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exam 2

Review Activity Exam II, BIO 114

1. DNA Substitution

  • Definition: A DNA substitution is a type of mutation where one nucleotide in the DNA sequence is replaced by another nucleotide.
  • Contrast between synonymous and nonsynonymous substitutions:
    • Synonymous Substitution: This type of mutation does not change the amino acid sequence of the protein. For example, if a codon for an amino acid is changed to another codon that codes for the same amino acid, it is a synonymous mutation.
    • Nonsynonymous Substitution: This mutation results in a change in the amino acid sequence of the protein. For example, if a codon changes from one that encodes an amino acid to a codon that encodes a different amino acid, it is a nonsynonymous mutation.

2. Evolutionary Processes

  • dN/dS Ratio: This ratio is a measure used to distinguish between different evolutionary processes acting on genes, specifically to assess the rate of nonsynonymous mutations (dN) compared to synonymous mutations (dS).
    • A ratio of dN/dS < 1 indicates purifying selection (selection against mutations).
    • A ratio of dN/dS = 1 indicates neutral evolution (no selection).
    • A ratio of dN/dS > 1 indicates positive selection (favoring beneficial mutations).

3. Types of Selection

  • Positive Selection: The process where favorable genetic variants increase in frequency in a population due to their advantageous traits.
  • Purifying Selection: The process that removes deleterious alleles from a population, thus conserving functionally important sequences.
  • Neutral Evolution: The hypothesis that most evolutionary changes at the molecular level are caused by random drift of mutant alleles that are selectively neutral.

4. Outcomes from Gene Duplication

  • Three possible outcomes include:
    1. Conservative Retention: One copy retains the original function, while the other either becomes nonfunctional or develops a new function.
    2. Neofunctionalization: One of the duplicated genes acquires a new function that was not present in the ancestral gene.
    3. Subfunctionalization: Each duplicate gene retains a subset of the original gene's functions, thereby splitting the functional duties.

5. Body-Plan Genes

  • Maternal Effect Genes: Genes expressed in the mother that influence the development of the embryo, affecting traits like body axis formation.
  • Segmentation Genes:
    • Gap Genes: Specify broad areas and lead to the formation of distinct body regions.
    • Pair Rule Genes: Define pairs of segments in the embryo.
    • Segment Polarity Genes: Establish anterior-posterior differences within individual segments.
  • Hox Genes: A group of related genes that control the body plan of the embryo along the head-tail axis, determining the identity of body parts.

6. Kimura’s Neutral Theory of Evolution

  • Definition: This theory posits that the majority of evolutionary changes at the molecular level are caused by random genetic drift rather than by natural selection. In this model, most mutations are selectively neutral and do not affect an organism's fitness.

7. Point Mutations

  • Five kinds of point mutations:

    1. Single Mutations: Changes at a single nucleotide position.
    2. Multiple Mutations: Changes occurring at multiple nucleotide positions simultaneously.
    3. Coincident Mutations: Mutations that occur in two or more genes simultaneously.
    4. Parallel Mutations: Independent mutations in different lineages that yield a similar trait.
    5. Reversions (Back Mutations): Mutations that revert a gene back to its original form.

  • Invisible Mutations: Those mutations that do not affect the phenotype and thus are not subject to selection pressures. Generally, synonymous mutations tend to be invisible.

  • Homoplasies: Arise in cases where mutations occur independently in different lineages, leading to similar characteristics without common ancestry.

8. Species Concepts

  • Morphological Species Concept: Defines species based on observable physical traits; commonly used for fossil species.
  • Biological Species Concept: Defines species as groups of interbreeding natural populations that are reproductively isolated from other such groups. Best for sexually reproducing organisms.
  • Lineage Species Concept: Species are defined as branches on the tree of life and are useful for asexual organisms and groups without clear reproductive boundaries.

9. Dobzhansky-Muller Model

  • Definition: A model of speciation that explains how genetic incompatibilities between diverging populations can arise. If two alleles at a single locus are fixed in separate populations, hybrid offspring might inherit incompatible combinations of alleles at different loci, leading to reduced fitness.

10. Isolating Mechanisms

  • Prezygotic Isolating Mechanisms: Mechanisms that occur before fertilization to prevent mating or fertilization (e.g., temporal, behavioral, mechanical isolation).
  • Postzygotic Isolating Mechanisms: Mechanisms that occur after fertilization that reduce the viability or fertility of hybrid offspring (e.g., hybrid inviability, hybrid sterility).

11. Hybrids and Hybrid Zones

  • Hybrids: Offspring resulting from the mating of individuals from two different species.
  • Hybrid Zone: A geographic area where interbreeding occurs between two distinct species, often resulting in a mixture of genetic and phenotypic traits.
  • Ring Species: A connected series of neighboring populations that can interbreed with each other, but the populations at the ends of the ring cannot interbreed.

12. Speciation Types

  • Allopatric Speciation: The formation of new species while geographically isolated from one another.
  • Sympatric Speciation: The formation of new species while sharing the same habitat.

13. Disruptive Selection and Polyploidy

  • Disruptive Selection: A type of selection that favors extreme phenotypes over intermediate phenotypes.
  • Polyploidy: A form of sympatric speciation that involves the duplication of chromosome sets, leading to organisms with more than two sets of chromosomes.
    • Autopolyploidy: A condition in which an organism has more than two sets of chromosomes all derived from a single species.
    • Allopolyploidy: A condition where two different species hybridize, and the resulting offspring have extra chromosome sets from both species.

14. Geological Concepts

  • Stratigraphy: The branch of geology concerned with the ordering and relative position of strata (rock layers) and their relationship to the geological time scale.
  • Radiometric Dating: A technique used to date materials such as rocks or carbon by measuring the radioactive decay of isotopes.
  • Radioisotopes: An isotope of an element that is unstable and can decay, releasing radiation.
  • Half Life: The time required for half of the radioactive atoms in a sample to decay.
  • Plate Tectonics: The scientific theory that explains the movement of the Earth's lithosphere which leads to geological phenomena such as earthquakes and the formation of mountains.

15. Mass Extinctions

  • Definition: Mass extinction is a significant and rapid decline in biodiversity on Earth, often marked by a high percentage of species loss within a relatively short time frame.
  • Causes of the Permian/Triassic Mass Extinction: Likely causes include volcanic eruptions, climate change, ocean acidification, and asteroid impacts.
  • Causes of the Cretaceous/Paleogene Mass Extinction: The leading hypothesis includes a massive asteroid impact (the Chicxulub crater) which led to drastic environmental changes, including wildfires, tsunamis, and 'nuclear winter' effects that altered ecosystems globally.

16. Paleozoic Transitions

  • Major Transitions: Highlights the evolution of fishes during the Devonian period and the subsequent colonization of land by both plants and animals, marking significant evolutionary adaptations and diversification.

17. Mesozoic Ecology

  • Post-Permian Atmospheric Crisis: The Mesozoic era saw the rise of dinosaurs and other reptiles as dominant terrestrial animal groups, along with significant plant diversification such as conifers and flowering plants.

18. Cenozoic Ecology

  • Ecological Developments: Characterized by the spread of grasslands, the evolution of mammals, and the occurrence of ice ages, leading towards the formation of the modern ecosystems that we recognize today.