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BIO120 > 21, 22, 1, 2, 3, 4, 5, 6 > Flashcards

21, 22, 1, 2, 3, 4, 5, 6 Flashcards

1
Q

Mutualism vs Symbiosis

A

symbiosis = living together
mutualism = beneficial interaction for both species

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1
Q

what does mutualism typically involve?

A

reciprocal exchange of goods or services between species

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2
Q

3 types of mutualisms

A
  • nutritional
  • defensive
  • dispersal
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3
Q

nutritional mutualisms

A
  • legumes and rhizobia: exchange fixed C for fixed N
  • plants and mycorrhizal fungi: exchange C for P
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4
Q

defensive mutualisms

A
  • ants and plants: exchange protection for food (eg extrafloral nectar) or housing
  • cleaner fish and client fish: exchange parasite removal for food
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5
Q

dispersal mutualisms

A
  • plants and animal seed dispersers: exchange seed dispersal for food
  • plants and animal pollinators: exchange gamete dispersal for food
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6
Q

mutualism between humans and free-living wild animals

A
  • Yao people in Mozambique harvest wild honey, but can’t find bees’ nests easily
  • honeyguides (Indicator indicator) eat bees wax and know where nests are, but can’t access them easily
  • honeyguides recognise the specific sound that Yao honey-hunters make to attract them
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7
Q

how would you change Lotka-volterra equations to model mutualism?

A
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8
Q

constraints of the Lotka-Volterra models of mutualism

A

both populations undergo unbounded exponential growth in an orgy of mutual benefaction

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9
Q

what limits the population growth of mutualists?

A
  • strong intra-specific competition
  • a third species such as a predator or a competitor
  • diminishing returns to mutualism as the population grows
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10
Q

invasions meltdown

A
  • positive feedback between mutualists tends to generate runaway population growth
  • if two invasive species interact as mutualists, they may facilitate each other’s spread
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11
Q

Spring ephemerals

A
  • perennial understory herbs that flower right after the snow melts, producing a short-lived ‘carpet of flowers’
  • have seeds dispersed by ants
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12
Q

elaiosome

A

fleshy appendage on seeds of spring ephemerals that attracts ants - rich in fats

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13
Q

experiment on seed dispersal by ants

A

Prof. F wanted to compare seed dispersal by a native seed-dispersing ant (Aphaenogaster rudis) and an invasive seed-dispersing ant, (Myrmica rubra)
- she placed one type of plant in each mesocosm, then added a bunch of native and invasive seeds for the ants to disperse
- with native ant, mostly native plants were dispersed
- with invasive ant, mostly invasive plants were dispersed

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14
Q

Myrmica rubra

A

native to Europe, where it disperses many seeds

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15
Q

Cleaner fish (Labroides dimidiatus)

A
  • Cleaner fish feed on ectoparasites on the bodies of client fish; cleaners gain food, clients benefit from fewer parasites
  • Cleaners often have “cleaning stations” (territories) that clients visit
  • Experimentally removing cleaner fish increases parasite (gnathiid) abundance on client fish
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16
Q

effect of the presence of cleaner fish in reefs

A

affects species diversity of other reef fish
- when cleaners were removed, the number of fish species went down
- when cleaners were added, number of fish species went up
- presence of cleaner fish attracts client fish

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17
Q

Darwin’s orchid, Angraecum sesquipedale

A
  • epiphytic orchid from Madagascar with a very long nectar spur
  • Darwin famously predicted that it must be pollinated by an insect with a very long proboscis (sucking mouthpart)
  • Alfred Russel Wallace drew a moth like this
  • Xanthopan morganii praedicta was discovered in 1903
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18
Q

Reciprocal adaptation (coevolution) between flowers and insects

A

how is long proboscis/floral tube beneficial?
- when nectar spur of the plant is longer than the mouthpart of the insect, this forces the insect to get deep into the flower in order to drink all the nectar
- this forces the insect to contact the pollen-receiving parts of the flower, improving pollination
- pollinators with longer mouthparts are able to get more food

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19
Q

Bacterial endosymbionts in aphids

A
  • aphids feed on phloem sap that is rich in sugars, but poor in essential amino acids
  • aphids have intracellular bacteria (Buchnera) that provide their hosts with essential amino acids
  • Buchner are vertically transmitted; they are passed in aphid eggs from mothers to offspring
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20
Q

what is a feature of vertically transmitted endosymbionts?

A
  • Buchnera has a much smaller genome than free-living bacteria (eg E.Coli); other endosymbiotic bacteria also have tiny genomes
  • in humans; mitochondrial genome is ~17000 base pairs (and encodes just 27 genes); nuclear genome is >3 billion base pairs
  • endosymbiotic bacteria lose genes that they no longer need
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21
Q

why do endosymbiotic bacteria lose genes that they no longer need

A
  • some functions unnecessary because bacteria are no longer free-living; bacteria protected inside host cells
  • other functions outsourced to host genome
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22
Q

are mutualisms often highly specialised?

A
  • Most aphid species have their own species of Buchnera bacteria
  • But most mutualisms are NOT tightly coevolved, species-specific interactions
  • Most mutualisms are horizontally transmitted; partners are acquired anew each generation
  • Mutualisms are rarely one-to-one interactions; usually many-to-many interactions
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23
Q

current areas of mutualism research

A
  • Understanding networks of interactions among large numbers of species
  • Microbiomes: this term refers to either all the microbes living together in a community (often, a host) or their collective genomes
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24
Q

do plants only have one pollinator species?

A

no, most plants have many pollinator species, and most pollinators visit many plant species

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25
Q

how can we characterise microbial diversity in a host (or environmental sample)?

A
  • culture-based methods
  • sequencing based methods
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26
Q

sequencing-based methods

A
  • Sequence a highly conserved (i.e., slowly
    evolving) gene, usually the bacterial 16S rRNA gene
  • Use DNA sequence data to identify microbes
  • Frees us from having to culture microbes in order to study them
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27
Q

mammal gut microbiomes reflect

A

diet, phylogeny, and morphology

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28
Q

Dispersal

A

movement from one population to another

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29
Q

dispersal allows organisms to:

A
  • colonise new areas
  • escape competition
  • avoid inbreeding depression
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30
Q

in animals, dispersal relies on

A

active movement - running, flying, etc

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31
Q

how are plants able to disperse?

A

they have evolved traits that aid dispersal:
- sweet, fleshy fruit is an adaptation that attracts animal seed disperses
- other seeds are dispersed by wind or water

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32
Q

Describe how dispersal is important for colonisation of new habitats

A
  • postglacial colonisation depends on plant and animal dispersal
  • most of Canada was under ice ~12,000 years ago
  • range shifts in response to climate change depend on dispersal
  • islands
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33
Q

Metapopulation

A

a population of populations - a collection of specially distinct populations that are connected via dispersal

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34
Q

how is dispersal involved in the formation of metapopulations?

A
  • dispersal connects populations
  • We call each spatially distinct population a patch
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35
Q

describe how metapopulation structure can allow population persistence even when individual populations are doomed

A
  • local populations can be reestablished by colonists from other populations after going extinct
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36
Q

source-sink dynamics

A
  • ‘Sinks’ are populations in small habitat patches that would go extinct, except …
  • Migrants from ‘source’ populations ‘rescue’
    these populations
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37
Q

Oceanic Island - single island level

A
  1. some prey colonize empty island
  2. prey quickly grow toward carrying capacity
  3. some predators arrive and reproduce rapidly
  4. predators drive prey to extinction
  5. predators starve, island is empty
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38
Q

single island system

A

At the island level, this system is inherently unstable: both species go extinct

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39
Q

archipelago of many such islands, each at a different stage, with some dispersal possible

A
  • a group of weakly coupled, locally unstable
    systems can be globally stable
  • The coupling is provided by occasional dispersal between islands
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40
Q

patch dynamics

A
  • akin to population dynamics, except:
  • instead of individuals in a population, we track patch occupancy through time
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41
Q

give a simple case for patch dynamics

A
  • a large number of identical patches
  • ignore population size within patches
  • populations within patches go extinct at some constant rate e
  • colonisation of patches is affected by P and 1-P
  • colonisation rate is thus cP(1-P), where c is a constant
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42
Q

colonisation of patches is affected by:

A
  • the fraction of currently occupied patches, P
  • higher P = more sources for colonisers
  • the fraction of empty patches, 1-P
  • as patches fill up, there are few patches available to colonise
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43
Q

Levin’s patch occupancy model

A

differential equations

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44
Q

equilibrium patch occupanc7

A

when overall colonisation rate and overall extinction rate intersect

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45
Q

what does meta population structure facilitate?

A

species persistence and coexistence
- of a single species (eg tiger salamanders)
- of predators and prey
- of competitors

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46
Q

describe how meta population structure facilitates coexistence of competitors

A
  • say A always outcompetes B within a habitat patch, so local coexistence is impossible
  • global coexistence requires:
  • A must sometimes go extinct in a patch or new patches must be created from time to time
  • B must be a better disperser than A
  • so B must be a fugitive, tramp, weedy, opportunistic, transient species
  • a competition-colonisation trade-off
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47
Q

Pikas as an example of meta populations

A
  • Bodie, California
  • mining ghost town
  • Andy smith’s pika research site
  • 1972 - present
  • tailing piles from hard-rock mining create many small replicated patches of pika habitat
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48
Q

general conclusions on species coexistence

A
  • populations can be driven to extinction in several ways
  • but these tendencies are countered and the paradox of the plankton is resolved
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49
Q
  • populations can be driven to extinction in several ways
A

Stochasticity: chance fluctuations in population numbers
- Competitive exclusion
- Through predator-prey (or host-parasite, etc.) interactions
- Allee effects at low density

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50
Q

but these tendencies are countered and the paradox of the plankton is resolved

A

Predation keeping competitive exclusion from going to completion (as in Paine’s sea star removal experiment)
- Non-equilibrial conditions, habitat patchiness, rescue-
by-migration, variation in life-history strategy (as in a competition-colonization trade-off)

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51
Q

meta community

A

a set of local communities linked by the dispersal of one or more of their constituent species

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52
Q

What determines the number of
species on an island?

A

Three processes:
* Colonization: a species can arrive on an island from elsewhere
* Extinction: a species can go locally extinct on an island
* In-situ speciation: a lineage can split in two on an island, but this is a very slow process …

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53
Q

MacArthur and Wilson’s theory
of island biogeography

A

Goal: predict the number of species on an island from the island’s size and isolation (distance from mainland)
* Ignored in-situ speciation; only considered colonization and extinction

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54
Q

draw theory of island biogeography in graphs

A
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55
Q

why colonisation rate decreases as no of species increases

A
  • the fewer the number of species, the more likely a migrant will be a new species
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56
Q

why extinction rate increases as no of species increases

A

more competition

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57
Q

near island vs far island

A
  • near island has higher colonisation rate than far island as it is easier to get to
  • so has more species at equilibrium
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58
Q

large island vs small island

A
  • extinction rate higher at small islands
  • have fewer resources and can support smaller population sizes
  • so have less species at equilibrium
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59
Q

is this model effective for species richness?

A
  • Mahler studied anolis lizards
  • species richness of anoles increase with area and decrease with isolation
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60
Q

when else does island biodiversity apply?

A

habitat fragmentation creates ‘islands’ of suitable habitat within an inhospitable matrix

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61
Q

Two core Tenets of evolution

A
  1. Living things change over time
  2. adaptations have arisen through natural selection
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62
Q

what does evolution challenge?

A

the view of special creation

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63
Q

define special creation

A

the direct creation of all living things in effectively their present form

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64
Q

state 5 important conclusions about evolution verified by scientific study

A
  1. organisms on earth have changed through time
  2. changes are gradual, not instantaneous
  3. lineages split by speciation, resulting in the generation of biodiversity
  4. all species have a singular common ancestor
  5. adaptations result from natural selection
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65
Q

evidence for organisms changing through time

A

fossil records

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66
Q

why are changes in traits in organisms gradual and not instantaneous?

A

processes of evolution take different amounts of time, but always have to work with pre-existing variation, limiting the rate of change.

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67
Q

biodiversity and adaptation are the

A

products of evolution

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68
Q

describe speciation

A

process by which one species bifurcates into two which do not go back together. iterative rounds of speciation give exponential growth of this process.

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69
Q

give 2 definitions of biodiversity

A
  • the diversity of life on earth
  • the number and kinds of living organisms in a given area
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70
Q

give 2 definitions of adaption

A
  • any trait that makes an organism better able to survive or reproduce in a given environment (noun)
  • the evolutionary process that leads to the origin and maintenance of such traits, reproducing and surviving better in an environment (verb)
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71
Q

major areas of evolutionary study

A
  • evolutionary history (i.e. patterns); reconstructing how life on earth happened
  • evolutionary mechanisms (i.e. processes); what gave rise to the life that we see
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72
Q

microevolution

A

evolutionary patterns and processes observed within species

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73
Q

macroevolution

A

evolutionary patterns and processes observed among species

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74
Q

draw a diagram for macro and microevolution, as well as evolutionary history and mechanisms

A
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75
Q

goals of evolutionary history

A

identify and understand long term patterns in evolution, including common ancestry

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76
Q

evolutionary history in practice

A

uses comparative data from sub-disciplines of systematics, biogeography, palaeontology, morphology, development and molecular biology

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77
Q

give 2 alternative terms for an evolutionary tree

A

a phylogenetic tree = a phylogeny

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78
Q

what is the purpose for evolutionary trees?

A

to reflect ancestor-descendant links

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79
Q

name of split points in evolutionary trees

A

nodes

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80
Q

can trees with different sets of species represent the same common ancestors?

A

yes - this also depends on rotation of branches on the tree

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81
Q

goals of evolutionary mechanisms

A
  • determine the particular processes responsible for evolutionary change
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82
Q

evolutionary mechanisms in practice

A
  • uses experimental and comparative studies of the genetics and ecology of populations
  • focuses primarily on the population level
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83
Q

state and describe the 4 approaches that are used to address scientific questions

A
  • observational - describe and quantify
  • theoretical - develop models (verbal, graphical, mathematical, computational)
  • comparative - obtain same data from many species
  • experimental - manipulate a system to address a specific hypothesis; requires an experimental design and statistical analysis
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84
Q

all good scientific theories have —- and the strongest studies use

A

testable and falsifiable hypotheses; more than one source of evidence

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85
Q

give 4 reasons as to why evolution is relevant?

A
  1. children’s questions/understanding life on earth
  2. medicine - mitigating effects of pathogens (eg variants of covid-19)
  3. agriculture
    - how can we design strategies to avoid herbicide and insecticide resistant superweeds/super pests?
    - what genes were important for crop evolution?
  4. climate change - selection pressures will be applied
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86
Q

public doubts about evolution

A
  1. extremely recent scientific concept (165 years is a brief time frame)
  2. very personal implications: direct ramifications about who we are and where we came from
  3. violates literal interpretations of religious texts
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87
Q

open questions in Darwin’s time

A
  1. where do species come from?
  2. how can we explain complex adaptations (ie traits with clear/elaborate function for the survival and reproduction of organisms)?
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88
Q

Paley’s argument from Design

A
  • Dominant view in European society - came from Natural Theology (branch of theology)
  • on a walk and you find a watch, with perfect hands for minutes and hours
  • they clearly have a specific function - somewhere on this planet must exist a ‘watchmaker’.
  • trees are adapted to have very specific functions, they are perfectly designed for their life and function
  • there has been a designer (ie God)
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89
Q

Jean Baptiste de Lamarck, 1744-1829

A

First to
- use term evolution
- provide a hypothesis for the causal mechanism (inheritance of acquired characters)

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90
Q

explain Lamarck’s example for the inheritance of acquired characters

A
  • giraffe feeds on leaves
  • will spend its whole life stretching its neck, allowing it to grow and reach further on the tree
  • this trait is passed on
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91
Q

give a summary of the theory for the inheritance of acquired characteristics

A

Organisms can change their phenotype within their generation; having changed within the generation, they pass this to offspring

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92
Q

draw a diagram for Lamarck’s theory

A
93
Q

who proved Lamarck wrong?

A

August Weismann’s Germplasm theory (1889)
- Inheritance only by germ cells (gametes); somatic cells do not function as agents of heredity, information only goes one way
- Thus genetic information cannot pass from soma to gametes and onto the next generation
- Modern interpretation in molecular terms: genetic information flows in one direction only: from DNA to protein but never in reverse

Therefore changes to the body cells would not be able to have an impact on gametes and be passed onto offspring

94
Q

what experiments did Weismann do to prove his Germplasm theory?

A

got a bunch of mice, chopped off their tails, and bred them together - the offspring still had normal sized tails

95
Q

describe Darwin and Wallace’s roles in developing the theory of evolution?

A
  • Darwin developed first comprehensive theory of evolution
  • Darwin and Wallace independently discovered the chief mechanism of evolution, Natural Selection
96
Q

Two major theses of Darwin and Wallace’s theory of evolution

A

All organisms have descended with modification from a common ancestor: thus, living things changed over time
The process leading to evolution is natural selection operating on variation among individuals

97
Q

describe the contents of Lyell’s book

A
  • argued for uniformitarianism
  • the forces and processes that shape the Earth’s surface are uniform through time (ie the forces we see today are the same as previous eons)
  • present day geological processes can explain the history of the Earth Gradualism of erosion, earthquakes, volcanoes
98
Q

Give the stages of Darwin’s development of this theory

A
  1. Exploration - voyage on HMS beagle around the world (1831-1836) as ship’s naturalist. Intellectual companion to Capt. Robert Fitzroy
  2. Gradualism - reads Lyell’s book ‘Principles of Geology’
  3. Species Vary - Variation patterns of Galapagos mockingbirds
  4. Struggle for existence - 1838, Darwin reads Malthus’ ‘An Essay on the principle of population’
99
Q

implications of Lyell’s book for Darwin

A
  1. the notion of a dynamic rather than a static world
  2. changes build up gradually, by the same mechanisms today as in the past
100
Q

implications of variation patterns of Galapagos mockingbirds for Darwin

A
  • there are 4 similar species endemic to the islands descended from a South American mainland ancestor
  • populations had very slightly different traits and were not constant
  • Darwin thus began to doubt the fixity of species
101
Q

Malthus’ essay on the principal of the population

A

there is a constant struggle for existence as populations could grow exponentially nut don’t due to limits on resources

102
Q

two key dates for Darwin and Wallace

A

July 1858 - Linnean Society presentation of Darwin-Wallace paper
Nov 1859 - publication of 490 pg book on Origin of the Species

103
Q

describe Darwin’s mechanism of Natural Selection (3)

A
  • Variation: individual variation in a population
  • Heredity: progeny resemble their parents Moree than unrelated individuals
  • fitness: some forms are more successful at (surviving and) reproducing than others in a given environment (i.e. some are more fit than others)

Natural selection is heritable variation in fitness

104
Q

state the 4 important elements of Darwin’s theory

A
  1. Evolution occurs primarily at the level of populations - individuals do not evolve
  2. Variation is not directed by the environment - individuals do not induce adaptive variation when needed
  3. Most fit type depends on the environment and changes from generation to generation
  4. ‘Survival of the fitter’ - evolution works with available variation, and will not necessarily achieve perfection
105
Q

State the implications of Darwin’s theory

A

The concept of a changing universe; a phenomenon with no purpose

106
Q

State the 4 sources of evidence for evolution:

A
  • Geology
  • Homology
  • Biogeography
  • Domestication
107
Q

Lessons from Geology

A
  1. Earth is very old - this allows for an immense amount of time for biological evolution
  2. Intermediate forms - evidence for transitional fossils linking features of seemingly dissimilar relatives (eg ungulates and whales, or tetrapods and fish)
  3. Fossils in younger strata increasingly resemble modern species in the same region - older strata show increasing differences
108
Q

Give an example of how discoveries of transitional fossils continue today

A

Tiktaalik roseae, discovered 2006
- has 2 legs and 2 fins
- nickname: fishapod

109
Q

Define homology

A

Similarity of traits in two or more species that is due to inheritance from a common ancestor

110
Q

Lessons from homology

A

Vestigial traits provide evidence of the evolutionary past:
- have no function/reduced function in extant organisms
- can only be explained by the presence of functional traits in ancestors, followed by evolutionary degredation

Homologous structures are ubiquitous across organisms:
- fundamental structural similarity reflects common ancestry
- homologous structures have evolved to serve very different functions

111
Q

Define a vestigial structure

A
  • features inherited from an ancestor, but reduced in morphology and function
  • are homologous to functional structures in related species
112
Q

Describe vestigial structures in Galapagos flightless cormorants compared to mainland cormorants

A

Mainland cormorants need to fly as they nest on trees; GF cormorants do not as they nest on rocks by the water. The wings of these two species, albeit varying in use, are homologous structures.

113
Q

what is a vestigial structure in cave-dwelling morphs of Astynax Mexicanus?

A

they have evolved to lose their eyes as they do not need them

114
Q

vestigial structures in humans

A
  • ear muscles
  • appendix
  • tailbone
  • goosebumps
115
Q

why is the presence of vestigial structures significant?

A
  • organismal features are consistent with modifications of pre-existing structures
  • this would not be expected if each organism was individually optimally designed
116
Q

describe homology in genes

A
  • approximately 500 genes are shared across all forms of life
  • there is a strong, shared constraint for genes involved in basic cellular function (eg transcription/translation)
117
Q

Lessons from Biogeography

A

Remote islands biotas:
- have continental affinities
- are dominated by good colonists
- have locally-differentiated species

biogeographically isolated regions:
- have species adapted to niches unusual for their group
- harbor endemic radiations of species that are convergent with radiations elsewhere

118
Q

3 main points of evidence from biogeography

A
  • geographically close organisms resemble each other
  • different groups of organisms adapt to similar environments in different parts of the world
  • geographically isolated regions have unusual organisms
119
Q

use Australia as an example of a location with an interesting Biogeography

A
  • although a continent, Australia is also an island
  • distinct flora and fauna with high endemism and many unique adaptations
  • australia has endemic radiations of species that are ecologically convergent with those of other continents
120
Q

what is Australia’s biological uniqueness a result of?

A

its long history of isolation from other land masses

121
Q

give a summary of evidence from domestication

A

Heritable variation can be selected on, leading to dramatic changes over generations

122
Q

define genotype

A

the genetic constitution of an organism
- defined in relation to a particular gene or gene combinations
- eg Aa, Bb

123
Q

define phenotype

A

feature of the organism as observed
- used when discussing a trait of an organism that varies
- eg size, fur colour, mRNA expression level

124
Q

define genome

A

the entirety of an organism’s DNA
- includes genes and non-coding regions

125
Q

state 3 sources of genetic variation

A
  1. mutation
  2. independent assortment
  3. recombination
126
Q

define a mutation

A

a stable change in the DNA sequence

127
Q

how often do mutations occur?

A

at a low rate
- mutation rate varies in ways that are partially predictable

128
Q

what are the different possible effects of mutations on fitness?

A
  • neutral (won’t matter for the fitness of the organism)
  • deleterious (weakly detrimental up to lethal)
  • beneficial
129
Q

state the 4 main characteristics of mutation

A
  1. mutation is an inevitable phenomenon, despite cellular mechanisms to correct errors during DNA replication
  2. mutation is not directed toward an outcome by the organism or by the environment
    - it is random with respect to effects on fitness
    - it is not ‘summoned’ to make things better
  3. rate depends on the type of mutation, and can also vary among genes
  4. the environment can affect the mutation rate (eg mutagens, high temp)
130
Q

what are the 4 types of mutation?

A
  1. point mutations (a simple substitution of a nucleotide)
  2. insertions/deletions (‘indels’) - adding/removing a nucleotide
  3. changes in repeat number
  4. chromosomal rearrangements (eg inversions)
131
Q

describe a mutation involving a change in repeat number

A
  • when there is a repeated motif (eg ATG) within the gene, the motif may accidentally be added/removed an extra time
  • the repeated motif makes it harder for the replicative machinery to replicate
132
Q

describe an example of a chromosomal rearrangement

A

inversions:
- flipping of the nucleotide sequence
- occurs when there is a double break in DNA strand; when enzymes try to put the two strands back together, it is hard to know which one was forward and which one was backwards

133
Q

give an example of a method that can be used to identify a new mutation?

A

a trio study:
- two parents (reproducing organisms) are selected
- their genome and the genome of their offspring is sequenced

134
Q

what is the rate of new mutation in humans?

A

per base pair of DNA: 16 in every billion nucleotides each generation

per individual genome (two copies of our 3 billion base pair genome): approx. 96 new mutations per zygote

for the entire human population (8 billion): every base pair in the genome mutated about 126 times over per generation

135
Q

why do some mutations not lead to amino acid changes?

A

we have more codons than amino acids - so sometimes mutations don’t make a difference to the amino acid sequence (= silent substitution)

136
Q

give an animal example of how single mutations can cause profound effects on traits

A
  • Antp Hox gene mutations in Drosophila
  • results in an extra pair of wings, for example, or a set of legs, instead of antennae, growing from the fly’s head
137
Q

describe G6DP deficiency in humans?

A

Glucose-6-phosphate dehydrogenase

most common enzyme deficiency in humans
- causes severe anemia
- also protects against malaria
- 2 amino acid replacement mutations in the coding sequence of G6PD are associated with disease allele (A-)

138
Q

what are polymorphisms?

A
  • A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population.
  • each allele must also occur in the population at a rate of at least 1% to generally be considered polymorphic.
139
Q

what are allozymes?

A

Alloenzymes are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus.

140
Q

give a flow chart for how mutations in G6PD lead to genetic variation

A

DNA (polymorphisms) -> proteins (allozymes) -> phenotype (polyphenisms)

141
Q

define independent assortment

A

the alleles of two (or more) different genes get sorted into gametes independently of one another.

142
Q

how does independent assortment in segregation during meiosis generate diversity?

A
  • allows different combinations of parental chromosomes
  • 2^n, where n=sets of chromosomes
143
Q

how can we tell if a mutation has increased or decreased fitness from a fitness distribution bar chart?

A

if the mutation leads to a fitness less than 1 (which is the fitness of the ancestor) then they are detrimental

144
Q

describe how recombination during meiosis (metaphase) further contributes to variation

A

there is synapsis of bivalents, leading to crossing over at chiasmata and recombinant chromosomes.

145
Q

how did scientists believe that heredity worked before Mendel?

A

performatifs (1700s):
- spermists/ovists believed only one parent contributed to inheritance

theory of blending inheritance (1800s)
- postulated that factors from both parents mix together irreversibly

146
Q

what is the problem with blending inheritance for evolution by natural selection?

A

there would be no way for a beneficial mutation to increase in frequency across generations

147
Q

describe Mendel’s experiment with diagrams

A
  1. hybrid cross of pure-breeding lines (yellow and green)
  2. self fertilised (all yellow)
  3. offspring were 3/4 yellow and 1/4 green
148
Q

state the key conclusions from Mendel’s pea experiments

A
  1. inheritance is determined by discrete particles, genes
  2. each diploid organism carries two copies (alleles) of each gene.
    - alleles can exhibit dominance/recessivity
    - gametes contain only one allele per gene
  3. gametes fuse to make offspring
    - sperm/pollen fuses with egg/ovule
  4. offspring inherit one gamete from each parent at random
    - one allele per gene at random from each parent
149
Q

describe phenotypic polymorphisms with simple mendelian genetic causes

A
  • common in nature
  • direct correspondence between trait and its genetic basis
  • easy to track selection and evolution
150
Q

what are the two types of genetic variation?

A

discrete variation:
- mendelian genetics
- genes of major effect, dominance, and recessiveness
- involves a spread of alleles and a change in allele frequency

continuous variation
- quantitative genetics
- many genes each with alleles of small effect, important environmental effects
- selection response as change in average trait value

151
Q

define discrete variation

A

Discrete variation refers to traits with a finite number of phenotypes, often controlled by single genes

152
Q

define continuous variation

A

Continuous variation, on the other hand, displays an infinite number of phenotypes across a continuum and is usually polygenic.

153
Q

how is the phenotype of a quantitative trait established?

A
  • often affected by many factors
  • complex polygenic inheritance
    AND
  • environmental factors
154
Q

define partial dominance

A

a form of Gene interaction in which both alleles of a gene at a locus are partially expressed, often resulting in an intermediate or different phenotype.

155
Q

define a polygenic trait

A

a characteristic that is influenced by two or more genes.

156
Q

locus

A

the location of the gene on a region of a chromosome

157
Q

What happened between the 1920s and the 1950s?

A
  • the creation of the mathematical evolutionary theory for population genetic change
  • initiated by Fisher, Haldane, and Wright
  • provided the foundations for Neo Darwinism and the New Synthesis
  • showed that continuous variation and Darwinian natural selection are entirely consistent with Mendel’s Laws
  • demonstrated the evolutionary significance of genetic variation
158
Q

state the 5 forces that influence patterns of genetic diversity and evolution and what effect they tend to have

A
  1. mutation - increases diversity
  2. recombination - increases diversity
  3. genetic drift - decreases diversity
  4. natural selection - increases/decreases diversity
  5. migration - increases diversity
159
Q

how does mutation influence patterns of genetic diversity?

A
  • increases genetic variation in populations
  • caused by errors during replication
160
Q

how does recombination influence patterns of genetic diversity?

A
  • increases genetic variation in populations
  • creates new combinations of alleles and mutations
161
Q

how does genetic drift influence patterns of genetic diversity?

A

defined as the change in the frequency of an existing gene variant (allele) due to random chance
- acts to decrease genetic variation in populations
- random sampling affects every generation
- more important for populations that are smaller

162
Q

three types of natural selection

A
  • negative (purifying) selection
  • positive (directional) selection
  • selection favouring diversity
163
Q

negative (purifying) selection

A
  • decreases genetic variation in populations
  • mutations that reduce fitness are removed by natural selection
164
Q

positive (directional) selection

A
  • decreases genetic variation in populations
  • mutations that increase fitness will eventually become fixed in a population
165
Q

selection favouring diversity

A
  • increases or retains genetic variation in populations
  • natural selection can act to maintain diversity over the long term (eg heterozygote advantage)
166
Q

how does migration (gene flow) influence patterns of genetic diversity?

A
  • increases genetic diversity in populations
  • migration influences the structuring of diversity over a large spatial scale
167
Q

describe the two metrics of genetic variation

A

Heterozygosity (H)
- fraction of individuals that are heterozygous, averaged across gene loci

Polymorphism (P)
- proportion of gene loci that have 2 or more alleles in the population
- a locus can be polymorphic without being heterozygous

168
Q

what maintains genetic variation?

A
  1. mutation-selection balance
  2. selection maintaining variation
169
Q

define fixation

A

occurs when a polymorphic locus becomes monomorphic due to the loss of all but one allele (can occur due to natural selection or genetic drift)

decreases differences between populations.

170
Q

mutation-selection balance

A
  • less fit types reintroduced by mutation
  • followed by selection acting to remove them
171
Q

selection maintaining variation

A
  • the maintenance of genetic variants at intermediate frequencies over long periods of time
172
Q

what are the two models of population genetic variation?

A
  • the “classical” theory asserted that most genetic variation within species is maintained by mutation-selection balance
  • the “balance” theory proposed that genetic variation is maintained primarily by overdominant selection or some other type of balancing selection.
173
Q

classical model

A
  • Morgan, muller
  • low heterozygosity
  • low polymorphism
  • wild type is ‘normal’ genotype
  • selection typically negative
174
Q

balance model

A
  • Dobzhansky, Ford
  • heterozygote advantage
  • high heterozygosity
  • high polymorphism
  • selection favours diversity
175
Q

define gene flow

A

movement of genetic material from one population to another

176
Q

how was genetic diversity studied before 1966?

A

morphological
- eg snail colour polymorphism
cytological
- eg chromosome inversions

177
Q

what was the early quantitative evidence for the existence of genetic variation?

A
  • rather than focussing on Mendelian discrete traits, there was a focus on continuous polygenic traits
  • selection experiments were done on different groups of organisms
  • these involved controlled breeding of individuals with particular traits for many generations

= artificial selection

178
Q

evolutionary responses of continuous traits

A
  • demonstrates existence of heritable variation in fitness-related phenotypes
  • due to many underlying genes
179
Q

give a summary of the artificial selection experiments that were done on quantitative traits

A
  • selection responses demonstrate that abundant genetic variation exists for polygenic quantitative traits
  • but often no information on P & H as key population genetic parameters
  • also comparative studies difficult as traits studied often are group specific

still no solution to the question: what maintains genetic variation?

180
Q

describe Richard Lewontin and the Electrophoresis Revolution

A
  • allozyme gel electrophoresis provided a way to ask
  • what proportion of genes are variable (p&h)?
  • addresses fundamental dispute between classical and balance schools
181
Q

advantages of studies of enzyme polymorphism

A
  • many loci can be examined
  • can be used in nearly any organism
  • loci co-dominant, heterozygotes can be identified
  • variation examined close to DNA level
  • provides genetic marker loci for other studies
182
Q

describe the neutral theory by Motoo Kimura

A
  • negative selection rapidly eliminates detrimental mutations
  • positive selection rapidly fixes beneficial mutations
  • the only mutations left to create genetic variation are selectively neutral
183
Q

describe DNA variation in maize vs teosinte

A
  • corn has reduced genetic diversity compared to its wild ancestor teosinte
  • a consequence of population bottlenecks during domestication
184
Q

describe human genetic variation

A
  • humans show a loss of genetic variation with increasing distance from East Africa
  • reflects founder events as humans migrated from source population
185
Q

describe comparisons of polymorphism in Arabidopsis lyrata

A
  • regions that were recently glaciated have lower DNA diversity
  • genetic drift following recolonisation
186
Q

draw a tree diagram for the various reproductive modes of organisms on earth

A

reproductive system - sexual/asexual
sexual system - hermaphrodite/dioecious
mating system - self fertilisation/cross fertilisation

187
Q

define parthogenesis

A

asexual reproduction in which an embryo develops from an egg without fertilisation

188
Q

define clonal propagation

A

asexual reproduction not involving an egg

189
Q

define a hermaphrodite

A

individual has both male and female reproductive parts.

190
Q

define dioecious

A

a characteristic of certain species that have distinct unisexual individuals

191
Q

3 characteristics of sexual reproduction

A
  • 2 parents contribute genetic material to offspring
  • meiotic, reductive division to form gametes
  • fusion of gametes
192
Q

3 characteristics of asexual reproduction

A
  • 1 parent contributes genetic material
  • no meiotic reductive division.
  • offspring are genetic replicas (clones) of parents
193
Q

give 2 examples of organisms which can reproduce either sexually or asexually

A

water fleas (daphnia)
water hyacinth (pontederia)

194
Q

two-fold cost of meiosis

A
  • compared to an asexual female, a sexual female contributes only 50% of her gene copies to the next generation
  • this transmission bias favours asexuals in competition with sexual females
195
Q

whereas asexual reproduction maintains favourable combinations of alleles, sexual reproduction

A

can continually recreate unfavourable combinations of alleles

196
Q

list the 6 costs of sex

A
  • time and energy to find and attract mates
  • increased energetic costs of mating
  • risk of predation and infection
  • cost of producing males
  • 50% less genetic transmission
  • break up of adaptive gene combinations through segregation and recombination
197
Q

state the 2 main benefits of sex

A

it allows for the bringing together of favourable mutations and the elimination of harmful mutations (independent assortment recombination)

198
Q

what are the benefits of genetic variation in variable/unpredictable environments known as?

A

lottery models
- tangled bank hypothesis
- red queen hypothesis

199
Q

tangled bank hypothesis

A

an evolutionary theory that suggests sexual reproduction increases genetic diversity, which is advantageous in complex and variable environments.

200
Q

in what environments is the tangled bank hypothesis applicable?

A

in spatially heterogeneous environments

201
Q

in what environments is the red queen hypothesis applicable?

A

in temporally heterogeneous environments

202
Q

red queen hypothesis

A

an evolutionary theory that suggests species must constantly adapt and evolve in order to survive while competing against other organisms that are also evolving.

203
Q

describe the evening primrose

A
  • 30% of Oenothera species are functionally asexual
  • over time, there have been many independent sexual-asexual transitions
204
Q

describe what experiments on asexual Oenothera have shown

A

asexual oenothera have:
- more premature stop mutations which lead to dysfunctional proteins
- higher rates of protein sequence evolution
- this implies a greater accumulation of deleterious mutations

205
Q

what is the effect of spatial heterogeneity in selection?

A

it can facilitate the evolution of sex

206
Q

describe what experiments were carried out on the rotifer Brachionus calyciflorus

A
  • planktonic freshwater animal
  • facultatively sexual with genetic variation for the propensity to reproduce sexually or asexually
  • each population consisted of two subpopulations, with migration performed manually between them
  • 10 replicate populations evolved under each of these conditions for ~70 generations
207
Q

draw diagrams for the experiments conducted on rotifer

A
208
Q

what were the results of experiments conducted on rotifers?

A

higher rates of sex are maintained in populations evolving in heterogenous habitats:
- sex declined rapidly over 12 weeks (70 generations) in homogeneous environments
- sex persisted at a much higher level with spatial heterogeneity

209
Q

describe the distribution of asexuality by parthenogenesis

A
  • sporadically distributed across the animal kingdom
  • more common in invertebrates, rare in vertebrates
210
Q

describe the distribution of asexuality by clonal propagation

A
  • much more common in plants
  • few species (if any) are exclusively asexual
211
Q

why are asexual species usually t the tips of phylogenies?

A
  • macroevolutionary pattern indicates higher extinction rate
  • low chance of long term evolutionary persistence
  • probably due to extremely low genetic variation and accumulation of deleterious mutations
212
Q

describe a rare case of ancient asexuality

A
  • bdelloid rotifers
  • males are unknown
  • no sex for millions of years
213
Q

outbreeding

A

mates are less closely related than random

214
Q

inbreeding

A

mates are more closely related than random

215
Q

in practice, there is a —– between outbreeding and inbreeding

A

continuum

216
Q

outcrossing

A
  • mating with someone else either by outbreeding or inbreeding
  • fusion of gametes from 2 parents, where gametes derive from meiotic reductive division
217
Q

selfing (self-fertilisation)

A
  • mating with yourself
  • most extreme form of inbreeding
  • NOT asexual reproduction
  • fusion of gametes from 1 parent
  • gametes derive from meiotic reductive division
218
Q

why is there plenty of potential for inbreeding?

A
  • local population substructure enhances mating among relatives
  • hermaphroditic organisms have the potential for self fertilisation (most plants, many animals)
  • in small populations, even random mating can lead to mating among relatives
219
Q

describe two inbreeding avoidance traits in flowering plants

A
  1. timing offset between male and female reproduction
    - pollen vs ovule maturation within a flower
    - when male vs female flowers open
  2. diverse morphological & physiological mechanisms to avoid selfing
    - self incompatibility
    - eg spacing of anther and stigma
220
Q

describe inbreeding avoidance behaviours in animals

A
  • dispersal by one sex
  • delayed maturation
  • extra pair copulation
  • kin recognition and avoidance
221
Q

what are the population genetic effects of inbreeding?

A
  • changes genotype frequencies: increases homozygosity, decreases heterozygosity (H)
  • does not directly change allele frequencies; does not change polymorphism (P)
222
Q

the effect of inbreeding on the rate of heterozygosity decline depends on

A

mating patterns

223
Q

define inbreeding depression

A

the reduction in fitness of inbred offspring compared to outcrossed offspring

224
Q

effects of inbreeding depression

A
  • lower viability (survival)
  • lower fertility (reproductive output)

strong inbreeding depression disfavours inbred offspring
- thus favouring outcrossed mating systems

225
Q

why can inbreeding reduce fitness?

A

due to homozygosity of recessive deleterious alleles

226
Q

what can reduce polymorphism?

A

competition between homozygous genotypes (selection) and genetic drift of small populations

227
Q

describe the transition from inbreeding depression to selfing

A
  • very common
  • associated with extensive phenotypic evolution
  • roughly 20% of plants and hermaphroditism animals are highly selfing
228
Q

describe the frequency in nature of selfing and outcrossing in the short term

A
  • if conditions are favourable selfing can spread via natural selection
    -> lack of reproductive assurance due to rarity of pollinators or mates
    -> transmission advantage from self and exported pollen
    -> low inbreeding depression
  • but harmful effects of inbreeding depression encourage outcrossing
229
Q

describe the frequency in nature of selfing and outcrossing in the long term

A
  • selfing leads to low diversity and inefficient selection
  • can drive higher extinction rates in selfing species
  • macroevolutionary pattern of greater prevalence of outcrossing
230
Q

describe the theory of automatic selection of a selfing gene by R.A fisher

A

table
- selfing variant has a transmission advantage

BIO120 (61 decks)

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