Reviewer 4th Quarter - Gen Bio
Taxonomy
● Terms
○ Taxonomy
■ Studies organism with the purpose of arranging them into groups.
○ Identification
■ Process of characterizing new organism
○ Classification
■ Process of arranging organisms into related groups. Uses the hierarchy of classification
that is accepted worldwide.
○ Systematics
■ Science that studies how living and extinct organisms are related to each other through
evolution
○ Hierarchy of Evolution
■ Concept that refers to how living things are grouped and organized at different levels, each
with its own features and evolutionary changes.
■ This system is called the genealogical hierarchy.
○ Phylogeny
■ Type of classification groups organisms based on evolutionary history or genealogy. It shows
how they are related, where they may have evolved from, and which species are their closest
relatives.
○ Phylogenetic Tree
■ AKA Tree of Life
■ Show the evolutionary pathways and connections among organisms
○ LUCA (Last Universal Common Ancestor)
■ Base of the Phylogenetic Tree
■ Can be branched into 3 domains: Archaea, Bacteria and Eukarya
○ Cladistics
■ Analytical method of refining the evolutionary classification of organisms
○ Cladogram
■ Show the shared characteristics
■ Diagram that represents an evolutionary relationship between different groups of taxa called
“clades”
○ Phenetics
■ AKA Numerical Taxonomy
■ Developed by Sneath and Sokal,
■ Classification method that groups organisms based on overall similarity in their characteristics
without considering evolutionary relationships
● Carolus Von Linnaeus “Carl Von Linnaeus”
○ May 23, 1707 - Jan 10, 1778
○ Swedish botanist/scientist
○ Laid The Foundation for Modern Taxonomy
○ Developed Linnaean Taxonomy
○ Developed Binomial Nomenclature
■ Binomial Nomenclature
● System in naming classified organisms
● Rules
○ Genus first letter is capitalized
○ Species name is lower case
○ The Genus species is typed in Italicized if Printed and Underlined if Written
● Cavalier Smith
○ Proposed 8 Kingdom classification (1993)
○ He split protista into 3 kingdoms
● Taxonomy Ranks (Do Ki Ph Cl O Fa G Spe)
Broadest Domain
Kingdom
Phylum
Class
Order
Family
Genus
Most Specific Species
● Linnaean System
○ Domain
■ Broadest
■ 3 Domains:
● Archaea
○ Single Celled
○ Multiply by: Binary Fission
○ Move by: Flagella
○ Lived in Extreme Environments
● Bacteria
○ Single Celled Prokaryotes
○ Common Shapes: Rod, Spherical, and Spiral)
○ Most Have Rigid Cell Wall
● Eukarya
○ Single-celled or Multicellular Eukaryotes
○ Kingdom
■ Based on molecular difference among organisms
■ Types
● Archaeabacteria
○ AKA Archaea
○ Prokaryotic microorganisms (Distinct from eubacteria)
○ Thrive in extreme environments
● Eubacteria
○ Prokaryotic
○ Much more common to find
○ Can be found in various environments
○ Classified by: Shape, Metabolism, and Genetic Structure
● Protista
○ Unicellular Organisms and some Multicellular Organisms
○ Classified by: Method of Obtaining Food and How They Move
● Fungi
○ Primarily Decomposer
○ Classified by: Reproductive Structure and Lifestyle
● Plantae
○ Photosynthetic Organism
○ Possess cell walls made of Cellulose
● Animalia
○ Multicellular, Eukaryotic, and Heterotropic
○ Classified by: Body Plan, Symmetry, and Developmental Patterns
○ Phylum
■ Archaebacteria
● Phylum Euryarchaeota
● Phylum Crenarchaeota
○ Mostly Found in Hot or Acidic Environment
○ Most are Thermophilic (Heat-Loving) and Acidophilic (Acid-Loving)
■ Eubacteria
● Phylum Firmicutes
○ Mostly Gram-positive
○ Have Ability to Form Endospores, That Enables Them To Live in Extreme
Environment
● Phylum Proteobacteria
○ Includes many important Pathogens (Ex. Salmonella, E. coli, and Vibrio Species)
○ Often Gram-negative
○ Has Wide Range of Metabolic Types
● Phylum Actinobacteria
○ Known for high G+C content
○ Can be Beneficial Soil Bacteria and Harmful Pathogens
● Phylum Cyanobacteria
○ AKA Blue-green Algae
○ Photosynthetic Bacteria
○ Essential role in Producing Oxygen
○ Found in Aquatic Environment
■ Protista
● Phylum Euglenophyta
○ Euglenoids
○ Characterized by: Ability to Photosynthesize
○ Have Flagella For Movement
● Phylum Dinoflagellata
○ Mostly Marine Plankton,
○ Some are Photosynthetic while some are Heterotrophic
○ Some species causes Algal Blooms (Red Tide)
● Phylum Chlorophyta
○ Green Algae (Similar in land plant through Photosynthetic Pigments)
○ Ex. Chlorella and Volvox
● Phylum Apicomplexa
○ Includes Parasitic Protist (Plasmodium)
○ Plasmodium - Causative agent of Malaria
● Phylum Ciliophora
○ Ciliates such as Paramecium
○ Uses Cilia For Movement and Feeding
○ Often Found in Freshwater
■ Fungi
● Phylum Ascomycota
○ Largest Phylum of Fungi
○ Includes Yeast and Molds
○ Reproduced Sexually via Ascospores
● Phylum Basidiomycota
○ Includes Mushroom and Puffballs
○ Produces Basidiospores
○ Play important role in Decomposing Organic Material
● Phylum Zygomycota
○ Includes fast growing molds (Rhizopus - Black Bread Mold)
○ Reproduce Sexually via Formation of Zygospores
● Phylum Chytridiomycota
○ Aquatic Fungi
○ Most are Parasitic (Batrachochytrium)
○ Affect Amphibian
■ Plantae
● Phylum Bryophyta
○ Non-vascular plant like Moss
○ Lacks Vascular Tissue for Transporting Water and Nutrients
○ Reproduces via Spores
● Phylum Pteridophyta
○ Ferns and Seedless Vascular Plants
○ Have Vascular Tissues
○ Reproduces via Spores
● Phylum Coniferophyta
○ Conifers like Pine Tree
○ Gymnosperms with Seeds Exposed to Cones
○ Woody Plants that Dominate Many Temperate Forest
● Phylum Angiosperms (Anthophyta)
○ Flowering Plants that produces seeds enclosed within Fruits
○ Further Divided into Monocots and Dicots
■ Animalia
● Phylum Porifera
○ Sponges
○ Has Sporus Bodies and Lack True Tissue
○ Usually Aquatic and Filter Feed
● Phylum Cnidaria
○ Includes Jellyfish, Coral and Sea Anemones
○ Has Radial Symmetry
○ Has Specialized Cell For Stinging (Cnidocytes)
● Phylum Arthropoda
○ Largest and Most Diverse Phylum
○ Includes insects, spiders and crustaceans
○ Has Segmented Body, Exoskeleton, and Jointed Limbs
● Phylum Chordata
○ Includes Vertebrates like Fish, Amphibians and Mammals
○ Some are Invertebrates like Tunicates and Lancelets
○ Class
■ Archaebacteria
● Phylum Euryarchaeota
○ Methanogens
■ Produces Methane
■ Usually Found in Anaerobic Environment
○ Halophiles
■ Salt-Loving Archaea
■ Lives in Environment with High Salinity
○ Thermophiles
■ Heat-loving Organisms
■ Survives in Extreme Hot Environment like Hot Springs
■ Eubacteria
● Phylum Firmicutes
○ Bacillus
■ Soil Bacteria
■ Can cause Disease but also used in Biotechnology
○ Clostridium
■ Includes pathogens like Clostridium botulinum, that causes Botulism
■ Includes Clostridium tetani, which causes Tetanus.
● Phylum Proteobacteria
○ Escherichia coli
■ E. coli
■ Common Bacterium in the Intestine
○ Salmonella
■ Major cause of Food Poison
○ Vibrio
■ Include Vibrio cholerae, causative agent of Cholera.
● Phylum Actinobacteria
○ Streptomyces
■ Soil-dwelling bacteria
■ Produce antibiotics.
○ Mycobacterium
■ Pathogens responsible for Tuberculosis and Leprosy.
● Hierarchy Of Evolution
○ Microevolution
■ Small-scale changes over short periods
■ Driven by mechanisms like natural selection, genetic drift, mutation, and gene flow.
■ Levels:
● Genes
○ Mutations and genetic recombination result in variations in genetic material, leading to
differences in traits.
○ Changes like mutations and mixing of genes create differences in traits.
● Cells
○ Genetic changes influence cellular processes, affecting an organism’s structure and
function.
○ These genetic changes affect how cells work, which can change how an organism looks
and functions.
● Organisms
○ Natural selection acts on individuals, favoring advantageous traits that enhance survival
and reproduction.
○ Natural selection helps individuals with helpful traits survive and reproduce more.
● Populations
○ As genetic variations accumulate, populations evolve, leading to observable changes in
traits over generations.
○ Over time, these changes add up, causing whole populations to evolve and show new
traits.
○ Macroevolution
■ Large-scale evolutionary changes that occur over long periods.
■ Focuses on the origin of new species, evolutionary trends, and mass extinctions.
■ Levels:
● Species
○ When populations become genetically distinct and reproductively isolated, new species
emerge through speciation.
○ When groups of organisms become so different that they can no longer breed with each
other, new species are formed. This is called speciation.
● Clades
○ Species with a common ancestor form clades, representing branches on the tree of life.
Understanding clades helps in studying evolutionary relationships.
○ Species that come from the same ancestor are grouped into clades. These clades are like
branches on the tree of life and help us understand how organisms are related.
● Lineages
○ Evolutionary lineages trace the ancestry and descent of organisms, often spanning
millions of years.
○ Lineages show the history of how organisms have changed and evolved over time,
often across millions of years.
●Biodiversity
○ Refers to the variety of living organisms on earth and interactions between them.
○ Includes species, ecosystems, and genetic variations.
● Bioinformatics
○ The application of computer science, mathematics, biological sciences, and analysis to interpret
different types of biological data.
● LEVELS OF ECOLOGICAL ORGANIZATION
○ Population
■ A group of individuals that belong in the same species and live in the same area.
■ ex. stray cats of new york city
○ Population Ecology
■ The study of how biotic (living) and abiotic (non-living) factors influence the density,
dispersion, and size of a population.
○ Community
■ In science definition:
● all populations of species that live in the same habitat and interact with each other.
■ In social studies:
● a group of people who live in the same place.
○ Ecosystem
■ A system that includes all living organisms and physical environment functioning together as a
unit.
● *Population have to be of the same species living in one place.
● *A community can have different species as long as they are living in the same place.
● *An ecosystem includes the animals and the environment.
●Evolution
○ Gradual process of change and development in living organisms over time.
○ Over many generations, this process leads to adaptations and the emergence of new species.
○ It is a continuous process that has resulted in the diversity of life forms.
● Evolutionary Theory
○ The unifying principle of all biological sciences.
○ It explains differences in structure, function, and behavior among life forms.
● DEVELOPMENT OF EVOLUTIONARY THOUGHT
○ Aristotle (c. 350 BCE)
■ “Species are identical and they tend to remain the same.”
○ Georges-Louis Leclerc, Comte de Buffon (AD 1749)
■ “As species change, they migrate to another environment.”
○ Jean-Baptiste Lamarck (1809)
■ “Species evolved from an existing species through environmental forces.”
■ “Traits can be passed to the next generation.”
○ Charles Lyell (1830)
■ “All changes in the environment are uniform and gradual.”
○ Charles Darwin (1859)
■ “Species evolved from one common ancestor.”
○ Alfred Russel Wallace (1859)
■ “Species evolved from the process of natural selection which causes variations.”
● LAMARCKISM
○ Jean-Baptiste de Lamarck (1744–1829)
■ A French naturalist.
■ Proposed:
● “Theory of Inheritance of Acquired Characteristics (1809)”
○ Also called soft inheritance.
○ Organisms can pass on traits they acquire during their lifetime to their offspring.
● “Theory of Use and Disuse”
○ Regular use of an organ leads to its development (hypertrophy).
○ Disuse leads to degeneration or loss (vestigial organs)
● Postulates of Lamarckism:
○ New Needs
■ Environmental changes create new needs for organisms.
○ Use and Disuse of Organs
■ New habits result in increased use of certain organs and disuse of others.
○ Inheritance of Acquired Characteristics:
■ Favorable traits acquired during an organism’s life are passed to offspring.
○ Speciation Through Accumulation:
■ Over generations, accumulated acquired traits lead to the formation of new species.
● Examples Supporting Lamarck’s Ideas
○ Deer to Giraffes:
■ Originally short-necked; necks grew longer due to reaching higher foliage after ground
vegetation disappeared.
○ Snakes:
■ Descended from reptiles with limbs (pentadactyl limbs); limbs lost due to disuse.
○ Horses:
■ Ancestors lived on soft ground with short legs; over time, longer legs evolved for survival on
dry, hard ground.
● Challenges to Lamarckism:
○ August Weismann (1892)
■ – Continuity of Germ Plasm Theory:
■ Proposed two types of cells in multicellular organisms:
● Germ Cells
○ Contain heritable information (passed to offspring).
● Somatic Cells
○ Affect only the individual, not passed to offspring.
● Concluded: Acquired traits in somatic cells cannot be inherited.
○ Pavlov (Russian Psychologist):
■ Trained mice to associate a bell with food.
■ Found that this learned behavior was not inherited in the next generation.
○ Kellogg and Bell Experiment:
■ Fed silkworm larvae a reduced quantity of mulberry leaves.
■ Larvae became smaller despite size normal feeding.
○ Castle and Phillips Experiment:
■ Transplanted ovaries of black guinea pigs into white guinea pigs before puberty.
■ All offspring were black, showing traits are inherited from germ cells, not influenced by the
host environment.
● Significance of Lamarckism
○ First comprehensive theory of biological evolution.
○ Explained the existence of vestigial organs due to disuse.
○ It explains the development of strong jaw muscles and claws in carnivores due to their continued
extra use.
○ It stimulated other biologists to look for the mechanism of organic mechanism.
● DARWINISM
○ Charles Darwin (1809–1882)
■ English naturalist.
■ Proposed:
● “Theory of Natural Selection”
● “Theory of Human Evolution”
■ He traveled on HMS Beagle, exploring South America, the Galápagos Islands, and more.
■ Influenced by:
● Alfred Russel Wallace’s essay: On the Tendency of Varieties to Depart Indefinitely
from the Original Type.
● Charles Lyell’s Principles of Geology.
● Postulates of Darwinism
○ Geometric Increase – Populations increase rapidly.
○ Limited Food and Space – Resources are limited.
○ Struggle for Existence – Organisms compete for survival.
○ Variations – No two individuals are exactly alike; variations exist naturally.
○ Natural Selection / Survival of the Fittest – Individuals with favorable traits survive and
reproduce.
○ Inheritance of Useful Variations – Favorable traits are passed to offspring.
○ Speciation – Accumulation of favorable traits leads to new species over time.
● Examples Supporting Darwin’s Ideas
○ Giraffes once had varying neck lengths.
○ Short-necked giraffes couldn’t reach food and died out.
○ Long-necked giraffes could feed on tall trees, survived longer, and reproduced.
■ Only long-necked giraffes remained — an example of survival of the fittest.
● Evidences in Favor of Darwinism
○ Close parallelism between natural selection and artificial selection.
○ Remarkable cases of resemblance (mimicry and protective coloration)
○ Replacement of earlier giant dinosaurs by small size carnivores reptiles due to scarcity of food,
space, and global cooling.
○ Pedigree of horse and other animals also support Darwinism.
○ Correlation between positions of nectaries and flower and length of proboscis and pollinating
insects which can be developed only gradually.
● Evidences Against Darwinism
○ Inheritance of Vestigial Organs
○ Inheritance of over-specialized organs see
○ Didn't explain the cause of variations and the mode of transmission of variations.
○ It didn't include the transitional stages which have no fossil records.
○ Did not differentiate between somatic and germinal variations.
○ It doesn't explain the evolution of terrestrial animals from aquatic animals.
● General Evidence of Evolution
○ The fossil record of change in earlier species.
○ The chemical and anatomical similarities of related life forms.
○ The geographic distribution of related species.
○ The recorded genetic changes in living organisms over many generations.
● Key Points of Natural Selection:
○ Natural Selection – Populations evolve to adapt via survival of the fittest.
○ Competition – Struggle arises due to limited resources.
○ Adaptation – Inherited traits that improve survival.
○ Variation – Differences in traits among individuals.
○ Overproduction – More offspring are produced than can survive.
○ Speciation – Formation of new species due to geographic, behavioral, or anatomical isolation.
