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Biology > Unit 3: Evolution > Flashcards

Unit 3: Evolution Flashcards

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1
Q

Evolution

A

change in biological entities over time (over generations)

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2
Q

Carolus Linnaeus

A
  • Father of Taxonomy (biological classification)
  • Promoted hierarchal, nested classification (and formal ranks)
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3
Q

Paleontology (fossils) and evolution

A
  • Rocks appear in layers: strata, as you go through strata, you go back in time
  • rocks of different age in the same location contain different species
  • Many species preserved as fossils are no longer seen on earth (extinct)
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4
Q

Lamarck’ ideas (1809)

A
  • Observed progressions of similar species in fossil records
    proposal: New species arise by modification of existing species
    1) Pattern
  • Living world made up of many separate lineages with independent origins
  • Each lineage progresses towards greater complexity/perfection
    2) Process
  • ‘use and disuse of parts’, with ‘inheritance of acquired characters’
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5
Q

Darwin - 2 main ideas

A

1) Pattern
- Living things united in one branching tree of relationships
- New lineages constantly being created by existing lineages splitting in two
- Each lineage progresses
Process of evolution
2) Process
- Evolution occurs primarily because of the action of natural selection
- Key point: individuals of a species belong to populations

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6
Q

Natural Selection - Ingredients

A

1) Heritable Variation
2) Excess Production
3) Differential Success

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7
Q

Heritable Variation

A
  • Individuals in a population are born differing in many traits
  • Many traits are passed on from parents to offspring (i.e. are heritable)
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8
Q

Excess Production

A
  • In any population, more offspring are produced than ‘needed’ to maintain it
  • When resources are limited, many of the offspring fail to survive/don’t reproduce
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9
Q

Differential Success (and fitness)

A
  • Because of their differing traits, some individuals are more likely than others to survive and reproduce
  • i.e. will produce more viable offspring on average
  • This is the concept of fitness
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10
Q

Evidence of Evolution

A

1) Natural selection in action
2) Evidence for a tree-of-life, and descent with modification
3) Analogous structures
4) Biogeography
5) The Fossil Record
6) Transitional forms
7) Modern whales

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11
Q

Natural selection in action

A

1) Warfarin resistance in rats
- Warfarin interferes with synthesis of blood-clotting agents, bleeding, death
- mutations in a gene associated with warfarin resistance
- Resistance increases rapidly in populations after poisoning program introduced
- Contingent on time and place
e.g. the gene variants that confer warfarin resistance happen to by disadvantageous when poison not being used
2) Soapberry bugs
- bug feeding on fruit of original host species
- flatter fruit becomes more common
- shorter beaks favored, to get to flat fruit
- Good example of “directional selection”

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12
Q

Evidence for tree-of-life, and descent with modification

A

1) Homology
- Similarity resulting from common ancestry
- E.g. standard anatomical homologies, vestigial structures, molecular homologies
- Ex: pentadactyl limb in mammals, common despite different functions, humans, cats, whales, bats
2) Vestigial structures
- Structures with little or no function, derived from more complex structures
- Ex: Remnant hind-limb bones in whales and same snakes
3) Molecular homologies
- Homologies at the biochemical level
- Ex: The universal genetic code
- Pseudogenes: Molecular vestigial features

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13
Q

Analogous Structures

A
  • Similar function, but no common underlying structure (similarity because of environment and not common ancestry)
  • Convergent evolution: When two species develop different structures that serve the same purpose because if similar environments
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14
Q

Biogeography

A
  • The geographic distribution of organisms
  • Some taxa are restricted to certain locations (endemic)
  • Explanation: Descent from a common ancestor that lived in that location
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15
Q

The Fossil Record

A
  • Descent with modification predicts ‘transitional forms’
  • Order or appearance in fossil record
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16
Q

Transitional forms

A
  • Ex: groups with major adaptations associated with an ‘unusual lifestyle’
  • Whales (fully aquatic mammals)
  • Birds (powered flight)
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17
Q

Modern Whales

A

Adaptations to being permanently aquatic:
- Lack hind-limbs
- Forelimbs lack distinct features
- Dorsal fin, caudal flukes
- Nostrils on top of head, etc.
- A series of many ‘transitional forms’ link modern whales to land-dwelling mammals

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18
Q

What is a population?

A
  • Localized group of interbreeding and interacting individuals
  • Each species is made up of one to many populations (that can interbreed when they meet)
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19
Q

Gene pool of a population/types

A
  • All alleles at all gene loci in all individuals
  • “Fixed” alleles: Whole population is homozygous at locus
  • Polymorphic loci: 2+ alleles in population, each present at some frequency
  • Most populations have thousands of polymorphic loci
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20
Q

Microevolution

A
  • Change in the frequencies of alleles over generations
  • At the extreme, ‘change’ can mean fixation of an allele, or loss (extinction) of an allele
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20
Q

Hardy-Weinberg Principle

A
  • Describes expected relationships between allele genotype frequencies when there is no evolution
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20
Q

Uses of Hardy-Weinberg Principle

A

1) Estimating allele and genotype frequencies
2) Populations with genotype frequencies that conform to the equation are said to be in Hardy-Weinberg equilibrium at that locus

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20
Q

Source of genetic variation

A
  • New alleles arise by mutation is existing alleles (A single mutation can result in a new allele)
  • Most mutations don’t meaningfully affect fitness: ‘neutral variation’
  • Some reduce fitness: harmful alleles
  • A very few alleles increase fitness: beneficial alleles
  • Alleles can also be introduced to a population from other populations
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20
Q

Hardy-Weinberg Equation

A

P^2 + 2pq + q^2 = 1
- P^2 and q^2 = Expected frequencies of the two homozygous genotypes
- 2pq = Expected frequency of heterozygotes

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21
Q

3 Causes if Microevolution

A

1) Natural selection
2) Gene flow
3) Genetic drift

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21
Q

Assumptions of Hardy-Weinberg

A

1) No net mutations
2) Random mating
3) No natural selection
4) Very large (infinite) population size
5) No migration
Violation of these assumptions usually signals evolutionary change

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22
Q

Gene Flow

A
  • Dispersal of gametes (e.g. pollen) or migration
  • Gene flow from populations with different allele frequencies, change in allele frequencies
  • Gene flow can introduce new alleles to a population
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23
Q

Random Genetic Drift

A
  • ‘Sampling error’: Random changes in allele frequencies over generations
  • Can lead to fixation (or extinction) of alleles in populations in the absence of natural selection
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24
Q

Drift, population size and frequencies

A
  • Rate of drift related to population size - faster in small populations than large
  • Random: Neutral allele frequency 0.5 is equally likely to eventually be fixed or to go extinct
  • In theory, chance of eventual fixation of a neutral allele in the same as its frequency
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25
Q

Genetic bottlenecks

A
  • Breeding population is very small for a time - genetic drift powerful: Allele frequencies change, many alleles fixed or go extinct
  • Lower genetic diversity overall, even if population late expands in numbers
  • Some rare alleles can increase in frequency = high frequencies of harmful alleles possible (even fixation of slightly harmful alleles)
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26
Q

Genetic bottlenecks - example

A

Greater Prairie Chickens of Illinois
- Lower genetic variability than larger
- Much reduced reproductive success (% eggs hatched)
- Fitness lowered by accumulated harmful alleles

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27
Q

Founder effect

A
  • Special case of the bottleneck
  • A FEW individuals found a new population
  • new population grows
  • Gene pool of new population reflects the small sample of alleles present in the founders
  • Some previously rare alleles end up being much more common in the new population
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28
Q

Founder effect example

A

High prevalence of particular genetic diseases in isolated human populations

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29
Q

Polygenic Inheritance

A
  • Phenotype influenced by several genes (alleles at several loci)
  • Smooth range of phenotypes (quantitative character)
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30
Q

Modes of Selection

A

1) Directional selection
2) Stabilizing selection
3) Disruptive selection
4) Sexual selection

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31
Q

Directional Selection

A
  • One end of distribution selected against
  • Classic response to changing environments
  • Ex: Soapberry bugs: flatter fruit causes shorter beaks, beak length in population falls
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32
Q

Stabilizing Selection

A
  • Extreme phenotypes selected against
  • often due to different, opposing selective forces
33
Q

Disruptive Selection

A
  • Intermediate phenotypes are selected against
  • Role in some speciation events
34
Q

Sexual Selection

A
  • Effectively, a special case of natural selection
  • Competition for mating opportunities
  • Results in adaptations that increase mating success
  • But (sometimes) actually reduce survival
    2 types:
  • Intrasexual selection
  • Intersexual selection
  • Many remarkable adaptations increase success during intersexual and
35
Q

Intrasexual selection

A

Competition within one sex (usually males) for mating opportunities

36
Q

Intersexual Selection

A

One sex (usually females) chooses mate from competing members of other sex

37
Q

Sexual Dimorphism

A

Common with sexual selection. Adaptation benefits only one sex, while both sexes would suffer any survival cost
- Distinct difference in size or appearance between the sexes of an animal in addition to difference between the sexual organs themselves

38
Q

Sickle Cell Anemia

A
  • Single locus recessive genetic disease
  • ss homozygotes - high mortality while young: Fitness of ss much lower than SS or Ss
  • But, Ss confers resistance to malaria
  • Malaria absent: SS and Ss similar fitness
  • Malaria prevalent: Ss confers higher fitness than SS
39
Q

What is a species?

A

1) Morphological species concept:
- Based on morphological similarity
- Molecular sequence similarity now also used
2) Biological species concept:
- Inter-fertility: Populations that interbreed to produce fertile offspring
- Reproductive Isolation: Do not normally successfully interbreed in nature with other species = no/few ‘Hybrids’

40
Q

Speciation

A
  • ‘Reproductive barriers’ inhibit gene flow between populations, allowing evolutionary divergence
41
Q

Types of reproductive barriers

A
  • Prezygotic Barriers: Act before fertilization
  • Habitat isolation
  • Temporal isolation
  • Behavioral isolation
  • Mechanic isolation
  • Gametic isolation (gamete incompatibility)
  • Postzygotic barriers: Act after fertilization
  • Hybrid inviability
  • Hybrid infertility (sterility)
  • Hybrid breakdown
42
Q

Hybrid Infertility Example

A
  • Horse and donkey mate
  • Mule: Vigorous, but infertile
  • Incompatible chromosome organizations
43
Q

Evolution of reproductive barriers

A
  • May arise ‘accidentally’ as a result of evolution in isolation
  • May evolve through natural selection to reduce interspecies mating that lowers reproductive success
44
Q

Types of Speciation

A

1) Allopatric speciation: Geographic barrier blocks gene flow between populations
- A barrier forms, or migrants cross existing barrier, founding new population
- Evolutionary change due to natural selection in both environments (adaptive evolution)
- Genetic drift (especially in small isolated populations)
2) Sympatric speciation: new species arise within range of parental population
- Requires a genetic barrier within a geographic region (ex. top vs bottom of a lake)
- Ex: disruptive selection: Favoring evolution of reproductive barriers between individuals with different phenotypes
- Polyploid speciation, especially in plants

45
Q

If contact is re-established between evolved allopatric populations

A

1) Complete reproductive barriers evolved: populations now classic biological species
2) Partial reproductive barriers evolved: Formation of hybrids where species contact
- Fusion: Hybrids form readily, have high fitness: The incipient species merge into one again
- Reinforcement: Hybrids have low fitness: Natural selection strengthens barriers: hybridization gradually ends: Two good biological species
- Long-lasting hybrids zone: (e.g. Hybrids have variable fitness, or are uncommon)

46
Q

Polyploid Speciation

A

Allopolyploid example (one mechanism)
- Viable but infertile hybrid
- Mitotic (or meiotic) error doubles chromosome number
- New fertile hybrid, reproductively isolated from both species A and species B
- Allopolyploid speciation is an example of ‘hybrid speciation’

47
Q

Systematics

A
  • Study of the diversity of life
  • Two components:
    1) Taxonomy: Naming and identification of taxa: Species and groups of species
    2) Estimation of evolutionary trees (Phylogenetic trees)
48
Q

Taxa

A
  • Taxa are named groups: collections of similar species
  • Domain, Kingdom, Phyla, Class, Order, Family, Genus, Species
  • Follow Binomial naming: Genus first, then species, in italics
49
Q

Phylogenetic Trees and Cladograms

A
  • ‘Tips’ represent examined units (often living species)
  • Branch point = ‘internal nodes’ represent ancestors
  • We usually don’t label internal nodes
50
Q

Cladogram vs Phylogram

A

Cladogram:
- Branch lengths have no particular meaning
Phylogram:
- Branch lengths represent (inferred) amount of evolutionary change
- Especially used for molecular phylogenies

51
Q

Different groups on trees

A
  • Monophyletic (clade): An ancestor and all of its descendants
  • Paraphyletic group: An ancestor and some, but not all, of its descendants
  • Polyphyletic group: A group that does not include its own most recent ancestor (2+ branches artificially grouped together)
52
Q

Taxonomy and Phylogeny

A
  • Taxa should be monophyletic groups where possible
  • Ex. Land plants (plantae) are a monophyletic group
  • Reptiles are a paraphyletic group
  • Ratites seem to be polyphyletic
53
Q

How do we infer phylogenies?

A
  1. Character states (possible homologies)
    - Morphological features, etc.
    - Identities in DNA/protein sequence
  2. Distribution of character states among organisms reflect evolutionary relationships
53
Q

Parsimony

A
  • Compare many (all) possible trees
  • Best inference is the tree that implies fewest evolutionary changes total
53
Q

Cladistic reasoning

A
  • Shared derived states imply relationships
  • Shared ancestral states do not
  • Outgroup comparison (usually) to distinguish ancestral and derived states
54
Q

Molecular sequence data

A
  • Phylogenies of living taxa usually estimated by comparing molecular sequences
  • A site in set of aligned DNA sequences is a character: Different bases at sites are the states
55
Q

Phylogenetic trees of molecular sequences

A
  • Most analyses use models of sequence evolution (rather than parsimony)
56
Q

Phylogenies of genes

A
  • Evolution of genes themselves often of interest
  • E.g. tracing history of gene duplication or of gene transfer between genomes
  • One of the many aspects of the disciplines of molecular evolution and genome evolution
57
Q

Lateral/Horizontal Gene Transfer

A
  • Transfer of genes between species
  • Quite common in unicellular organisms
58
Q

Fossils

A
  • preserved remnants (traces) of past life
  • petrified organic material
  • Casts
  • Trace fossils (footprints, etc.)
  • Info about past ecosystems, climate, sea levels, etc. and dating of geological record
  • More direct view of evolutionary history then from living organisms
  • Most are found in sedimentary rock
59
Q

Index Fossils

A
  • Common, widespread fossils characteristic of particular periods of earth’s history
  • Crucial for ‘relative dating’ in geological record
60
Q

The geological record

A
  • Earth is around 4.6 billion years old
  • (Microbial) life arose around 3.5+ billion years ago
  • Fossils of animals and plants common in the last 550 million years: “Phanerozoic Eon”
  • Phanerozoic divided into three ‘Eras’: Each era subdivided into several ‘Periods’
61
Q

Periods of the Phanerozoic Eon

A
  • Cenozoic era
  • Mesozoic era
  • Paleozoic era
62
Q

Mass Extinctions

A
  • Many species extinct in a very short time
  • Causes: large environmental changes
  • Ex:
  • Massive volcanic activity
  • Impact by asteroid or comet
  • Major importance in history of life
  • 5 big ones; most making ends of Eras/Periods
63
Q

End-Permian Mass Extinction

A
  • Around 250 million years ago
  • Most devastating mass extinction
  • Extinction of around 90% of species on earth
  • Many large taxa went totally extinct (e.g. around 50% of Families)
64
Q

End-Cretaceous Mass Extinction

A
  • Around 65 million years ago
  • Most recent ‘big’ mass-extinction
  • Extinction of around 50% of species on earth
  • E.g. dinosaurs (other than birds)
  • Several marine invertebrate group
65
Q

Adaptive radiations

A
  • Rapid speciation and evolutionary change in underexploited habitats
  • Regional: e.g. colonization of new island chains
    World-wide:
  • Following mass extinction events
  • Only surviving lineages can radiate
  • Replacement in fossil record
66
Q

Regional adaptive radiation example

A
  • Hawaiian ‘silversword alliance’
  • Plant group, endemic to Hawaii (very isolated, ‘young’ island group)
  • Around 50 species: great variation in size, shape
  • All descended from one species, in last 5 million years
67
Q

How do complex adaptations evolve?

A

Darwinian evolution proposes:
- Evolution through many small steps
- Every ‘step’ should improve fitness
Some mechanisms for evolution of complex adaptations:
1) Intermediates that are actually capable of functioning
2) Modification of existing structures with different functions
3) Larger ‘steps’ (than imagined by Darwin)
(Changes in developmental regulation, origin of novel genes, e.g. gene duplication)

68
Q

Functioning Intermediates

A
  • In many cases, simpler forms of complex structures are functional
  • Evidence: Organs of different complexity in related species
  • Stepwise evolution plausible
69
Q

Modification of Existing Structures

A

Exaptation:
- Structures adapted for one function are coincidently useful for another function
- Evidence: Feathers in non-flying dinosaurs, later useful for flying

70
Q

The Evolution of Developmental Regulation

A
  • Mutations affecting genes that control development
  • Small genetic change can result in large, coordinated changes in phenotype
    E.g. Homeotic genes
  • e.g. Hox genes - control identity of segments along developing animal body (fruit fly)
71
Q

New genes (e.g. gene duplication)

A
  • Gene duplication event
  • Over time, independent evolutionary change (one can acquire new function)
  • The two related genes in one genome are paralogs
72
Q

Three domain scheme

A
  • Bacteria
  • Archaea
  • Eukarya
    Note: bacteria, archaea and most eukaryotic groups are microbial life-forms
  • Bacteria and Archaea are two very different kinds of ‘prokaryotic’ cells
73
Q

Importance of prokaryotes (Bacteria and Archaea)

A
  • On Earth for around 3.5 billion years
  • Responsible for most of biological activity in many ecosystems
  • More prokaryotes than human cells in body
  • Cause many major diseases and infections
  • Biotechnology
74
Q

Bacteria

A
  • Includes almost all well-known prokaryotes
  • E.g. all known disease-causing species
75
Q

Bacterial cell envelope

A

Usually two bounding membranes: Plasma membrane and outer membrane
- Peptidoglycan wall between the membranes (complex polymer of sugar and amino acids)

76
Q

Important groups of bacteria

A
  • Spirochetes
  • Gram-positive bacteria
  • Cyanobacteria (photoautrophs)
  • Proteobacteria
77
Q

Archaea

A
  • Many are extremophiles
  • E.g. Some are extreme thermophiles (some grow at 110 degrees)
  • many are methanogens - produce methane as a waste product of energy metabolism
78
Q

Archaea - cell envelope

A
  • No ‘outer membrane’ ; no peptidoglycan
  • Cell membrane lipids are chemically different from those of bacteria and eukaryotes
79
Q

Similarities between Archaea and Eukaryotes

A
  • Eukaryotic (-like) RNA polymerase
  • Core histones associated with DNA
    Archaea are more closely related to eukaryotes than bacteria
80
Q

The origin of eukaryotic cells

A

1) Endomembrane system, including nuclear envelope evolves conventionally (not by symbiosis)
2) Endosymbiotic alpha proteobacterium becomes mitochondrion (many eukaryotes, including animals)
3) Endosymbiotic cyanobacteria becomes plastid (some eukaryotes, including plants)

81
Q

Some prokaryotic-like features of mitochondria and plastids

A
  • Divide by binary fission
  • Have (prokaryotic-like) ribosomes
  • Have their own genomes:
    Encode some RNAs, and proteins that are translated on the organelle ribosomes
82
Q

‘Protists’

A
  • Most of eukaryotic diversity
  • Abundant in most ecosystems
  • Important photosynthesizers (algae)
  • The major predators of prokaryotes
  • Parasitic protists cause some major diseases (e.g. malaria)
  • Protists are a paraphyletic group
83
Q

Origins of animals and fungi

A
  • Phylogenies of molecular sequences show that animals and fungi are quite closely related
  • … but independently evolved from single-celled protist ancestors
  • Plants evolved from photosynthetic ‘green algal’ protists

Biology (5 decks)

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