Chapter 33. Evolution
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4. Neo-Darwinian Evolutionary Theory
5. Phylogenetic Tree of Life and Evolution
1. Darwinian Biology
⑴ Before Darwin
① Linnaeus: Thought that diversity of species is the created form of species
② Cuvier
③ James Hutton (1726-1797): Gradualism
○ It took much more than 6,000 years for the current landscape to form
○ Natural changes are gradual, not abrupt
④ Charles Lyell (1797-1875): Uniformitarianism
○ The speed of past changes is the same as the speed of current changes
⑤ Jean Babtiste de Lamarck (1744-1829): Inheritance of Acquired Characteristics
○ Hypothesized that organs used frequently develop while unused organs degenerate
○ In 1809, in “Philosophie Zoologique,” he claimed that organisms on Earth can change over time
○ Recent emphasis on the heredity of acquired traits
⑥ Thomas Malthus (1766-1834): “An Essay on the Principle of Population”
○ Population growth is geometric, food production is arithmetic
○ Darwin connected Malthus’s ideas to the survival of the fittest in natural selection
⑵ Darwin
① Natural Selection: Traits that enable survival thrive in populations and change over time.
② Mayer’s Logical Inference
○ Observation 1: If all individuals reproduce successfully, the population size grows exponentially
○ Observation 2: Most populations remain stable in size
○ Observation 3: Resources are limited
○ Inference 1: Only some survive, leading to competition for resources
○ Observation 4: Population members have diverse traits
○ Observation 5: A significant portion of variations within a population are hereditary
○ Inference 2: Traits with higher survival and reproductive probabilities exist
○ Inference 3: Differential survival and reproduction lead to gradual changes in populations over generations
⑶ Evidence for Evolution
① Ongoing Natural Selection (Microevolution)
○ Example: Finch populations
○ Example: Evolution of drug resistance in HIV
② Homology
○ Anatomical Homology
○ Example 1: Mammalian forelimbs: Different functions but shared origin (homologous structures)
○ Example 2: Tail: Humans have vestigial coccyx like primates, but no tail
○ Example 3: Piloerector muscles (arrector pili): Tiny muscles at the base of hair, contract to make hair stand on end
○ Example 4: Thorns of roses and tendrils of grapes
○ Ontogenetic Homology (Haeckel’s Recapitulation Theory): Individual development recapitulates ancestral development.
○ Example: All chordates develop pharyngeal pouches like in a single common ancestor, shared developmental path with tails
○ Vestigial Organs: Present in modern plants but no longer serve a function
○ Examples: Human appendix, human tailbone
③ Analogous Organs: Not evidence of evolution, refers to convergent evolution
○ Example: Vines of ivy and vines of grapes
④ Molecular Biology Evidence (Similarity of DNA)
○ Example: Birds of the same genus have more similar DNA sequences
○ Example: Human (100%) - Chimpanzee (99.01%) - Gorilla (98.90%) - African Monkey (96.66%)
⑤ Biogeographical Evidence
○ Examples: Related species found in close geographical proximity (Galápagos and Ecuador finches)
○ Example: Ancestral human fossils found in Africa, where hominids resided
○ Example: Pacific snapping shrimp and Atlantic snapping shrimp were the same species before the formation of the Isthmus of Panama 3 million years ago
⑥ Fossil Record
○ Example: Sequence of evolutionary changes in the horse lineage
⑷ Validity of Alternative Evolutionary Hypotheses
① Static Model: Earth is much older than 6,000 years, and species clearly change over time (rejected)
② Transformism: Evidence of flexible relationships between organisms is abundant (rejected)
③ Individual Type Theory: Universality of DNA, genetic code, and cellular composition provide evidence for a single origin of life (rejected)
④ Without Evolution, it’s difficult to explain the universality of DNA and protein mechanisms
2. Microevolution
⑴ Definition: Change in gene pool (less controversial)
① Natural selection manifests as phenotypic changes, while microevolution manifests as changes in allele frequencies within a population.
⑵ Gene Pool and Allele Frequency
① Population: A group of individuals (same species) capable of producing offspring
② Population Genetics
③ Gene Pool
④ Allele Frequency
○ The sum of frequencies of all alleles is 1
○ For 2 alleles, in Mendelian genetics, with dominant allele frequency A and recessive allele frequency a:
○ Dominant genotype ratio: A2 + 2Aa
○ Recessive genotype ratio: a2
⑶ Hardy-Weinberg Law
① Conservation of Allele Frequencies: Mendelian genetic processes alone cannot alter allele frequencies (Hardy-Weinberg equilibrium)
② (p + q)2 = p2 + 2 · p · q + q2 = 1 (where p and q are frequencies of 2 alleles)
③ Conditions for Hardy-Weinberg Equilibrium
○ Large population size where probability can work
○ Random mating
○ Absence of migration and gene flow
○ No mutations
○ No natural selection
○ If any of these conditions is violated, evolution occurs
⑷ Microevolution: When Hardy-Weinberg Equilibrium is Broken
① Genetic Drift: Phenomenon where allele frequency changes in a small population
○ In small populations, alleles can be lost or fixed due to the finite number of mates each generation
○ Types: Bottleneck effect (dramatic and temporary decrease in population size, leading to changes in allele frequency) and founder effect (small group isolates from a larger population, forming a new gene pool)
○ Random events: A carrier of a rare allele might not reproduce
② Non-random Mating: Mating that is not random
○ Homogamy (non-homosexuality)
○ Sexual Selection (intersexual selection): Selection of mates to maximize reproductive ability; e.g., sexual dimorphism
○ Heterogamy (intersexual selection): Tendency for organisms to mate with individuals resembling themselves
○ Artificial selection for quality improvement
③ Mutation
○ Substitution rate in mammalian DNA sequences: 3 ~ 5 × 10-9 substitutions/nucleotide/year
○ Substitution rate in human influenza virus DNA sequences: 2 × 10-3 substitutions/nucleotide/year
④ Gene Flow (Migration)
⑤ Natural Selection: Favorable mutations increase in frequency, unfavorable mutations decrease; no new traits are created
○ Stabilizing Selection: Selects intermediate phenotypes, stabilizes gene pool
○ Directional Selection: Selects one extreme phenotype, gene pool shifts in a specific direction
○ Disruptive Selection: Selects both extreme phenotypes, gene pool splits into two distinct groups
○ Increased effects of natural selection
○ When dominant phenotype is detrimental: Heterozygotes also suffer elimination
○ When environment changes rapidly
○ Examples: Increased UV radiation ⇒ increased vitamin D, decreased folic acid
○ Low UV ⇒ Light skin (optimal vitamin D)
○ High UV ⇒ Dark skin (optimal folic acid)
⑥ Hybridization: Reproduction between different species
⑸ Conservation of Genetic Variation
① Diploidy
② Sexual Recombination
③ Balancing Selection
○ Heterozygote Advantage: When heterozygotes are more fit than homozygotes
○ HbA: Adult hemoglobin, HbS: Sickle cell hemoglobin
○ HbA/HbA: Malaria sensitivity
○ HbA/HbS: Malaria resistance
○ HbS/HbS: Anemia
○ Frequency-Dependent Selection
④ Neutral Mutation
⑹ Consequences of Genetic Variation
① Homologous Genes
② Orthologous Genes (Parallel Homologs): Genes that originated from a common ancestral gene but diverged during speciation
③ Paralogous Genes (Serial Homologs): Genes within a single species that are duplicated, creating 2 alleles
⑺ Evolutionary Fitness
① Fitness: Normalized value between 0 and 1 that represents the ratio of the number of offspring with a specific genotype to the number of parents with that genotype
○ Biological meaning: Relative survival and reproduction ÷ reproductive capability
○ Meaning of normalization: Adjusts the factor to make the most common genotype’s fitness 1
○ Higher fitness means better survival and reproduction
② Adaptive Traits: Traits that enhance an organism’s fitness in a given environment
③ Selection Coefficient: Difference in fitness between two organisms
○ Ranges from 0 to 1
3. Evolutionary Development
⑴ Evolutionary Process = Speciation ← Subspeciation + … + Subspeciation ← Common Ancestor (Common Ancestral Theory), (subject to controversy)
⑵ Biological Species Concept : Group of organisms capable of interbreeding and producing fertile offspring in nature
① Prezygotic Barrier : Prevents mating from occurring
○ Geographic Isolation : No contact between different species
○ Temporal Isolation : Different species breed at different times
○ Behavioral Isolation : Differences in mating behaviors
○ Mechanical Isolation : Differences in reproductive structures
Example : Reproductive structures of insects that fit together like locks and keys
○ Gametic Isolation : Proteins on the surface of eggs do not allow sperm from different species to fertilize
○ Reinforcement of Isolation : Prezygotic barriers are stronger in cases where genetically close species coexist in the same area
○ Due to strong selection pressure preventing hybridization among closely related species
② Postzygotic Barrier : Hybridization occurs but hybrids are sterile
○ Hybrid Breakdown (hybrid vigor lost) : Developmental failure due to incomplete genetic information
Example : Cross between goat and sheep produces offspring but they die at an early developmental stage
○ Hybrid Sterility : Hybrids cannot undergo meiosis due to lack of homologous chromosomes
○ Hybrid Disintegration : First-generation hybrids are healthy but subsequent generations experience reduced survival and reproduction
③ Example 1: Liger
○ Offspring of a tiger and a lion
○ Not a biological species due to lack of fertility
○ Tigers and lions are not the same species
④ Example 2: Mule
○ Offspring of a female horse and a male donkey
○ Not a biological species due to lack of fertility
○ Female horse and male donkey are not the same species
⑶ Limits of Biological Species Concept
① Cases where Biological Species Concept cannot be applied
○ Asexual reproduction
○ Difficulty in confirming reproductive compatibility between organisms
○ Cases of fossil species
② Alternative species concepts
○ Morphological Species Concept
○ Conventional species concept based on external characteristics
○ Most commonly used species concept in classification
○ Pros : Applicable to asexual organisms and fossil organisms where biological species cannot be verified
○ Cons : Does not always reflect evolutionary independence.
○ Example : Estimating relationships when reconstructing the emergence and migration of ancestral humans
○ Example : Wolves and dogs are not considered the same species despite being capable of interbreeding
○ Paleontological Species Concept
○ Ecological Species Concept
○ Based on ecological similarity
○ Classifies organisms with similar ecological niches as the same species
○ Phylogenetic and Ontogenetic Species Concept
○ Groups organisms with the same evolutionary history using morphological and DNA sequence data
○ Species with the same genetic characteristics that diverged from a common ancestor
⑷ Mechanisms of Speciation
① Allopatric Speciation : Speciation due to geographical isolation within a single population
② Sympatric Speciation : Speciation occurring within the same geographical area
○ Type 1: Sexual Selection : Occurs when individuals with specific genetic traits are more likely to mate
○ Type 2: Habitat Differentiation : Subpopulations exploit different habitats or resources
○ Type 3: Polyploidy : Occurs due to errors in chromosome addition during cell division
○ Autopolyploidy
○ Allopolyploidy : Forms from hybrids of different species and undergoes various processes to become a polyploid
○ Around 50% of flowering plants are derived from polyploidy
○ Example: Canola : A hybrid of kale and turnip, canola results from an error in chromosome segregation, resulting in a triploid with restored fertility
○ Principle of Trait Substitution : Trait differentiation tends to be higher in sympatric populations than in allopatric ones
③ Adaptation Radiation : Process where life forms evolve into various directions to adapt to their environment
○ Natural selection improves adaptation to current conditions rather than past improvement
○ Natural selection does not drive progress towards a goal
④ Theory 1: Gradualism or Gradual Evolution Theory
○ Proposed by Darwin
○ Theory that small changes accumulate gradually over millions of years leading to speciation
⑤ Theory 2: Punctuated Equilibrium Theory
○ Proposed by Stephen Jay Gould
○ Suggests that after rapid changes in form, there is little change over time due to the absence of intermediate forms in the fossil record
○ Currently combined with the Evo-devo theory, related to homeobox genes
⑥ Rebuttal of Punctuated Equilibrium Theory
○ Genetic changes are fundamentally gradual and lack direction
○ In stable environments, gradual genetic changes lead to minimal species change
○ In changing environments, specific genetic changes in individuals lead to rapid species change
○ Earth’s history shows rapid environmental changes, leading to punctuated equilibrium
⑸ Factors Influencing Speciation Rate
① Species Richness : Higher speciation rate within a lineage with more species
② Range Size
③ Behavior
④ Environmental Change
⑤ Generation Time
4. Evo-devo Evolutionary Theory
⑴ Evo-devo (Evolutionary Developmental Biology) Theory
⑵ HOX Genes and deep relationship
⑶ Supports the Punctuated Equilibrium Theory
5. Tree of Life and Evolutionary Theory
⑴ Common Characteristics of Organisms : Because they originated from a common ancestor
① All organisms have the same basic biochemistry and share the same types of macromolecules
② All organisms are composed of cells and have a bilayer lipid membrane as their outer boundary
③ Eukaryotic cells share almost identical organelles
⑵ Phylogenetic Tree : Represents the path of evolution as a branching tree
⑶ Phylogenetic Methods : Molecular Clock
① Tracking using rRNA : rRNA has the slowest evolutionary rate
○ Hemoglobin, cytochrome c, fibrinogen, histone proteins can also be used
○ Mitochondrial DNA generally mutates about 10 times faster than nuclear DNA
② Principle of Parsimony (Minimum Evolution) : Choose the phylogenetic tree
with the fewest trait changes
○ DNA-DNA hybridization experiment : Closer relationships have higher DNA melting temperatures (Tm)
③ Characteristics
○ Ancestral forms are positioned lower, closer relationships are placed closer
○ Slowly evolving sequences allow tracking of distant evolutionary history
○ Over long periods, substitution rates slow due to synonymous substitutions in nucleotide and amino acid sequences
Note: The error rate of DNA polymerase is constant during replication of genes
④ Clades
○ Monophyletic Clade : Common ancestor and all its descendants
○ Paraphyletic Clade : Includes common ancestor and some of its descendants
Example : Birds evolved from reptiles, but birds are excluded from the paraphyletic reptile group
○ Polyphyletic Clade : Includes groups with different common ancestors
⑤ Derived Traits
○ Primitive Character : Trait shared by all groups derived from a common ancestor
○ Derived Character : Trait present in a group but absent in its ancestors
○ Synapomorphy : Unique trait found only in a specific clade, used as evidence in building phylogenies
○ Paraphyletic Clades
⑤ Traits Based on Clades
Figure 1. Phylogenetic Tree
Input: 2015.07.09 14:56
Updated: 2019.02.05 12:24