Comprehensive Guide to Evolution and Biological Classification

Posted on Aug 23, 2024 in Biology

Biological Classification and Evolution

Terms

  1. Phylogeny: Evolutionary history and relationships (e.g., domains)

  2. Phylogenetic Tree/Cladogram: Diagram reconstructing history based on morphology/physical behavior

  3. Heterotrophic: Consumers (cannot produce their own food)

  4. Autotrophic: Producers (can produce their own food – e.g., photosynthesis in plants)

  5. Cephalization: Cluster/concentration of sensory organs (e.g., brain, nerves)

Binomial Nomenclature

Developed by Carl Linnaeus, binomial nomenclature uses genus and species names to name organisms (e.g., Homo sapiens, Escherichia coli).

Taxonomy

Taxonomy classifies organisms according to the presence/absence of shared characteristics.

  • Kingdom – Phylum – Class – Order – Family – Genus – Species
    • e.g., King Phillip Came Over For Grape Soda

Kingdom (Domain Eukarya)

  1. Protista: Widest variety, unicellular, heterotrophic and autotrophic, motility (pseudopodia, cilia, flagella), disease-associated (dysentery, malaria)

    1. e.g., seaweed, slime molds

  2. Plantae: Multicellular, autotrophic (photosynthesis)

    1. e.g., flowering plants, ferns, mosses, algae

  3. Fungi: Heterotrophic, decomposers, cell walls contain chitin, secrete hydrolytic enzymes (extracellular digestion)

    1. e.g., mold, yeast, mushrooms

  4. Animalia: Multicellular, heterotrophic, sexual reproduction (diploid stage – two sets of chromosomes), monophyletic (traced back to a common ancestor)

    1. Multi-branched phyla: Porifera, Cnidaria, Platyhelminthes, Nematoda, Annelida, Mollusca, Arthropoda, Echinodermata, Chordata
    2. Classified by anatomical features (common structures → DNA data, embryonic development)
    • Primitive: No symmetry, no cephalization, two cell layers (endo, ecto), no true tissues, life in water, sessile
    • Complex: Bilateral symmetry, cephalization, three cell layers (endo, meso, ecto), tissues and organs, life on land, motile

Domain (Derived from Common Ancestors)

  1. Bacteria: Unicellular, prokaryotes, peptidoglycan, facultative anaerobes, decomposers, binary fission, conjugation and transformation, pathogens (disease-causing)

  2. Archaea: Unicellular, prokaryotes, no peptidoglycan

    1. Methanogens: Obtain energy by producing methane from hydrogen
    2. Halophiles: Thrive in high salt conditions
    3. Thermophiles: Thrive in high temperatures (e.g., hot springs)

  3. Eukarya: Eukaryotes, no peptidoglycan

BacteriaArchaeaEukarya
No nucleusNo nucleusNucleus
No organellesNo organellesOrganelles
No intronsIntrons (some)Introns

Levels of Organization

  1. Cells: Basic unit of life (e.g., neuron)

  2. Tissues: Group of similar cells performing a particular function (e.g., muscle tissue)

  3. Organs: Group of tissues performing related functions together (e.g., heart)

Gastrulation

Gastrulation is the process of germ layer formation during embryonic development.

  1. Ectoderm: Outermost layer (e.g., skin and nervous system)

  2. Endoderm: Innermost layer (e.g., viscera or guts)

  3. Mesoderm: Middle layer (e.g., blood and bones)

Symmetry

  • Bilateral: Symmetrical halves
  • Radial: Symmetry around a central axis

Evidence of Evolution

Fossil Records

Fossil records reveal the existence of species (extinction and evolution).

  1. Radiometric Dating: Measures the absolute age of fossils based on the natural decay of radioisotopes.

    1. Half-life: Time it takes to decay to half its products (e.g., Carbon-14 = 5730 yrs.)

  2. Law of Superposition: Determines a fossil’s relative age (lower layer of rock = older)

  3. Carbon Dating: Measuring the ratio of carbon in fossils (organisms stop accumulating carbon after death).

    1. Carbon-14 decays into N-14, causing a shift in the carbon ratio after death.

Comparative Anatomy

  1. Homologous Structure: Traits with similar structures but different functions (common ancestry)

    1. e.g., human hands, cat paws, whale fins, bat wings

  2. Analogous Structure: Similar functions but different structures (suggests adaptation)

    1. e.g., insect, bird, and bat wings

  3. Vestigial Structure: Evidence of evolved structures

    1. e.g., the appendix in humans evolved from being necessary to becoming useless

Comparative Biochemistry/Molecular Biology

Common ancestors have similar biochemical pathways (e.g., humans and bacteria with glycolysis).

  1. Cytochrome c: Present in all aerobic organisms

Comparative Embryology

Closely related organisms have similar stages of embryonic development.

  1. e.g., vertebrates begin with gill pouches on their throats – gills for fish and Eustachian tubes in mammal ears

Biogeography

Biogeography is the study of geographic distribution (current forms arose from ancestral forms).

  1. e.g., Marsupials in Australia, Pangaea

Theories of Evolution

Lamarck

Lamarck proposed the inheritance of acquired characteristics”use and disuse”

  1. Organisms choose to change in response to the environment.
  2. e.g., giraffes get their long necks from stretching their necks for food in high trees.

Darwin

Darwin proposed the theory of natural selection/descent with modification (mechanism for how populations evolve).

  • Natural Selection: Organisms don’t evolve; the frequency of an allele being passed on within a population changes.
    • Populations grow (overpopulate) and result in competition; variations inherited make for an unequal ability to survive (some more favorable than others).
    • Best-fit individuals pass on their favorable traits (accumulate to become dominant) and continue to reproduce more offspring.

Types of Selection

Stabilizing (Purifying) Selection

Eliminates”extreme” of a population, favors the more common intermediate form.

  1. e.g., humans – majority birth weights around 6-8 lbs (greater mortality in smaller and larger infants)

Diversifying/Disruptive Selection

Increases the extremes (more successful) at the expense of an intermediate.

  1. Arises new species

  2. Balanced Polymorphism: Two or more phenotypic variations in a single population of a species (each has an advantage and adapts).

    1. e.g., variety of snail shell colors

Directional Selection

One favored phenotype replaces another in a gene pool (rapid shifts in allele frequencies).

  1. e.g., antibiotic resistance in bacteria, peppered moths

Sexual Selection

Based on variation in secondary sexual characteristics (competing and attracting mates).

  1. e.g., antlers, horns, strength, canines, large stature

  2. Sexual Dimorphism: The difference in appearance between males and females.

    1. e.g., Peacocks – females blend into the environment to protect their young, while males are bright-colored and flashy to attract females.

Artificial Selection/Breeding

Favorable traits are selected by humans.

  1. e.g., dogs, racehorses (speed), hens (production)
  2. e.g., cabbage, Brussels sprouts, kale, cauliflower were bred from the wild mustard plant (with different traits selected)

Sources of Variation

Geographic Variation “Cline”)

Two different variations of a single species adapt to different environments.

  1. e.g., white rabbit in the north, grey/brown rabbits in the south

Sexual Reproduction

Recombination of alleles during meiosis and fertilization.

  1. Independent Assortment, crossing over, random fertilization

Outbreeding

Mating within one species that is distantly related (opposite of inbreeding).

  1. e.g., dominant male lions mate with young maturing lions from another pride, humans

Diploidy

2n condition maintains and hides a huge pool of alleles that may be harmful/unfavored but advantageous in changing conditions.

Heterozygotic Organisms

Preserves multiple alleles to increase reproductive success and advantageous genotypes.

  1. e.g., sickle cell anemia:

    1. Ss (heterozygous) – does not have sickle cell (mild), resistant to malaria
    2. SS – does not have sickle cell, susceptible to malaria
    3. ss – has sickle cell

Frequency-Dependent Selection (Minority Advantage)

Decreases the frequency of more common phenotypes.

  1. e.g., predators develop”search image” that allow them to hunt particular prey.

    1. If the prey types differ, the more common type will be preyed upon (will continue when the less common become more common).

Evolutionary Neutral Traits

Traits have no selective advantages.

  1. e.g., different human blood types

Population Evolution

Genetic Drift

Change/fluctuation in allele frequency due to chance.

  1. Bottleneck Effect: Natural disasters reduce the size of a population randomly (certain alleles may be under or overrepresented afterward).

  2. Founder Effect: Small populations break away from larger ones to colonize a new area.

    1. e.g., Amish settlers, Polydactyly

Gene Flow

Movement of alleles in or out of a population, migration of fertile individuals.

  1. e.g., pollen, chimpanzees

Mutations

Changes in genetic material (raw material).

  1. e.g., a single mutation can introduce new alleles into a population

Nonrandom Mating

Individuals choose mates for specific reasons/traits (eliminates unfit traits).

Speciation

Speciation occurs when two populations evolve and take several forms that they can no longer interbreed.

  1. Allopatric Speciation: A physical barrier prevents species from breeding so that they evolve on their own in different conditions (geographical isolation).

  2. Sympatric Speciation: No geographical isolation.

    • Polyploidy: A cell has more than two complete sets of chromosomes.
      • Occurs during nondisjunction

    • Habitat Isolation: Two organisms in the same area do not interact.

      • e.g., different snake species/same genus live in the same area, but one lives on land, and the other lives closer to water.

    • Behavioral Isolation (Mating Behavior): Leads to reproduction.

      • e.g., fireflies send out blinking patterns to attract females; if reciprocated, then breeding will occur.

    • Temporal Isolation: Depends on the time of year.

      • e.g., white rabbits mate from November-April, brown rabbits mate from May-October

    • Reproductive Isolation: Difference that prevents reproduction.

      • Prezygotic Barriers: Cannot happen before mating.

        • e.g., a small male cannot mate with a large female due to size difference
      • Postzygotic Barriers: Prevents the production of fertile offspring after mating (the produced zygote is sterile).

Evolutionary Patterns

Evolutionary patterns describe how species evolve into new species from speciation.

Image result for patterns of evolution

Divergent Evolution

A population becomes isolated from the rest and is exposed to new selective pressures.

  1. e.g., Allopatric and Sympatric Speciation

Convergent Evolution

Unrelated species occupy the same environment and experience similar pressures (unrelated species exhibiting similar characteristics).

  1. e.g., fins of a shark and whale (analogous structures form)

Parallel Evolution

Two species have similar evolutionary adaptations after divergence (similar environments and pressures).

  1. e.g., marsupial and placental mammals

Co-evolution “Evolutionary Arms Rac”)

Reciprocal adaptations made from two sets of species.

  1. e.g., predator-prey relationships (one adapts, forcing the other to adapt as well to increase survival)

Adaptive Radiation

Newly emerged species from a common ancestor introduced to a new environment fill an ecological niche.

  1. e.g., Darwin’s 14 Galapagos finches

Theories of Evolutionary Rate

Gradualism

The theory that organisms descend from common ancestors gradually.

  1. Big changes happen by accumulating many smaller ones (fossil records refute – missing link)

Punctuated Equilibrium

New species evolve after a long period of stasis.

  1. Large changes occur rapidly at different times.
  2. Allopatric model supported → new species arises in a different place and expands their range and outcompeting abilities to replace ancestral species (develop better traits).

Evo-Devo

Evo-devo is the study of how gene sequences can regulate others and change the forms and functions of organisms (why we can share DNA with common ancestors).

Gene Regulation

Similar DNA in particular structures, but genes are up/down-regulated to create different outcomes.

  1. Homeotic Genes: Regulatory genes that control the spatial organization of body parts.

    1. Hox genes: Provide positional information for developing embryos.

  2. Heterochrony: Evolutionary change in the rate of developing body parts.

    1. e.g., chimps and humans – the genome signals to stop skull development before we develop powerful teeth/jaws like chimps.

Origin of Life

Early Earth

Early Earth lacked free oxygen.

  • Oparin and Haldane: Organic molecules arose and developed without free oxygen.
  • Sidney Fox: Started with organic molecules and produced membrane-bound cell-like structures (proteinoid microspheres).

Miller-Urey Experiment

Modeled early Earth conditions by using atmospheric gases and a spark to simulate lightning and UV lights (tested the Oparin-Haldane hypothesis).

  1. Proved energy could have converted atmospheric molecules into organic molecules (amino acids).

Endosymbiotic Theory

The first cells on Earth were anaerobic, heterotrophic prokaryotes that absorbed organic molecules from”primordial sou” (life in water) as a nutrient source.

  1. Eukaryotes arose when free-living mitochondria and chloroplasts were enveloped by larger prokaryotes (beneficial symbiotic relationships became permanent).
  2. Evidence: Mitochondria and chloroplasts have their own DNA, the DNA is closely similar to prokaryotic DNA (wrapped in histones), organelles have double membranes (prokaryotic cell membrane, enveloped host cell membrane).

RNA World Hypothesis

The first genetic substance was not DNA (complex) but RNA (simple).

  1. Ribozyme: Catalyzes reactions, transmits information generationally, removes its own introns/self-splices, joins amino acids to form polypeptides.

Panspermia

Life originated from microorganisms in outer space that initiated life on reaching a suitable environment.

  1. Explains how life arose on Earth but not how life arose itself.

Hardy-Weinberg Equilibrium

Hardy-Weinberg equilibrium describes stable, non-evolving populations (allelic frequencies do not change).

  • Large population (no genetic drift), isolated population (no migration), no mutations, random mating, no natural selection

Calculations

Calculate the frequency of alleles within a population (p = dominant, q = recessive).

  1. p + q = 1
    p2 + 2pq (heterozygous) + q2 = 1

Example

If 9% of the population has blue eyes, what percentage of the population is heterozygous and homozygous for brown?

  1. If 9% is blue (recessive) → √q2 = √0.09 = 0.3
  2. p + q = 1 → p + 0.3 = 1 → p = 0.7

Heterozygous brown → 2pq → 2(0.7)(0.3) = 0.42 (42%)

Homozygous brown → p2 = 0.72 = 0.49 (49%)

Determining if a Population is in Hardy-Weinberg Equilibrium

–

Ex. Straight hair is dominant (IsIs), curly hair is recessive (IcIc), wavy hair is heterozygous (IsIc), a population of 1,000 individuals, 245 have straight, 393 had curly, and 362 had wavy


Allelic Frequencies:

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  • If there are 1,000 individuals then you divide the total by 2,000 since every individual contains 2 alleles per phenotype

bNEypyCxROf7sBGEcGeRh9kXaf1fK2NmCWz-lF0a


  • Degrees of freedom = n -1 (“n” being the total number of genotype classes)


The Null Hypothesis (H0) → interpret the chi-square value by considering the degrees of freedom and focusing on the probability of chance

  • hypothesis is rejected (does not follow the chi-square value) = population is not in Hardy-Weinberg Equilibrium (evolution occurring)