Chapter 33. Evolution
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4. Evo-devo 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
○ Hypothesized that 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 grows geometrically (exponentially), while food production grows arithmetically.
○ Through Malthus’s An Essay on the Principle of Population, Darwin was led to the idea that, in the struggle for existence, favorable variations are more likely to survive.
⑵ Darwin
① Natural Selection: Traits that enable survival thrive in populations and change over time.
② Mayr’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 (→ maybe controversial) changes in populations over generations
⑶ Evidence for Evolution
① Ongoing Natural Selection (Microevolution)
○ Example: Guppy 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: Goosebumps: The arrector pili (piloerector) muscle is a tiny muscle at the base of each hair; when it contracts, the hair stands up, making the body appear larger under stress and helping conserve heat.
○ Example 4: Thorns of roses and tendrils of grapes
○ Ontogenetic Homology (Haeckel’s Recapitulation Theory): Individual development recapitulates ancestral development.
○ Example: Derived from a single common ancestor, all chordate embryos form pharyngeal slits and share a developmental pathway in which they possess a tail during early embryonic stages.
○ Vestigial organs
○ Example: Although flowering plants do not undergo alternation of generations, they form tiny gametophytes within the flower (egg cell: a vestigial organ).
○ Example: the human appendix; the human coccyx (tailbone).
③ Analogous organs: not evidence of common ancestry; refers to convergent evolution.
○ Example: the tendrils of peas and grapes.
④ Molecular evidence (similarity of DNA)
○ Example: birds within the same genus have more similar DNA sequences.
○ Example: human (100%) – chimpanzee (99.01%) – gorilla (98.90%) – African monkeys (96.66%).
⑤ Biogeographic evidence
○ Example: related species are found near one another (Galápagos finches and those of Ecuador).
○ Example: fossils of human ancestors are found in Africa, where apes live.
○ Example: Pacific and Atlantic pistol shrimps were a single species 3 million years ago, before the Isthmus of Panama formed.
⑥ Fossil record
○ Example: the sequence of evolutionary changes in the horse lineage.
⑷ Validity of Alternatives to Evolutionary Hypotheses
① Static Model (rejected): Because Earth is much older than 6,000 years, and species clearly change over time.
② Transformism (rejected): Because evidence of flexible relationships between organisms is abundant.
③ Individual Type Theory (rejected): Because universality of DNA, genetic code, and cellular composition provide evidence for a single origin of life.
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 allele frequencies is 1 (A + a = 1).
○ In a two-allele Mendelian locus, let A be the dominant-allele frequency and a the recessive-allele frequency.
○ Dominant phenotype proportion: A2 + 2Aa (i.e., A2 + 2·A·a).
○ Recessive phenotype proportion: 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 changed due to the finite number of mates each generation
○ Type 1. Bottleneck effect: A dramatic, temporary reduction in population size (e.g., due to fire or flood) that causes the frequencies of some alleles to increase while others decrease or are lost.
○ Type 2. Founder effect: When a small number of individuals become isolated from a large population, forming a new, small population whose gene pool differs from that of the original.
○ Type 3. Chance event: A case where carriers of a rare allele happen not to reproduce.
② Selective mating: Nonrandom mating.
○ Intrasexual selection (≠ homosexuality)
○ Sexual selection (intersexual choice): choosing mates to maximize reproductive success; e.g., sexual dimorphism between males and females in animals.
○ Assortative mating: a tendency to mate with partners who resemble oneself.
○ Artificial/selective breeding for quality (trait) improvement.
③ Mutation
○ Substitution rate in mammals: 3–5 × 10-9 substitutions per nucleotide per year.
○ Substitution rate in human influenza virus: 2 × 10-3 substitutions per nucleotide per year.
④ Gene flow (migration)
⑤ Natural selection: advantageous variants increase in frequency, disadvantageous variants decrease; it does not create new traits.
○ Stabilizing selection: selects intermediate phenotypes → stabilizes the gene pool.
○ Directional selection: selects one extreme phenotype → shifts the gene pool in a particular direction.
○ Disruptive (diversifying) selection: selects both extreme phenotypes → divides the gene pool into two groups.
○ When the effect of natural selection is stronger:
○ When a dominant phenotype is selected against (because heterozygotes are also eliminated).
○ When the environment changes rapidly.
○ Example: UV ↑ ⇒ vitamin D ↑, folate ↓
○ Low UV favors light skin (adequate vitamin D).
○ High UV favors dark skin (adequate folate).
⑥ Hybridization: Reproduction between different species
⑸ Conservation of Genetic Variation
① Diploidy
② Sexual Recombination
③ Balancing Selection
○ Heterozygote advantage (overdominance): When heterozygotes have higher fitness/survival than either homozygote in diploids.
○ HbA: adult hemoglobin; HbS: sickle-cell hemoglobin.
○ HbA/HbA: susceptible to malaria.
○ HbA/HbS: resistant to malaria.
○ HbS/HbS: anemia (sickle-cell disease).
○ Frequency-dependent selection.
④ Neutral Mutation
⑹ Results of genetic variation
① Homologous gene (homolog): A gene derived from a single ancestral gene.
② Orthologous gene (ortholog): Genes that originated from the same ancestral gene but diverged during speciation.
③ Paralogous gene (paralog): Within a species, a gene that has duplicated, yielding two copies (alleles) of the gene.
⑺ Evolutionary fitness
① Fitness: (number of individuals in the offspring generation with a given genotype) ÷ (number of individuals in the parental generation with that genotype), normalized to a value between 0 and 1.
○ Biological meaning: relative survival and reproduction / reproductive ability.
○ Meaning of normalization: typically multiply by a proportional factor so that the genotype with the highest reproductive success has fitness 1.
○ Implication: the greater the fitness, the more favorable the survival and reproduction.
② Adaptive trait: A trait that increases an individual’s fitness in a given environment.
③ Selection coefficient: The difference in fitness between two individuals; takes a value between 0 and 1.
3. Macroevolution
⑴ Macroevolution = speciation ← microevolution + … + microevolution ← a single common ancestor (common descent hypothesis), (much debated).
⑵ Biological species concept: a population whose members can interbreed in nature and produce fertile offspring.
① Prezygotic reproductive barriers: fertilization does not occur.
○ Spatial (geographical) isolation: individuals of different species do not come into contact.
○ Temporal isolation: the timing of reproduction differs by species.
○ Behavioral isolation: differences in courtship behavior.
○ Mechanical isolation: differences in the structure of reproductive organs.
○ Example: the genitalia of certain insects fit like a lock and key.
○ Gametic isolation: egg-surface proteins that bind sperm do not permit sperm from other species.
○ Reinforcement: when two genetically very similar species inhabit the same area, prezygotic isolation becomes stronger, because strong selection acts to prevent hybrid production between sympatric species.
② Postzygotic reproductive barriers: fertilization occurs, but the hybrid cannot reproduce.
○ Reduced hybrid viability (hybrid zygote inviability): development fails due to incompatible/incomplete genetic information.
○ Example: a goat–sheep cross can form an embryo, but it dies at an early developmental stage.
○ Reduced hybrid fertility (hybrid sterility): because the hybrid’s chromosomes lack homologous pairs, it cannot undergo meiosis.
○ Hybrid breakdown: the F1 hybrids are healthy, but later generations show reduced survival and fertility.
③ Example 1. Liger
○ Offspring born to a tiger and a lion.
○ Infertile, so it is not a biological species.
○ Tigers and lions are not the same species.
④ Example 2. Mule
○ Offspring born to a mare and a jack (male donkey).
○ Infertile, so it is not a biological species.
○ Mares and male donkeys are not the same species.
⑶ Limits of Biological Species Concept
① Cases where the Biological Species Concept (BSC) cannot be applied:
○ Asexual reproduction
○ It is not feasible to test mating/interbreeding ability among all organisms.
○ Fossil species
② Alternative species concepts
○ Morphological species concept
○ A conventional species concept based on external (morphological) traits
○ The most widely used species concept in taxonomic classification
○ Advantage: can be applied to asexual organisms or fossil organisms where the biological species concept cannot be verified.
○ Disadvantage: does not always reflect evolutionary independence.
○ Example: when inferring relatedness while reconstructing the emergence and migration routes of ancestral humans
○ Example: Although wolves and dogs can interbreed, they are not regarded as the same species.
○ Paleontological species concept
○ Ecological species concept
○ Premise: Organisms are morphologically and physiologically similar.
○ If they occupy the same ecological niche, they are classified as the same species.
○ Phylogenetic/embryological species concept
○ Groups with the same evolutionary history, inferred from morphological data and DNA sequences, are regarded as the same species.
○ Species that diverged from a common ancestor and have the same genetic characteristics.
⑷ Mechanisms of Speciation
① Allopatric Speciation: Speciation due to geographical isolation within a single population
② Sympatric speciation: speciation that occurs within the same geographic area
○ Type 1. Sexual selection: occurs when individuals with certain heritable traits obtain more mates.
○ Type 2. Habitat differentiation: a subpopulation exploits habitats or resources not used by the parent population.
○ Type 3. Polyploidy: arises from errors during cell division that add extra sets of chromosomes.
○ Autopolyploid.
○ Allopolyploid: a polyploid formed from a hybrid produced by mating between two different species, via various subsequent processes.
○ About 50% of flowering plants originate from polyploidy.
○ Example. canola: the hybrid of kale and turnip; due to a mitotic error in which nuclear division succeeds but cytokinesis fails, the chromosome number doubles to a diploid state and fertility is restored.
○ Principle of character displacement: sympatric populations tend to show greater trait divergence than allopatric populations.
③ Adaptive radiation: the process by which living organisms evolve along multiple lineages to adapt to their environments.
○ Natural selection favors what is well-adapted to the present; it is not an improvement over the past.
○ Natural selection does not produce progress toward a predetermined goal.
④ Theory 1. Gradualism (the gradual evolution model)
○ Advocated by Darwin.
○ The theory that small changes accumulate slowly, leading to speciation over millions of years.
⑤ Theory 2. Punctuated equilibrium
○ Proposed by Stephen Jay Gould.
○ Based on the scarcity of transitional fossils, it posits that species undergo rapid morphological change and then persist with little further change.
○ Recently integrated with evo-devo (evolutionary developmental biology); related to the homeobox.
⑥ Critiques of punctuated equilibrium
○ Genetic change is fundamentally gradual and directionless.
○ If environmental change is minimal, directionless genetic variation results in little change at the species level.
○ If environmental change is great, individuals with particular genetic changes are more likely to survive, and species-level change proceeds rapidly.
○ Because Earth’s history includes many abrupt environmental shifts, punctuated patterns are observed.
⑸ Factors influencing the speciation rate
① Species richness: the more species within a lineage (clade), the higher the speciation rate.
② Size of geographic range.
③ Behavior
④ Environmental change
⑤ Generation time
4. Evo-devo Evolutionary Theory
⑴ Evo-devo (Evolutionary Developmental Biology) Theory
⑵ Deeply related to HOX (Homeobox) genes.
⑶ Supports the Punctuated Equilibrium Theory
5. Phylogenetic Tree of Life and Evolution
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 lipid bilayer 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 instead of rRNA.
○ 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
○ Looking back far into the past, multiple substitutions (“multiple hits”) cause the observed substitution rates of nucleotide and amino-acid sequences to slow down.
○ Note: The error rate of DNA polymerase remains constant when replicating genes.
④ Clade
○ Monophyletic clade: a single common ancestor and all of its descendants.
○ Paraphyletic clade: a clade that includes a common ancestor and only some of its descendants.
○ Example: Birds evolved from reptiles, yet “Reptilia” is treated as a paraphyletic group that excludes birds.
○ Polyphyletic clade: a grouping that includes taxa with different common ancestors.
⑤ Derived characters
○ Ancestral/primitive character: a trait shared by all taxa derived from a single ancestor.
○ Derived character: a trait present in the taxon but absent in the ancestral group.
○ Synapomorphy (shared derived character): a distinctive trait unique to a particular clade; a clue for establishing monophyletic groups.
○ Paraphyletic clade
⑥ Characters by clade
Figure 1. Phylogenetic Tree
Input: 2015.07.09 14:56
Updated: 2019.02.05 12:24