Biology Chapter 22: Descent with Modification

Chapter 22: Descent with Modification

• Scientists who influenced Darwin: Hutton, Cuvier, Lyell, Wallace
• Darwin's voyage on the HMS Beagle and publication of "The Origin of Species" in 1859
• Definition of evolution: the process by which species accumulate differences from their ancestors as they adapt to different environments over time
• Population changes over time genetically, not individually
• Natural selection: the process in which individuals with certain inherited traits tend to survive and reproduce at higher rates
• 4 observations of natural selection:
  • Individuals in populations vary in their inherited traits
  • All species can produce more offspring than the environment can support
  • Individuals with inherited traits that increase survival and reproduction in an environment tend to produce more offspring
  • The unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations
• Artificial selection: humans modifying species through breeding individuals with desired traits

Evidence of Evolution

• Direct observation: antibiotic resistance, birds' beak size and fruit size
• Homology: similarity from common ancestry
  • Anatomical homology: homologous structures
  • Comparative embryology
  • Vestigial structures: goosebumps, wisdom teeth, ear muscle, tailbone of human
  • Molecular homology: DNA
• Fossil records: the age of fossil records is about 3.5 billion years ago
• Biogeography: the scientific study of the geographic distribution of species (continental drift and the distribution of modern living organisms)

Homologous vs. Analogous Structures

• Analogous traits: result of similar environments (not due to common ancestry)
• Convergent evolution: the evolution of similar features in distantly related groups
• Examples: dolphin and shark body shapes, sugar glider and flying squirrel

Chapter 23: The Evolution of Populations

• Macroevolution vs. microevolution
• Microevolution: changes in allele frequencies in populations over generations
• Three mechanisms that cause allele frequency change:
  • Natural selection
  • Genetic drift
  • Gene flow
• Genetic variation: the differences in genes or other DNA sequences among individuals
• Sources of genetic variation:
  • Mutation
  • Gene duplication
  • Sexual reproduction
• Gene pool: consists of all copies of every allele in all members of the population

Hardy-Weinberg Equilibrium

• If a population is not evolving, genotype and allele frequencies will be constant from generation to generation
• Equilibrium conditions:
  • No mutation
  • Random mating
  • No natural selection
  • Extremely large population size
  • No gene flow
• Hardy-Weinberg equation: p + q = 1
• Applying the equation: need to work on practice questions

Natural Selection

• Natural selection is the only mechanism that consistently causes adaptive evolution
• Relative fitness: the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals
• Patterns of natural selection:
  • Directional
  • Disruptive
  • Stabilizing
• Sexual selection: a process in which individuals with certain heritable traits are more likely to obtain mates than other individuals of the same sex
• Heterozygote advantage: occurs when heterozygotes have a higher fitness than both kinds of homozygotes

Genetic Drift

• A process in which chance events cause allele frequencies to fluctuate unpredictably from one generation to the next
• Tends to reduce genetic variation through the random loss of alleles
• The smaller the sample, the greater the chance of random deviation from a predicted result
• Founder effect: occurs when a few individuals become isolated from a larger population
• Bottleneck effect: occurs when there is a drastic reduction in population size due to a sudden change in the environment

Gene Flow

• Consists of the movement of alleles among populations
• Can lead to genetic variation and change in populations

Chapter 24: The Origin of Species

• Speciation: the process by which one species splits into two species
• Microevolution vs. macroevolution: macroevolution refers to broad patterns of evolutionary change above the species level
• Biological species concept: defined by the populations' ability to interbreed and produce fertile offspring
• Morphological species concept: mainly depends on anatomical physical features
• Ecological species concept: defines species by its ecological niche

Reproductive Isolation

• Results when biological barriers impede members of two species from interbreeding and producing fertile offspring
• Prezygotic and postzygotic isolations
• Prezygotic isolation:
  • Habitat isolation
  • Temporal isolation
  • Behavioral isolation
  • Mechanical isolation
  • Gametic isolation
• Postzygotic isolation:
  • Reduced hybrid viability
  • Reduced hybrid fertility
  • Hybrid breakdown

Speciation

• Two ways of speciation: allopatric vs. sympatric speciation
• Allopatric speciation: populations are geographically isolated
• Sympatric speciation: speciation occurs in populations that live in the same geographic area
• Polyploidy: instant speciation, common in plants
• Sexual selection: speciation is driven by mate choice for certain traits
• Habitat differentiation: the exploitation of new habitats or resources

Chapter 25: The History of Life on Earth

• The formation of earth: about 4.6 billion years ago
• The oldest prokaryote fossils: 3.5 billion years ago
• The oldest eukaryote fossils: 1.8 billion years ago
• The first genetic material on earth: more likely RNA
• Radiometric dating: how fossils are dated, using radioactive isotope
• Geologic record: Cambrian explosion (Many animal phyla appear suddenly in the fossils of the Cambrian period)

Endosymbiosis

• Origin of eukaryotic organisms
• Both mitochondria and plastids are thought to have descended from bacteria
• Serial endosymbiosis: the hypothesis stating that mitochondria evolved before plastids through a sequence of endosymbiotic events

Mass Extinctions

• Occur when large numbers of species rapidly become extinct worldwide
• Five mass extinctions have been documented
• Paved the way for adaptive radiation (a rapid period of evolutionary change where many new species arise and adapt to different ecological niches)

Chapter 26: Phylogeny and the Tree of Life

• Phylogeny: the evolutionary history of a species or group of related species
• Phylogenetic tree: the evolutionary history of a group of organisms can be represented in a branching diagram
• Biological classification system:
  • Domain-Kingdom-Phylum- Class-Order-Family-Genus-Species
  • Binomial nomenclature: by Carolus Linnaeus in the 18th century

Homology vs. Analogy

• Homology is similarity due to shared ancestry
• Analogy is similarity due to convergent evolution

Phylogenetic Tree

• Only monophyletic groups, consisting of the ancestor and all of its descendants, are clades
• A paraphyletic group consists of an ancestral species and some, but not all, of the descendants
• A polyphyletic group includes distantly related species but not their most recent common ancestor

Chapter 27: Bacteria and Archaea

• Prokaryotes:
  • Single-celled organisms that make up domains Bacteria and Archaea
  • First organisms to inhabit Earth
  • Most are unicellular but some species form colonies
  • Smaller and simpler than eukaryotic cells
  • Shapes: cocci, bacilli, spirals
  • Structures: nucleoid, plasmid, pili, fimbriae, capsule, ribosome
• Reproduce quickly by binary fission
• Genetic recombination by transformation, transduction, conjugation
• Different ways to obtain energy:
  • Phototrophs
  • Chemotrophs
  • Autotrophs
  • Heterotrophs
• Two domains with prokaryotes: bacteria and archaea
• Bacteria: gram positive vs. negative, Cyanobacteria are photosynthetic
• Archaea: extremophiles (live in extreme environments), methanogens
• The commonalities and differences between bacteria and archaea
• The roles of prokaryotes:
  • Pathogen
  • Mutualistic organisms
  • Decomposers

Descent with Modification

• Scientists who influenced Darwin: Hutton, Cuvier, Lyell, Wallace, etc.
• Darwin's 5-year voyage on the HMS Beagle as a naturalist led to the publication of "The Origin of Species" in 1859
• Definition of evolution: the process by which species accumulate differences from their ancestors as they adapt to different environments over time
• Populations change over time genetically, not individuals

Natural Selection

• The process by which individuals with certain inherited traits tend to survive and reproduce at higher rates because of those traits
• 4 observations (or inferences) of natural selection:
  • Individuals in populations vary in their inherited traits
  • All species can produce more offspring than the environment can support, leading to a struggle for existence
  • Individuals with inherited traits that increase survival and reproduction in an environment tend to produce more offspring
  • The unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations
• Artificial selection: humans can modify species through breeding only individuals with desired traits

Evidence of Evolution

• Direct observation: antibiotic resistance, birds' beak size and fruit size
• Homology: similarity from common ancestry, including:
  • Anatomical homology (homologous structures)
  • Comparative embryology
  • Vestigial structures (e.g. goosebumps, wisdom teeth, ear muscle, tailbone of humans)
  • Molecular homology (DNA)
• DNA provides strong evidence that all living organisms came from a common ancestor
• Fossil records: age of fossil records is about 3.5 billion years old
• Biogeography: the scientific study of the geographic distribution of species, including continental drift and the distribution of modern living organisms

Homologous vs. Analogous Structures

• Analogous traits are the result of similar environments, not common ancestry (convergent evolution)
• Examples of analogous structures: streamlined body shapes of dolphin and shark, sugar glider of Australia and flying squirrel of North America
• Examples of homologous structures: wings of birds and forelimbs of mammals (e.g. flippers of whales)

Microevolution vs. Macroevolution

• Microevolution: changes in allele frequencies in populations over generations, evolution at its smallest scale
• Macroevolution: broad patterns of evolutionary change above the species level, the formation of new species

Mechanisms of Evolution

• Three mechanisms that directly cause allele frequency change:
  • Natural selection
  • Genetic drift
  • Gene flow
• Genetic variation: the differences in genes or other DNA sequences among individuals, required for a population to evolve
• Sources of genetic variation: mutation, gene duplication, sexual reproduction

Hardy-Weinberg Equilibrium

• If a population is not evolving, genotype and allele frequencies will be constant from generation to generation
• Equilibrium conditions: no mutation, random mating, no natural selection, extremely large population size, no gene flow
• In real populations, allele and genotype frequencies often do change over time
• Hardy-Weinberg equation: p + q = 1, p² + 2pq + q² = 1

Natural Selection

• The only mechanism that consistently causes adaptive evolution
• Relative fitness: the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals
• Patterns of natural selection: directional, disruptive, and stabilizing
• Sexual selection: a process in which individuals with certain heritable traits are more likely to obtain mates than other individuals of the same sex
• Heterozygote advantage: occurs when heterozygotes have a higher fitness than both kinds of homozygotes

Genetic Drift

• A process in which chance events cause allele frequencies to fluctuate unpredictably from one generation to the next
• Tends to reduce genetic variation through the random loss of alleles
• The smaller the sample, the greater the chance of random deviation from a predicted result
• Founder effect: occurs when a few individuals become isolated from a larger population
• Bottleneck effect: occurs when there is a drastic reduction in population size due to a sudden change in the environment

Gene Flow

• Consists of the movement of alleles among populations
• Causes allele frequencies to change in a population

Speciation

• The process by which one species splits into two species
• Microevolution vs. macroevolution: macroevolution refers to broad patterns of evolutionary change above the species level
• Biological species concept: defined by the populations' ability to interbreed and produce fertile offspring
• Morphological species concept: mainly depends on anatomical physical features
• Ecological species concept: defines species by its ecological niche

Reproductive Isolation

• Results when biological barriers impede members of two species from interbreeding and producing fertile offspring
• Prezygotic and postzygotic isolations
• Prezygotic isolation: block fertilization, including:
  • Habitat isolation
  • Temporal isolation
  • Behavioral isolation
  • Mechanical isolation
  • Gametic isolation
• Postzygotic isolation: occurs after fertilization, including:
  • Reduced hybrid viability
  • Reduced hybrid fertility
  • Hybrid breakdown

Speciation

• Two ways of speciation: allopatric vs. sympatric speciation
• Allopatric speciation: populations are geographically isolated
• Sympatric speciation: speciation occurs in populations that live in the same geographic area
• Polyploidy: instant speciation, a process that can form a new species within a single generation without geographic separation
• Sexual selection: speciation is driven by mate choice for certain traits
• Habitat differentiation: the exploitation of new habitats or resources

The History of Life on Earth

• The formation of earth: about 4.6 billion years ago
• The oldest prokaryote fossils: 3.5 billion years ago
• The oldest eukaryote fossils: 1.8 billion years ago
• The first genetic material on earth: RNA (self-replication, central roles in protein synthesis, catalytic ability)
• Radiometric dating: how fossils are dated, using radioactive isotopes
• Geologic record: Cambrian explosion (many animal phyla appear suddenly in the fossils of the Cambrian period)

Endosymbiosis

• Origin of eukaryotic organisms
• Both mitochondria and plastids are thought to have descended from bacteria
• Serial endosymbiosis: the hypothesis stating that mitochondria evolved before plastids through a sequence of endosymbiotic events
• Evidence: mitochondria and plastids are similar to bacterial cells in their membrane protein, replication mechanisms, DNA structures, ribosomes, RNA sequence, etc.

Mass Extinctions

• Occur when large numbers of species rapidly become extinct worldwide
• Five mass extinctions have been documented
• Paved the way for adaptive radiation (a rapid period of evolutionary change where many new species arise and adapt to different ecological niches)

Phylogeny and the Tree of Life

• Phylogeny: the evolutionary history of a species or group of related species
• Phylogenetic tree: a branching diagram that represents the evolutionary history of a group of organisms
• Biological classification system: Domain-Kingdom-Phylum-Class-Order-Family-Genus-Species
• Binomial nomenclature: by Carolus Linnaeus in the 18th century

Bacteria and Archaea

• Prokaryotes: single-celled organisms that make up domains Bacteria and Archaea
• First organisms to inhabit Earth
• Most are unicellular but some species form colonies
• Smaller and simpler than eukaryotic cells
• Shapes: cocci, bacilli, spirals
• Structures: nucleoid, plasmid, pili, fimbriae, capsule, ribosome
• Reproduce quickly by binary fission
• Genetic recombination by transformation, transduction, conjugation
• Different ways to obtain energy: phototrophs, chemotrophs, autotrophs, heterotrophs
• Two domains with prokaryotes: bacteria and archaea

Bacteria and Archaea

• Bacteria: gram positive vs. negative, Cyanobacteria are photosynthetic
• Archaea: extremophiles (live in extreme environments), methanogens
• The commonalities and differences between bacteria and archaea
• Both have a plasma membrane, no nuclear envelope
• Different composition of cell wall (most bacterial cell walls contain peptidoglycan while Archaeal walls lack this material)
• The roles of prokaryotes: pathogen, mutualistic organisms, decomposers

Descent with Modification: A Darwinian View of Life

• Charles Darwin's publication of "The Origin of Species" in 1859 started a scientific revolution in evolutionary biology
• Darwin's ideas developed gradually, influenced by other works and his own travels

Evolution

• Evolution refers to the process by which species accumulate differences from their ancestors as they adapt to different environments over time
• Evolution can be viewed as both a pattern and a process
• The pattern is revealed by scientific data showing that life has evolved over time
• The process consists of the mechanisms that cause the pattern of change
• Descent with modification is a phrase summarizing Darwin's view of life

Scala Naturae and Classification of Species

• Greek philosopher Aristotle believed that species were fixed and unchanging
• Aristotle arranged species on a scale of increasing complexity called the scala naturae
• Carolus Linnaeus developed a nested classification system grouping similar species into increasingly inclusive categories
• Binomial format for naming species (e.g., Homo sapiens) is still in use today

Ideas About Change over Time

• Fossils provide evidence of species that have changed over time
• Paleontology, the study of fossils, was developed in large part by Georges Cuvier
• Cuvier observed that older strata contain fossils less similar to current organisms than more recent strata
• Cuvier speculated that boundaries between strata represent sudden catastrophic events
• Darwin was influenced by scientists proposing that slow, continuous processes caused change on Earth
• James Hutton and Charles Lyell proposed that Earth's geologic features were formed gradually
• Darwin reasoned that the Earth must be older than the widely accepted age of a few thousand years
• If true, gradual processes could also account for substantial biological change

Lamarck's Hypothesis of Evolution

• Jean-Baptiste de Lamarck proposed two principles to explain evolutionary change
  • Use and disuse: body parts used extensively become larger and stronger, unused parts deteriorate
  • Inheritance of acquired characteristics: modifications acquired in one's lifetime can be passed to offspring
• This mechanism is not supported by experimental evidence

Darwin's Research

• Charles Darwin had a consuming interest in nature throughout his life
• He studied medicine and theology before taking a position as naturalist on the HMS Beagle
• During his travels on the Beagle, Darwin collected specimens of South American plants and animals
• He noted that fossils resembled living species from the area in which they were found, and living species resembled other species from areas nearby
• On the Galápagos Islands, Darwin collected many similar but different species of birds, some unique to individual islands
• Animals unique to the islands resembled species on the nearby mainland of South America
• Darwin hypothesized that species from the mainland colonized and diversified on the islands

Descent with Modification

• Darwin used descent with modification to describe his view of life
• All organisms are related by descent from a common ancestor that lived in the past
• Related organisms living in different habitats gradually accumulated diverse modifications to fit them to specific ways of life
• Large morphological gaps between related groups are explained by branching and extinction events

Artificial Selection, Natural Selection, and Adaptation

• Humans modify species through artificial selection, breeding only individuals with desired traits
• Crops, livestock animals, and pets often bear little resemblance to their wild ancestors
• Natural selection is a process in which individuals with inherited traits that increase survival and reproduction in an environment tend to survive and reproduce at higher rates

Key Features of Natural Selection

• Individuals with certain heritable traits survive and reproduce at a higher rate than other individuals
• Natural selection increases the frequency of adaptations that are favorable in an environment
• If the environment changes, natural selection may drive adaptation to new conditions, giving rise to new species

Evolution is Supported by Scientific Evidence

• Direct observations of evolutionary change

• Homology, similarity resulting from common ancestry

  • Anatomical and molecular homologies
    • Vestigial structures are remnants of features that served a function in the organism's ancestors
  • Molecular homologies, including the genetic code shared by all life

• The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time

• Biogeography, the scientific study of the geographic distribution of species, provides support for evolution### Understanding Continental Drift and Species Distribution

• The study of continental drift and modern species distribution helps predict when and where different groups evolved

• Freshwater fish in the family Galaxiidae live in South America and Australia, separated by wide stretches of open ocean

• These fish species share a common ancestor dating back to the time when the continents broke away from Pangea

Characteristics of a Scientific Theory

• A scientific theory accounts for many observations and data
• A theory attempts to explain and integrate a great variety of phenomena
• Darwin's theory of evolution by natural selection integrates diverse areas of biological study
• The theory stimulates many new research questions
• Ongoing research adds to our understanding of evolution

Descent with Modification: A Darwinian View of Life

• Charles Darwin's publication of "The Origin of Species" in 1859 started a scientific revolution in evolutionary biology
• Darwin's ideas developed gradually, influenced by other works and his own travels

Evolution

• Evolution refers to the process by which species accumulate differences from their ancestors as they adapt to different environments over time
• Evolution can be viewed as both a pattern and a process
• The pattern is revealed by scientific data showing that life has evolved over time
• The process consists of the mechanisms that cause the pattern of change
• Descent with modification is a phrase summarizing Darwin's view of life

Scala Naturae and Classification of Species

• Greek philosopher Aristotle believed that species were fixed and unchanging
• Aristotle arranged species on a scale of increasing complexity called the scala naturae
• Carolus Linnaeus developed a nested classification system grouping similar species into increasingly inclusive categories
• Binomial format for naming species (e.g., Homo sapiens) is still in use today

Ideas About Change over Time

• Fossils provide evidence of species that have changed over time
• Paleontology, the study of fossils, was developed in large part by Georges Cuvier
• Cuvier observed that older strata contain fossils less similar to current organisms than more recent strata
• Cuvier speculated that boundaries between strata represent sudden catastrophic events
• Darwin was influenced by scientists proposing that slow, continuous processes caused change on Earth
• James Hutton and Charles Lyell proposed that Earth's geologic features were formed gradually
• Darwin reasoned that the Earth must be older than the widely accepted age of a few thousand years
• If true, gradual processes could also account for substantial biological change

Lamarck's Hypothesis of Evolution

• Jean-Baptiste de Lamarck proposed two principles to explain evolutionary change
  • Use and disuse: body parts used extensively become larger and stronger, unused parts deteriorate
  • Inheritance of acquired characteristics: modifications acquired in one's lifetime can be passed to offspring
• This mechanism is not supported by experimental evidence

Darwin's Research

• Charles Darwin had a consuming interest in nature throughout his life
• He studied medicine and theology before taking a position as naturalist on the HMS Beagle
• During his travels on the Beagle, Darwin collected specimens of South American plants and animals
• He noted that fossils resembled living species from the area in which they were found, and living species resembled other species from areas nearby
• On the Galápagos Islands, Darwin collected many similar but different species of birds, some unique to individual islands
• Animals unique to the islands resembled species on the nearby mainland of South America
• Darwin hypothesized that species from the mainland colonized and diversified on the islands

Descent with Modification

• Darwin used descent with modification to describe his view of life
• All organisms are related by descent from a common ancestor that lived in the past
• Related organisms living in different habitats gradually accumulated diverse modifications to fit them to specific ways of life
• Large morphological gaps between related groups are explained by branching and extinction events

Artificial Selection, Natural Selection, and Adaptation

• Humans modify species through artificial selection, breeding only individuals with desired traits
• Crops, livestock animals, and pets often bear little resemblance to their wild ancestors
• Natural selection is a process in which individuals with inherited traits that increase survival and reproduction in an environment tend to survive and reproduce at higher rates

Key Features of Natural Selection

• Individuals with certain heritable traits survive and reproduce at a higher rate than other individuals
• Natural selection increases the frequency of adaptations that are favorable in an environment
• If the environment changes, natural selection may drive adaptation to new conditions, giving rise to new species

Evolution is Supported by Scientific Evidence

• Direct observations of evolutionary change

• Homology, similarity resulting from common ancestry

  • Anatomical and molecular homologies
    • Vestigial structures are remnants of features that served a function in the organism's ancestors
  • Molecular homologies, including the genetic code shared by all life

• The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time

• Biogeography, the scientific study of the geographic distribution of species, provides support for evolution### Understanding Continental Drift and Species Distribution

• The study of continental drift and modern species distribution helps predict when and where different groups evolved

• Freshwater fish in the family Galaxiidae live in South America and Australia, separated by wide stretches of open ocean

• These fish species share a common ancestor dating back to the time when the continents broke away from Pangea

Characteristics of a Scientific Theory

• A scientific theory accounts for many observations and data
• A theory attempts to explain and integrate a great variety of phenomena
• Darwin's theory of evolution by natural selection integrates diverse areas of biological study
• The theory stimulates many new research questions
• Ongoing research adds to our understanding of evolution

Descent with Modification

• Scientists who influenced Darwin: Hutton, Cuvier, Lyell, Wallace, etc.
• Darwin's 5-year voyage on the HMS Beagle and publication of "The Origin of Species" in 1859
• Definition of evolution: the process by which species accumulate differences from their ancestors as they adapt to different environments over time
• Populations change over time genetically, not individuals

Natural Selection

• The process in which individuals with certain inherited traits tend to survive and reproduce at higher rates because of those traits
• 4 observations of natural selection:
  • Individuals in populations vary in their inherited traits
  • All species can produce more offspring than the environment can support, and many of these offspring fail to survive and reproduce
  • Individuals with inherited traits that increase survival and reproduction in an environment tend to produce more offspring than other individuals
  • The unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations
• Artificial selection: humans can modify species through breeding only individuals with desired traits

Evidence of Evolution

• Direct observation: antibiotic resistance, birds' beak size and fruit size
• Homology: similarity from common ancestry
  • Anatomical homology (homologous structures)
  • Comparative embryology
  • Vestigial structures (e.g. goosebumps, wisdom teeth, ear muscle, tailbone of human)
  • Molecular homology (DNA)
• Fossil records: 3.5 billion years ago
• Biogeography: the scientific study of the geographic distribution of species (continental drift and the distribution of modern living organisms)

Evolution of Populations

• Microevolution vs. macroevolution
• Three mechanisms that cause allele frequency change:
  • Natural selection
  • Genetic drift
  • Gene flow
• Genetic variation: the differences in genes or other DNA sequences among individuals
  • Sources of genetic variation: mutation, gene duplication, sexual reproduction
• Gene pool: consists of all copies of every allele in all members of the population
• Hardy-Weinberg Equilibrium:
  • If a population is not evolving, genotype and allele frequencies will be constant from generation to generation
  • Equilibrium conditions: no mutation, random mating, no natural selection, extremely large population size, no gene flow

Natural Selection (continued)

• Relative fitness: the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals
• Patterns of natural selection:
  • Directional
  • Disruptive
  • Stabilizing
• Sexual selection: a process in which individuals with certain heritable traits are more likely to obtain mates than other individuals of the same sex
• Heterozygote advantage: occurs when heterozygotes have a higher fitness than both kinds of homozygotes (e.g. sickle cell anemia)

Genetic Drift

• A process in which chance events cause allele frequencies to fluctuate unpredictably from one generation to the next
• Tends to reduce genetic variation through the random loss of alleles
• The smaller the sample, the greater the chance of random deviation from a predicted result
• Founder effect: occurs when a few individuals become isolated from a larger population
• Bottleneck effect: occurs when there is a drastic reduction in population size due to a sudden change in the environment

Gene Flow

• Consists of the movement of alleles among populations

Origin of Species

• Speciation: the process by which one species splits into two species
• Microevolution vs. macroevolution
• Biological species concept:
  • Defined by the populations' ability to interbreed and produce fertile offspring
  • Limitations: cannot be applied to fossils or asexual organisms
• Morphological species concept:
  • Mainly depends on anatomical physical features
  • Not as accurate as the biological species concept, but still useful in fossil data, asexual species, and species that we can't observe their reproductive activity
• Ecological species concept: defines species by its ecological niche

Reproductive Isolation

• Results when biological barriers impede members of two species from interbreeding and producing fertile offspring
• Prezygotic and postzygotic isolations
• Prezygotic isolation:
  • Habitat isolation
  • Temporal isolation
  • Behavioral isolation
  • Mechanical isolation
  • Gametic isolation
• Postzygotic isolation:
  • Reduces hybrid viability
  • Reduces hybrid fertility
  • Hybrid breakdown

Speciation

• Two ways of speciation: allopatric vs. sympatric speciation
• Allopatric speciation: populations are geographically isolated
• Sympatric speciation: speciation occurs in populations that live in the same geographic area
• Polyploidy: instant speciation, common in plants
• Sexual selection: speciation is driven by mate choice for certain traits
• Habitat differentiation: the exploitation of new habitats or resources

History of Life on Earth

• Formation of earth: about 4.6 billion years ago
• Oldest prokaryote fossils: 3.5 billion years ago
• Oldest eukaryote fossils: 1.8 billion years ago
• The first genetic material on earth: likely RNA
• Radiometric dating: how fossils are dated, using radioactive isotopes (e.g. Carbon 14)
• Geologic record: Cambrian explosion (many animal phyla appear suddenly in the fossils of the Cambrian period)
• Endosymbiosis:
  • Origin of eukaryotic organisms
  • Serial endosymbiosis: the hypothesis stating that mitochondria evolved before plastids through a sequence of endosymbiotic events

Phylogeny and the Tree of Life

• Phylogeny: the evolutionary history of a species or group of related species
• Phylogenetic tree: represents the evolutionary history of a group of organisms in a branching diagram
• Biological classification system:
  • Domain-Kingdom-Phylum-Class-Order-Family-Genus-Species
  • Binomial nomenclature: by Carolus Linnaeus in the 18th century
• Homology vs. Analogy:
  • Homology is similarity due to shared ancestry
  • Analogy is similarity due to convergent evolution
• Phylogenetic tree:
  • Only monophyletic groups, consisting of the ancestor and all of its descendants, are clades
  • A paraphyletic group consists of an ancestral species and some, but not all, of the descendants
  • A polyphyletic group includes distantly related species but not their most recent common ancestor

Bacteria and Archaea

• Prokaryotes: single-celled organisms that make up domains Bacteria and Archaea
• Characteristics:
  • Smaller and simpler than eukaryotic cells
  • Shapes: cocci, bacilli, spirals
  • Structures: nucleoid, plasmid, pili, fimbriae, capsule, ribosome
  • Reproduce quickly by binary fission
  • Genetic recombination by transformation, transduction, conjugation
  • Different ways to obtain energy: phototrophs, chemotrophs, autotrophs, heterotrophs
• Two domains with prokaryotes: Bacteria and Archaea
• Commonalities and differences between Bacteria and Archaea:
  • Both have a plasma membrane, no nuclear envelope
  • Different composition of cell wall (peptidoglycan in bacteria, lacking in archaea)
• Roles of prokaryotes: pathogens, mutualistic organisms, decomposers

Protists

• An informal term for eukaryotes that are not plants, animals, or fungi
• Characteristics:
  • Have a nucleus and membrane-enclosed organelles
  • Most are unicellular, but some are multicellular
  • Nutritionally diverse (photoautotrophs, heterotrophs, mixotrophs)
• Endosymbiosis: a relationship between two species where one organism lives inside the cell or cells of the other
• 4 groups:
  • Excavata (Trypanosoma, Euglena)
  • SAR (Diatoms, brown algae, water molds, Dinoflagellates, Plasmodium, Paramecium)
  • Archaeplastida (red and green algae, Charophytes, Volvox)
  • Unikonta (Amoeba, slime mold)

Fungi

• Heterotrophs that absorb nutrients from outside their bodies
• Characteristics:
  • Mostly multicellular, but some are unicellular (e.g., yeast)
  • Cell walls made of chitin
  • Sexual and asexual reproduction
• Body structure:
  • Hyphae: tubular cell walls strengthened with chitin, divided into cells by septa
  • Mycelium: an interwoven mass formed by hyphae, maximizing surface area for absorption
• Roles:
  • Decomposers
  • Mutualists
  • Pathogens (e.g., ringworm, yeast infection)
  • Medicine (e.g., penicillin)

Mutualism of Fungi

• Mycorrhiza: mutually beneficial relationships between fungi and plant roots
• Lichen: symbiotic associations between photosynthetic microorganisms and fungi
• Fungus-farming ants: some fungi share digestive services with animals

Plant Diversity

• Role of plants: oxygen production, food sources, habitat for land organisms
• Similarities between plants and green algae:
  • Multicellular, eukaryotic, photosynthetic autotrophs
  • Cellulose cell walls
  • Chloroplasts
• Differences:
  • Alternation of generations
  • Walled spores produced in sporangia
  • Apical meristems
  • Cuticle and stomata unique to plants

Evolution of Plants

• From cyanobacteria to green algae to land plants
• Four groups of plants:
  • Nonvascular plants (Bryophytes, Mosses)
  • Seedless vascular plants (ferns)
  • Gymnosperms (naked seeds)
  • Angiosperms (flowers, double fertilization, nearly 90% of living plants)

Seed Plants

• Sporophyte-dominated life cycle
• Characteristics:
  • Reduced gametophytes
  • Heterospory
  • Ovules
  • Pollen
• Pollination: transfer of pollen to ovules
• Seeds:
  • Consist of embryo and nutrients surrounded by a coat
  • Can remain dormant for years
  • Can be transported long distances by wind or animals
• Gymnosperms:
  • Naked seeds exposed on sporophylls (e.g., conifers)
• Angiosperms:
  • Seed plants with reproductive structures called flowers and fruits
  • 90% of all plants

Plant Structure

• Hierarchical organization: cell – tissue – organ – organism
• Plant organs:
  • Roots (root system)
  • Stems and leaves (shoot system)
• Root functions:
  • Anchoring the plant
  • Absorbing minerals and water
  • Storing carbohydrates
• Stem functions:
  • Elongating and orienting the shoot
  • Maximizing photosynthesis
• Leaf functions:
  • Main photosynthetic organ
  • Exchanging gases
  • Defending against herbivores and pathogens

Plant Tissues

• Dermal tissue: protective outer coating
• Vascular tissue: facilitates transport of materials and provides mechanical support
• Ground tissue: specialized cells for storage, photosynthesis, and support
• Meristem tissue: for growth and development

Plant Cells

• Parenchyma: performs most metabolic functions
• Collenchyma: provides flexible support
• Sclerenchyma: rigid cells with secondary cell walls containing lignin
• Water-conducting cells of the xylem: tracheids, vessel elements
• Sugar-conducting cells of the phloem: sieve-tube elements, companion cells

Resource Acquisition and Transport

• Xylem: transports water and minerals from roots to shoots
• Phloem: transports photosynthetic products from where they are made to where they are needed
• Stomata: pores necessary for CO2 diffusion into photosynthetic tissues
• Mycorrhizae: fungal associations increase surface area for absorbing water and minerals
• Aquaporins: transport proteins facilitating water passage across cell membranes

Soil and Plant Nutrition

• Essential elements: 17 chemical elements required for plant life cycle
• 9 macronutrients: required in large amounts
• 8 micronutrients: required in small amounts
• Plant mutualism with soil bacteria: rhizobacteria and endophyte
• Nitrogen fixation: required for plants to acquire nitrogen as nitrate

Angiosperm Reproduction

• Angiosperm anatomy:
  • Flowers: reproductive shoots of the angiosperm sporophyte
  • Four parts of flowers: carpels, stamens, petals, sepals
• Angiosperm life cycle:
  • Gametophyte development
  • Sperm delivery by pollen tubes
  • Double fertilization
  • Seed development
• Pollination: transfer of pollen from anthers to stigma
• Double fertilization: fusion of gametes
• Fruits: mature ovary of a flower, protects seeds and aids in seed dispersal

Chapter 32: Animal Diversity

• Common characteristics of animals: can move and capture prey, multicellular, no cell walls, heterotrophic, eukaryotes
• Animals evolved from flagellated protists, with choanoflagellates as the closest living relatives
• The Cambrian explosion marks a period of rapid animal diversification
• Animal body plan: radial symmetry vs. bilateral symmetry, with most animals evolving to have bilateral symmetry for faster movement and formation of a head with sensory organs and central nervous system

Embryo Development

• Animal zygotes undergo cleavage, a succession of cell divisions without growth between divisions
• Cleavage leads to the formation of a blastula, often in the form of a hollow ball of cells

Animal Tissues

• Only a few groups have no tissue (e.g., sponges)
• Most animals have germ layers that give rise to the tissues and organs (diploblastic: ectoderm and endoderm/triploblastic: ectoderm, endoderm, and mesoderm)
• Body cavity: coelom (a cavity surrounded by tissues derived from mesoderm), hemocoel (filled with hemolymph), or no cavity at all (e.g., flatworms)

Protostome vs. Deuterostome Development

• In protostome development, the blastopore becomes the mouth
• In deuterostomes, the blastopore becomes the anus (e.g., echinoderms and chordates)

Chapter 33: Invertebrate Animals

• Invertebrates: animals without a backbone
• Porifera (sponges): simplest animals, filter feeders, no tissue
• Cnidarians: true tissues, gastrovascular cavity, polyps and medusa life forms, nematocysts, radial symmetry
• Lophotrochozoans: have a lophophore for feeding or a trochophore larval stage
• Flatworms (platyhelminthes): flat body form for large surface area (e.g., planarians, tapeworms)
• Molluscs: muscular foot, visceral mass, mantle (major groups: Gastropoda, Bivalvia, Cephalopoda)
• Annelids: segmented worms, have a coelom (e.g., leeches, earthworms)
• Ecdysozoans: cuticle, molting
• Nematodes: have hemocoel (e.g., roundworms)
• Arthropods: segmented body, exoskeleton, jointed appendages, open circulatory system with heart and hemolymph (example groups: Pancrustaceans including insects, Chelicerates, Myriapods)
• Deuterostomes: formation of the anus from the blastopore, radial cleavage
• Echinoderms: water vascular system, tube feet

Chapter 34: Vertebrate Animals

• Common characteristic of chordates: bilateral, deuterostome development, mostly vertebrates with two groups of invertebrates
• Four characteristics of chordate embryos: notochord, dorsal nerve cord, pharyngeal pouches (slits), post-anal tail
• Chordates:
  • Lancelet, tunicates: invertebrates
  • Hagfishes and lampreys: lacking jaws
  • Sharks and rays: oil in the liver to maintain buoyancy
  • Ray-finned and lobe-fin fish: swim bladder for buoyancy
  • Amphibians: need water and land for living, metamorphosis, frogs, and salamanders
  • Reptiles: scales, shelled and amniotic eggs, ectothermic
  • Birds: endothermic, direct descendants of dinosaurs
  • Mammals: mammary glands, hair, endothermy (high metabolic rate)

Chapter 40: Animal Form and Function

• Tissues: groups of cells with a similar appearance and function
• Four types of tissues:
  • Epithelial tissue: covers the outside of the body and lines the organs and cavities within the body
  • Connective tissue: holds many tissues and organs together in place (e.g., tendons, ligaments, bone, adipose tissue, blood)
  • Muscle tissue:
    • Skeletal muscle: responsible for voluntary movement
    • Smooth muscle: responsible for involuntary body activities such as digestive system movement or uterus contraction
    • Cardiac muscle: responsible for contraction of the heart (striated with intercalated disc)
  • Nervous tissue: functions in the receipt, processing, and transmission of information

Homeostasis

• Automatic tendency to maintain a constant and optimal internal environment
• Positive and negative feedback

Chapter 41: Animal Nutrition

• Variation in diet: herbivores, carnivores, omnivores
• Food processing: ingestion, digestion, absorption, and elimination
• Most complex animals have a digestive tube with two openings (alimentary canal)
• Advantages of having a complete digestive system: specialized regions with diverse functions
• Digestive system in human:
  • Oral cavity: salivary glands, amylase which breaks down starch
  • Pharynx: the junction that opens to the esophagus and the trachea
  • Esophagus: connects to the stomach, food is pushed to the stomach by peristalsis (by alternating waves of smooth muscle contraction), valves called sphincters regulate the movement of material between compartments
  • Stomach: gastric juice, chyme, breaks down proteins, mucus protects the stomach lining
  • Small intestine: most enzymatic hydrolysis of macromolecules occurs here (pancreas produces trypsin and chymotrypsin, bile facilitates fat digestion (made by liver and stored in gall bladder), huge surface area due to villi and microvilli
  • Large intestine: absorbs water and salts, includes colon, cecum, and rectum

Chapter 42: Circulation and Respiration

• Open and closed circulatory system
• Insects, other arthropods, and some molluscs: open circulatory systems with hemolymph
• Annelids, cephalopods, and vertebrates: closed circulatory systems
• Human cardiovascular system:
  • Heart
  • Blood vessels:
    • Arteries: carry blood away from the heart to capillaries
    • Veins: return blood from capillaries to the heart
    • Capillaries: where chemical exchanges occur
  • Blood:
    • Plasma: liquid matrix
    • Platelets: fragments of cells involved in clotting
    • Red blood cells (erythrocytes): transport oxygen
    • White blood cells (leukocytes): defense

Chapter 43: Immune System

• Examples of pathogens: agents that cause disease such as viruses, bacteria, fungi
• Innate immunity:
  • Non-specific, active immediately upon infection
  • Barrier defenses (skin, mucus, body fluids)
  • Cellular defense (neutrophils, macrophages, dendritic cells, eosinophils, natural killer cells)
  • Inflammation: histamine triggers blood vessels to dilate and become more permeable
  • Interferons: provide innate defense by inhibiting the replication of viruses
• Adaptive immunity:
  • Activated after the innate response
  • Develops more slowly
  • Enhanced by previous exposure to the pathogen
  • T cells (mature in thymus)
  • B cells (mature in bone marrow)

Chapter 44: Osmoregulation

• Osmoregulation: controls solute concentrations and balances water gain and loss
• Animal’s nitrogenous waste: consumption of proteins and nucleic acids causes nitrogenous waste
• Excretory systems:
  • Filtration: filtering of body fluids
  • Reabsorption: recovering valuable solutes
  • Secretion: adding nonessential solutes and wastes to the filtrate
  • Excretion: processed filtrate containing nitrogenous wastes is released from the body
• Kidney: the excretory organs of vertebrates and some other chordates, function in excretion and osmoregulation
• Nephrons: the functional units of the vertebrate kidney

Chapter 45: Hormones

• Hormone: a secreted molecule that circulates through the body and stimulates specific cells
• Communication and control in animals:
  • Endocrine system: chemical signaling by hormones
  • Nervous system: a network of specialized cells (neurons) that transmit signals along dedicated pathways
• Feedback regulation:
  • Negative feedback: the response reduces the initial stimulus (more common)
  • Positive feedback: reinforces a stimulus to produce an even greater response (e.g., oxytocin causes the release of milk, causing greater suckling by offspring, which stimulates the release of more oxytocin)
• Hypothalamus: coordinates endocrine signaling, signals from the hypothalamus travel to the pituitary gland
• Posterior pituitary: stores and secretes hormones that are made in the hypothalamus
• Anterior pituitary: makes and releases hormones under regulation of the hypothalamus