetables)

Phylum: Basidiomycota
-Most mushrooms, shelf fungi, and puffballs
-Most familiar, called “club fungi”
            -account for almost a third of all identified fungi
-Fruiting bodies are visible
-Many are poisonous (genus Amanitas)
Example - Amanita Muscaria - hallucinogenic mushroom, often for drug-use

Phylum: Zygomycota
-Black bread mold
-Decomposes bread, fruits, vegetables, and decaying animals
-Produces a fuzzy, black growth on its substrate
-Form a zygospore as part of their sexual reproduction, but can reproduce asexually also
-Harmful if eaten!


Plantae: otherwise known as plants...

-trees, herbs, bushes, grasses, vines, ferns, mosses, and green algae
-scientific study of plants is called botany
-350,000 species of plants

Body plan-
-Multicellular with cell walls made of cellulose

Divergent event/evolution-
-There are claims that all plants evolved from a single type of algae that originally came from bacteria
-Evolved through endosymbiotic events between 2500 and 1000 million years ago
-Main difference is the cell wall and chloroplasts that allow plants to perform photosynthesis

-Autotrophic – able to make their own source of energy (glucose) from the sunlight, water, and carbon dioxide (photosynthesis)

-Intracellular – use digestive enzymes to break down food
-Absorb nutrients from digested food

-Gases enter and exit plants through stomata in leaves
-Water and dissolved minerals enter plants through their roots from the soil
-Travel upward in the plant in xylem vessels
-Transpiration – evaporation of water from leaves
-Water column stays intact because of cohesion property of water
-Carbohydrates travel downward in phloem
-Water pressure forces substances from cell to cell

-Passive – releases energy that is captured and stored in plants
-Energy stored in the form of glucose is released for use in plant metabolism
-Glucose is broken down, releases carbon dioxide
            -if oxygen is present, products will be used in mitochondria
            -if oxygen is not present, fermentation occurs
-Light and dark reactions (photosynthesis)
            -light reactions use light energy from the sun and water to produce ATP and NADPH
            -dark reactions (Calvin Cycle) uses the ATP and NADPH from the light cycle and carbon dioxide to produce G3P that is used to produce sugars

-no brain, but DNA in the nucleus codes for proteins that allow all cell functions to occur properly

            -kalanchoe leaves perform mitosis at meristems along their leaf margins that produce little plants that fall off and can be independent 
            -rhizome underground stems arch over and take root at their tips, growing a new plant
            -sporophytes, conifers (staminate and ovulate cones), flowers (pollination)

-Rosaceae Rosa
-Pinaceae Pinus

Phylum: Bryophyta
-Non-vascular plants – cannot transport fluids through their bodies
-Must rely of surrounding moisture to do this job for them
-Lay foundations for other plant growth, prevent erosion, and contribute to green appearance of forests
-Reproduce by spores, never have flowers
-Grow low to the ground, on moist rocks, and on other plants
-Example - Moss

Phylum: Coniferophyta
-Reproduce from seeds instead of spores
-Seeds are “naked” – not covered by an ovary
-Seeds are produced in a cone-like structure called a conifer
-Never have flowers
-Have needle-, scale-, or awl-like leaves
-Grow in extreme conditions, can survive in extreme cold

Phylum: Anthophyta
-Flowering plants
            -Class: Monocotyledonae
-Have an embryo with a single seed leaf
-Narrow leaves with parallel veins and smooth edges
-Hollow or soft stems
-Flowers are arranged in threes
 -Example - Orchids

            -Class: Dicotyledonae
-Presence of two seed leaves
-Broad leaves with net-like veins
-Example - Rhododendron catawbiense


Animalia (Metazoa): otherwise known as animals...
-Animalia cells do not contain cell walls that characterize plant cells
-Nine to 10 million species of animals
-THE most complex organisms on Earth

Body plan-
-ALL are multicellular

Divergent event-
-Charles Darwin’s Theory of Evolution
            -natural selection (survival of the fittest)
-Developed from the first organisms on Eath (bacteria)
-Grew more and more complex
-Related to fungi more than any other kingdom
-Only the ones who had the traits for their environment survived and moved on to reproduce

-ALL are heterotrophs (obtain energy from or by consuming other organisms)
-ALL require oxygen for metabolism

-Intracellular – most have a digestive system
            -consists of: mouth, esophagus, stomach, liver, small/large intestine, pancreas, colon, rectum

-Closed AND open
            -Closed – blood closed at all times within vessels of different size and wall thickness, blood pumped by heart through vessels, does not fill body cavities
            -Open – pumped by heart into body cavities where tissues are surrounded by blood
-pumps, three- and four-chamber hearts

-Gills – extracts dissolved oxygen from water
            -fish, other aquatic animals
-Book lungs – look like books, maximize surface area with air/gas exchange
-Lungs – mouth, nose, oropharynx, nasopharynx, larynx, trachea, bronchi, bronchioles, alveoli
            -tetrapods, few fish, few snails
            -two lungs on either side of heart in complex mammals (humans)

            -frontal, parietal, occipital, temporal lobes
-Nerve net
            -simple nervous system found in cnidaria and echinodermata phyla
            -found in insects such as the cockroach

-Oryctolagus cuniculus (Rabbit)

-Chinchilla lanigera (Chinchilla)

Phylum: Nematoda
-80,000 known parasitic worms
-Bilaterally symmetrical
-Body cavity is pseudocoel (its body flied is under high pressure)
-No circulatory system
-Feed on everything
-Don't usually live in dry places
Example- Roundworm

Phylum: Mollusca
-110,000 known species
-Most diverse in the world
-Mantle with cavity used for breathing and excretion
-Has a pair of kidneys
-Most have a shell of some sort
-Pearls from oysters were among the earliest forms of money
Example- Snail

Phylum: Annelida
-15,000 individual segmented worms
-Body possesses three separate sections: a prosomium, a truck, and a pygidium
-Has a true closed circulatory system
-No true respiratory organs
Example- Common earthworm

Phylum: Chordata, Subphylum: Vertebrata
-50,000 species of animals
-Structure is composed of numerous tissues and organs
-Have vertebrae - hollow structures which combine to make the spinal column
            -made of cartilage or bone and cartilage
            -surrounds and protects the central nerve cord

Class: Myxini
-Live in deep water
-Feed on carrion (dead, rotting flesh) as well as polychaete worms
-Use tentacles around their mouths to locate prey
-Single nostril opens into pharynx
-Example- Hagfish

Class: Cephalspidomorphi
-Hatch/breed in fresh water, mature in marine
-Parasitic as adults - have a suction-like mouth that grasps onto other fish and puts a hole in their skin
-Have buccal glands that secret an anticoagulant to ensure free-flowing food source
-Larvae are called ammocoetes
-Example- Lamprey

Class: Chondrichthyes
-Paired nostrils
-Skeleton is completely cartilage - no endoskeletal bone
-No swim bladder
-Example- Stingray

Class: Osteichthyes
-Endoskeleton made up of bone
-Jaws and paired appendages
-Arose in freshwater, moved into saltwater
-Example- Ocean Sunfish

Class: Amphibia
-Ectothermic - regulates body temperature by moving to different climates within its environment (cold-blooded)
-Eggs must be laid in water or in a very moist environment
           -young develop with gills and live in the water as tadpoles
-Example- Poison Dart Frog

Class: Reptilia
-Some of the first land-only vertebrates
-Ectothermic, heliotherms - can regulate body temperature using solar radiation
-Example- American Crocodile

Class: Aves
-Four-chambered heart
-Bill instead of teeth
-Endothermic - able to maintain a constant body temperate, regardless of its surroundings
-Example- Bald Eagle

Class: Mammalia
-Has hair/fur
-Mammary glands to give milk to young
-Dental bones
-Example- Dogs (Yorkshire Terrier)