Midterm Flashcards
1
Q
Species
A
-Groups of similar individuals
2
Q
Interpretations of diversity: Special creation
A
- species were created recently
- species are unchanging, look the same (phenotypes)
- variation=imperfection, Adam and Eve’s bad decision
- Linnaean classification=tried to pick the most perfect example as key comparison to make, orignal perfect specimen or type
3
Q
Research from the Canadian National Collection of Insects
A
- moth named after Donald Trump
- Neopalpa donaldtrumpi
4
Q
Interpretations of diversity: Evolution
A
- living species arose from a single common ancestor over millions of years
- species have been modified (evolved) through time
- “descent with modification”
- variation=opportunity to change over time
- 3 major categories: anagenesis, extinction, cladogenesis
- proposed in late 1700s and early 1800s
- Comte du Buffon, Jean-Baptiste Lamarck (his explanation came closest), Erasmus Darwin, Charles Darwin
- volume of evidence
- natural selection as mechanism for “survival of the fittest”
5
Q
Anagenesis
A
- Change through time
- ex) one lineage is getting smaller and the other larger through time
- species formation without branching of the evolutionary line of descent
- ex) humans have changed drastically through time (don’t look like chimpanzees)
6
Q
Cladogenesis
A
- speciation
- from common ancestor
- ex) lineages no longer mating together so can be independent and different
- the formation of a new group of organisms or higher taxon by evolutionary divergence from an ancestral form
7
Q
Extinction
A
Lineages disappear
8
Q
Artificial selection
A
- process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits by choosing which typically animal or plant males and females will sexually reproduce and have offspring together
- select particular traits
9
Q
Tree thinking
A
-Darwin introduced the metaphor of the “Tree of Life”
10
Q
What are the two grand questions of evolutionary biology?
A
1) What are the causes of evolution?
2) What has been the history of life?
11
Q
What are some popular perceptions of life?
A
- fact of evolution widely accepted, sometimes unconsciously
- human evolutionary past often invoked to explain modern human behaviour or physical ailments like feet/back/knee problems (humans not meant to wear shoes), obesity (wheat belly), type 2 diabetes (non-hereditary)
- extreme is the “Paleofantasy” perspective
12
Q
Popular perceptions: Paleofantasy perspective
A
- modern humans evolved in Paleolithic
- cultural change has since outpaced evolutionary change leading to a “gene-culture mismatch”
- ex) sugar cravings appropriate in environments where starvation is a real possibility
- “paleosolutions” = run barefoot, eat raw food, cut out wheat
- stasis
13
Q
Stasis
A
- stability through time, some species don’t change much through time
- species are identifiable with ancestors that lived millions of years ago
14
Q
What is the evidence for evolution?
A
1) change through time: micro-evolution in extant lineages, vestigial organs, paleontology
2) common ancestry: biogeography, clinal variation within species, homology
15
Q
Evidence for evolution: Change through time - Micro-evolution
A
- evolutionary change within a species or small group of organisms, especially over a short period
- domesticated species (pigeons, dogs=greatest domestic variation, might be reproductive isolation between chihuahua and Great Dane due to size differences)
- extreme body size variation in wild animals (pigmy hippo 385kg vs hippopotamus 3000kg, anglerfish female 1000x larger vs parasitic male)
- introduced species (beak length in Florida soapberry bugs decreased with introduction of flatter fruit source) = organisms need to respond quickly to changing environments
- microbial evolution = antibiotic/pesticide resistance (penicillin overuse and bacteria became resistant to drug), host switches (influenza epidemic, H1N1), evolution within hosts (HIV, several strains of HIV-1 have diverged rapidly since transfer=hinders vaccine development, each originated from a chimpanzee, group M is most common strain, AIDS=symptom of HIV, evolves within hosts, leads to collapse of immune systems)
16
Q
Evidence for evolution: Change through time - Vestigial organs
A
- organs that have no current use but reflect their ancestors
- eyes in cavefish
- limbs in snakes
- wings in flightless birds
- tailbone in humans
17
Q
Evidence for evolution: Change through time - Paleontology
A
- the branch of science concerned with fossil animals and plants
- extinct species=dinosaurs and Pleistocene megafauna (species of very large mammals like mammoths)
- George Cuvier=listed 23 extinct species in 1801, proved Irish Elk extinct in 1812, would prove that extinct existed, belief at the time was that God’s creation was no longer perfect if this were true
- law of succession
- transitional forms (also support common ancestry), are the missing links
18
Q
Law of succession
A
Fossil and living organisms from the same region are related and are distinct from those in other regions
19
Q
Transitional forms
A
- intermediate form between dinosaurs and birds is Archaeopteryx
- Durodon and Basilosaurus are an intermediate species between mammals and whales
- Archaeopteris is an intermediate form between ferns and seed plants
- are the “missing links”
20
Q
Evidence for evolution: Common ancestry - Biogeography
A
- study of the distribution of species and ecosystems in geographic space and through geological time
- similar species in geographic proximity
- “species flocks” = different groups fill same niche on different continents or different lakes
- terrestrial organisms on “islands” habitable surrounded by inhabitable land
- Honeycreepers in Hawaii (different beak phenotypes for specialization in modes of feeding and diets on the island, different colours for different mating systems, rapid evolution of distinct calls and colour patterns)
- silverswords and tarweeds, Hawaii
- finches, Galapagos
- anole lizards, Caribbean
- birds of paradise, New Guinea
- Rift Lake cichlid fish, Lake Victoria cichlids (Lake Victoria completely dry as recently as 14 700 years ago, many now extinct but Nile perch (predator) populations dropped and cichlids increasing due to hybridization, ancient hybridization between 2 lineages provided genetic diversity that allowed adaptive radiation of 700 species in 150 000 years)
21
Q
Evidence for evolution: Common ancestry - Clinal variation and discontinuities
A
- a measurable gradient in a single character (or biological trait) of a species across its geographical range
- most evident in ring species (gulls across northern hemisphere, greenish warblers, salamander Ensatina eschholtzii, buckeye butterflies)
22
Q
Ring species
A
- a connected series of neighbouring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two “end” populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each “linked” population
- distribution pattern=donut
- island of inappropriate habitat in the middle of the ring
- gulls across northern hemisphere
- greenish warblers(both forms co-occur or overlap in Siberia but don’t reproduce with one another, inhabitable environment is a deforested gap)
- salamander Ensatina eschholtzii
- buckeye butterflies (northern and southern form with continuous gene flow, in cuba 2 species coexist where area of range overlap)
23
Q
Evidence for evolution: Common ancestry - Homology
A
- similarity in form despite difference in function
- similarity due to common ancestry
- evidence from morphology (similar bone structure in human, mole, horse but different arrangement and function), embryology (early development in snake, human, cat all look similar, all have a tail and pharyngeal pouch) and molecular biology (genetic code, gene sequences, biochemical pathways, similar amino acids in all species, utility of model organisms,
24
Q
2 major hypotheses in the Origin of Species
A
1) descent with modification
- species lineages change over time and are derived from common ancestral lineages
2) natural selection
- the main mechanism for the evolutionary divergence of lineages and explains adaptations
25
Conditions (testable hypotheses) for evolution by natural selection
1) phenotypic variation in a given trait exists among individuals of a population
2) phenotypic variation is heritable (traits inherited by parents and passed on to offspring)
3) more offspring are produced than can be supported by the resources available in the environment (Frequency of phenotypes are not going to change if resources are unlimited, but where it is limited, heritable traits that are better adapted will increase in frequency and the less adaptable will disappear from the population)
4) differential survival and reproduction based on phenotypic variation
* if one of these fail, then natural selection is not occurring in that population
26
Major components of Darwinian fitness
- survival (viability)
| - number of offspring (fecundity)
27
Darwinian fitness
- Overall Fitness=viability x fecundity
- Fitness = lifetime contribution of genes to next generation
- relative measure
- if doesn’t survive, individual can’t contribute to the next generation
- this provides the lifetime contribution of genes to the next generation
- only meaningful in comparisons of phenotypes in the same population only in context of a particular population
- the genetic contribution of an individual to the next generation's gene pool relative to the average for the population, usually measured by the number of offspring or close kin that survive to reproductive age
28
Malthus and reproduction
- Observed population of Ireland where there were too many people in a population and not enough food to feed everyone (Potato famine)
- Exponential population growth and resources that the population depends on is constant or linear, then you reach a disequilibrium =struggle for survival
- Some phenotypes will be preferred or selected over others
29
“Struggle for survival”
- every organism produces more gametes than offspring and more offspring than survive
- small variation in phenotype may affect survival and reproduction
30
Fitness sub-components
- survival to adulthood
- ability to evade predators
- courtship and mating
- successful reproduction
- quantity of offspring produced
31
Polymorphic traits
- traits attributed to two or more genes and can be measured quantitatively (variable traits)
- Take population and put it in an environment of variation in fitness (AA more frequent, Aa medium, aa poor)
- Next generation, frequency of aa will go down (will still be some ) and heterozygotes reproduce with each other to still form some aa, more fit Aa
32
Flower colour in snap dragons
- pink (dominant) vs yellow (recessive) flowers
- phenotypic variation: yellow and white flowers (condition 1)
- heritable variation: ss=yellow, Ss and SS=white (condition 2)
- fitness differences: bee visits and seed set (condition 3)
- association between fitness and heritable phenotype (condition 4)
- observe the number of pollinator visits and see which attracts most often = fitness
- natural selection shifted the frequency distribution of flower colour
33
Continuous traits
- displays a range of expression (such as weight, height, etc.) rather than an all-or-none appearance (such as white or red)
- height in humans separated by sex, follows normal bell distribution
- if there is a variation in fitness, height distribution is shifted to the right towards taller individuals in the next generation
34
Galapagos finch beaks
- phenotypic variation in beak depth (condition 1)
- parental phenotype predicts offspring phenotype
- variation in beak depth is heritable (condition 2)
- Showed beak depth was highly correlated with the average of the two parents
- Access large and hard seeds with bigger beaks =selection
- another bird species introduced that was already feeding on the large and hard seeds so finches could not adapt to the larger beaks due to lack of larger seeds
- severe drought reduced seed abundance, seeds are large and hard, strong selection on foraging
- survival low but nonzero (condition 3)
- finches with deeper beaks more likely to survive drought and reproduce in the future (condition 4)
- survivors passed on larger beaks to their offspring
- natural selection shifted average beak length
35
Properties of natural selection
- acts on individuals, affects populations
- acts on phenotypes, changes allele frequencies
- acts on individuals, not for the good of the species (what helps the current generation may be reversed for the next generation, only produces the best at the given moment)
- is not random, but not goal directed
- existing traits and new genes = novel phenotypes
- not perfect
36
Conceptual changes with Darwinism
- tree thinking
- population thinking (variation=opportunity, small changes accumulate to generate large scale patterns)
- natural selection explains speciation, change within species and extinction
- speciation is gradual (varieties to subspecies to species)
- difficulty in species definitions explained
37
Why Darwin?
- naturalist
- theoretical leanings (geology, math)
- experimentalist (breeding pigeons, measuring survival in birds)
- right time (age of exploration), right place
38
Five sub-theories in the Origin of Species
1) evolution (first Darwinian revolution, organisms are not constant through time)
2) common descent (=common ancestor)
3) multiplication of species (formation of many different species through domestication and artificial selection)
4) gradualism (changes occur gradually through time)
5) natural selection (increasing controversy, force in changing organisms through time)
39
Controversy about natural selection - Religious beliefs
- constant world
- unique position of man
- created world
- wise and benign creator (created things a certain way and shouldn’t be able to improve it by natural selection)
40
Controversy about natural selection - Secular beliefs (no religious beliefs)
- essentialism (for every species, there are a set of attributes which are necessary for its identity and function, if a bird has no feathers is it really a bird)
- physics envy (biology not easily reducible to a small number of mathematical principles, some physicists/chemists did not consider biology to be a real scientific discipline)
- teleology (organisms and structures were designed with a specific purpose in mind, they have a destiny, vultures=remove the dead from environment)
- political ideology
41
Controversy about natural selection - Secular beliefs (no religious beliefs): Political ideology
- Nazi Germany favoured Eugenics, firm belief in teleology (chose which children survived based on phenotypes)
- Pre-Soviet Russia a leader in genetics (crop breeding genetics for Russian climate)
- Stalin and communist leaders denounced and jailed geneticists, based agricultural policies in Russia and China on Lamarckian beliefs (own individual wealth should not be based on who’s children we are but instead from the collective communities, Lamarckian belief=children raised in hardship are expected to rise to the occasion, overcome it and have children that are also tough)
- Nikolai Vavilov=bourgeois geneticist, established worlds first seed bank
- Trofim Lysenko=crop breeding under this leader, used Lamarckian logic to breed for cold tolerance and fudged data, disastrous crop improvement programs, crop failures, food shortages and starvation
42
Lamarckian beliefs
a theory of evolution based on the principle that physical changes in organisms during their lifetime, such as greater development of an organ or a part through increased use, could be transmitted to their offspring
*extreme values
43
Controversy about natural selection - Missing/incorrect data
- origin of variation
- inheritance of variation, particularly for continuous traits
- age of earth
44
Alternatives to Natural Selection - Neo-Lamarckism
- combined elements of natural selection and Lamarckism
- “soft” inheritance
- very widespread
- even Darwin (by pushing ourselves to have the best athletic performance, we can somehow pass on these traits to our children)
45
Alternatives to Natural Selection - Orthogenesis
- mutations are directional rather than sporadic/random
- mostly palaeontologists
- variation internally generated
- fixed direction of change in species
- could explain extinct forms
- ex) horses started small then got larger, mutations themselves did this
46
Alternatives to Natural Selection - Mutationism and macroevolution
- spontaneous variants defined as “mutants”
- discrete variation
- mutations of large effects define new species
- chromosomal rearrangements known to simultaneously produce both major phenotypic effects and reproductive isolation
- chromosomal rearrangements=“hopeful monsters”
- ex) mutations in fly wings allowed fleas (no wings) to create a new species (are closely related to flies)
47
Foundations for consensus
1) hard inheritance
- Mendel and Weismann (mouse tails, chop off tail of parent and young still born with tail)
- organisms inherit traits from parents with only modest or no influence from the environment in which their parents lived
- genes are hardwired
2) revised calculations of the earth’s age
- understanding of sun changed
- evolution of diversity of life
3) contributions by geneticists
- chromosomal recombination allows for variation to be passed down the generations
- most mutations of small effect
- inheritance of continuous (polygenic) traits
- theory of population genetics (use of mathematical equations)
4) contributions by “naturalists”
- systematics and paleontology
- macro-evolutionary patterns in the fossil record
- geographic variation among populations
- individual variation within populations
48
Evolutionary synthesis
- second Darwinian revolution
- mutual education between geneticists and naturalists (looking at mutants, field work)
- Mayr=came up with biological species concept, great historian of entire period
- T Dobzhansky=Drosophila genetics, genetic variants in wild populations, ardent naturalist, familiar with population genetic theory
- incorporated mathematical theory of population genetics
- genetics, natural selection and chance events combine to cause adaptive evolution
- data from many different fields
49
Genetic variation
- ultimately a result of mutation
- per gene mutation rates=1 in 10 000 to 1 in 10 000 000
1) point mutation=creates new alleles (alternate forms of a single gene)
2) chromosomal inversion=alleles inside inversion are transmitted together as a unit
3) gene duplication=redundant genes may acquire new functions through accumulation of additional mutations
4) genome duplication=may create new species, massive gene duplication, first discovered in plants
50
Why the 1000 fold difference in gene mutation rates? Why may one gene undergo mutation more than another?
- some DNA sequences more prone to changes than others (repetitive DNA sequences)
- genes are not all the same size (bigger genes=more nucleotides=better chance of mutation)
- a less essential gene for survival more likely to pick up mutation
- more carefully conserved genes are those protected the most from mutation
- age=sloppier mutation
51
Genetic variation in the wild
1) Classical School
- a few rare mutants
- most of the population remains stable, no mutation
- evolution waits for mutational variation
- ex) Drosophila in lab
2) Balance School
- much allelic variation
- lots of phenotypic variation in population
- constantly changing population
- evolution waits for environmental change (dry vs wet year)
- ex) Drosophila in natural populations
52
Genetic variation in the wild: Visible polymorphisms
- shell banding patterns in snails (can track colour over time , see if one phenotype did better than another)
- stripes on garter snakes
- coat colour in mice (blend in with soil)
- need breeding studies to confirm genetic basis
53
Genetic variation in selection experiments
- Maize=selection on seed oil
- 3-fold difference in oil content after 60 years (generations) due to selection compared to the original population
- either due to new mutations or presence of already high oil content seed individuals
54
Genetic markers
- a gene or short sequence of DNA used to identify a chromosome or to locate other genes on a genetic map
- revolutionized the study of evolutionary genetics
- molecular phenotypes
- heritable and polymorphic (variable traits)
- reflect allelic (DNA) variation at a locus
- allow direct measurement of genetic differences without breeding experiments
55
Why are genetic markers useful?
- many species difficult to rear in captivity
- complex inheritance of many traits
- breeding experiments not often feasible
56
What do genetic markers characterize?
1) genetic variation = conservation biology, can indicate how healthy a population is, prevent disease
2) short-term processes = selection, migration, hybridization, mating patterns
3) long-term processes = range expansion / contraction, long-term demography, speciation, phylogenetics
57
Mutation and markers: Allozymes
- variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus
- protein coding locus
- alleles are allozymes, may be neutral or under selection
- important tool to understand genetic variation in populations
- lots of enzymes have allelic variation in population all the time, allows for heterozygosity
58
Mutation and markers: Introns
- introns = non-coding DNA sequences, neutral regions
- they take up space
- mutations accumulate over time
- phylogenetic analysis (measurable genetic variation useful for analysis)
- molecular clock (can give you the amount of time two individuals shared a common ancestor last)
59
Mutation and markers: Tandem repeats
- neutral regions containing repeats of the same nucleotide sequence
- repeat number highly variable among individuals
- STR=microsatellites
- changes rapidly
- can detect mutations from parent to offspring
- applications=paternity, forensics, population differentiation
60
Mutation and markers: DNA fragments
- mutations can add or subtract restriction sites
- numerous variable bands within species
- separation and breaking of DNA into pieces
61
Hardy Weinberg Law
- states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences
- relates Mendelian segregation to genotypic frequencies in ideal situation
- works because transmission of alleles to gametes is predictable
- useful null hypothesis
- 2 allele case: p^2+2pq+q^2
62
Assumptions of Hardy Weinberg Law
1) no mutation
2) random mating
3) infinitely large population
4) no migration
5) no selection
6) (diploid organism, sexual, non-overlapping generations)
63
What is the maximum heterozygosity?
0.5 when 2 alleles are present
64
Quantifying selection: Construction of mines
- Soil piles of metals and debris not needed
- Little grows on these piles, but in Britain after hundreds of years, some select few plants started to invade them
- These flower at a different time than members of the same species in the surrounding area
- If transplanted from pile, they would grow slowly and be out-competed
- Interpretation=can grow in area where others couldn’t, but cost is rapid growth needed to compete with other plants
- Suggested that mechanism for changing the flower time resulted in less pollen being transferred to other flowers (reproductive isolation)
65
Quantifying selection: Moths in UK
- melanic frorm "carbonaria" (darker form) unknown in UK prior to 1848
- by 1860s, frequency of carbonaria in some industrial regions above 80%
- in agricultural areas, carbonaria remained rare
- as industrialization continued in UK, carbonaria spreads due to soot covered trees
- visualization to predators like birds increased predation of the lighter coloured moths
- an example of a polymorphism
- In 30 years, complete flip from which allele is the most common and which is the most rare (from Carbonaria to the white form today)
66
Polymorphism
the occurrence of different forms among the members of a population or colony, or in the life cycle of an individual organism
67
Quantifying selection
- s=1-w of least fit phenotype
- a direct measurement to compare survival or reproduction by phenotypes or genotypes
- S (selection) can be compared among different populations of pigeons and flowering plants
- W (fitness, omega) cannot be compared among different populations
68
Direct measurement of selection: Feral pigeons in California
- wild type=blue-grey with white rump, recessive
- other type=blue rump, dominant
- white rump helps pigeons avoid falcon attacks compared to blue bar phenotype
- pleiotropic traits
69
Pleiotropic traits
Producing or having multiple effects from a single gene
70
Viability fitness and reproductive success
-fitness = performance / best performing phenotype in population
71
Lifetime fitness
w of lifetime = (w viability x w reproductive) / highest multiple wv x wr in population
72
Mean fitness of population (w bar)
w bar = w(aa)*p^2 + w(Aa)*2pq + w(AA)*q^2
73
Frequency in next generation (frequency of AA, Aa and aa corrected for selection)
```
freq(AA)= p^2 * (wA1A1 / w bar)
freq(Aa)= 2pq * (wA1A2 / w bar)
freq(aa)= q^2 * (wA2A2 / w bar)
```
74
Directional selection
- a mode of natural selection in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype
- the fitness of the population is highest when the population is "fixed" for the favoured allele
- recessive alleles change slowly when rare
- dominant alleles change slowly when common
75
How is genetic variation maintained?
- directional selection eliminates variation
- high variation in nature
- neutralists=molecular (marker) variation results from mutation and drift, new mutations causes high variation in nature, rare alleles exist in heterozygotes, North American perspective
- selectionists=non-directional selection maintains genetic variation, European perspective
76
Genetic drift
-variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce
77
Non-directional selection: Overdominance
- heterozygote advantage
- ex) sickle cell anemia = heterozygote favoured in regions with malaria (immune)
- ex) Colias butterflies = Mutation in enzyme phospoglucose isomerase enzyme (PGI), Converts glucose-6 phosphate to fructose-6 phosphate (=glycolysis), One allele is heat stable (not temperature dependent) and another allele more enzymatically efficient (can convert glucose to fructose faster) but at high temperatures it becomes inefficient, Growing season is short so advantage if you have an efficient enzyme at low temperatures to maximize the total amount of daylight hours, Brood 2 doesn’t need an enzyme that has an advantage at lower temperatures in the morning and night since longer days, so the allele that is not temperature dependent is lost, Brood 1 has a lot of heterozygotes since allele not dependent on temperature is needed for shorter days
78
Non-directional selection: Negative frequency dependence
- fitness of each phenotype negatively related to its frequency
- ex) parasite-host interactions, rare prey advantage
- ex) cultivated bananas= Don’t have seeds since are triploid so don’t undergo meiosis, Represent a single variety of banana (95%), A pathogen killing this banana variety, Whole industry will collapse due to this pathogen, Has already happened with a different banana variety
- ex) elderflower orchid in Europe = Produce flowers and attract pollinators but don’t feed (no nectar) them and pollen is inaccessible to pollinators, Instead they stick the pollen sack onto the pollinators, Mimic real elder flowers phenotype to trick pollinators, For pollinators, orchids are a waste of time and energy since no rewards, Some produce pheromones or mimic a female insect to attract the males to the flower, Male fitness, More frequent the yellow morph, a rewardless flower, the less successful the orchid is to spread their pollen since pollinator will figure out the orchid is cheating
79
Non-directional selection: Alternative equilibria
- increasing variation within populations may maintain within species
- underdominance=heterozygote disadvantage
- positive frequency dependence
- ex) Mullerian mimicry in Heliconius butterflies = Have toxins inside butterflies that can make birds sick when eat them, Mimic each other to take advantage of learning the cues of birds on one species and then mistake a different butterfly with same markings so avoid them =avoid predation =positive frequency dependence
80
Underdominance
- the selection against the heterozygote, causing disruptive selection and divergent genotypes
- heterozygote disadvantage
81
Positive frequency dependence
-the fitness of a phenotype or genotype increases as it becomes more common
82
Non-directional selection: Trade-offs
- balance between sexual selection and natural selection
- alleles that enhance one fitness component but decrease another may be maintained at intermediate frequency
- ex) mating displays
- Ex) Swordail fish = Have long extension of caudal fin (sword), Dance around female, Females prefer mates with longer swords, Second class of males=Pygmy males are small with no sword and female-like, Difference is an a single locus S_ =displaying male and ss =Pygmy male , Females never mate with Pygmy males if given a choice, Sometimes they don’t have a choice if she can’t see the display due to murky water and can’t distinguish if the phenotype preferred is displayed, Advantage in murky water=Pygmy males since they mature more quickly due to being small, reach sexual maturity faster and fitness is longer, While displaying males spend their time displaying, the predators can get to them, Pygmy males=sneaker male strategy, when female is distracted by predator or displaying by another male, they sneak up behind her and mates
83
Non-direction selection: Varying selection
- spatial or temporal variation in selection pressure is likely common
- muddy stream, lots of predators=pygmy males dominate
- clear stream, not many predators = displaying males
84
Selection overall (summary)
1) H-W equations can be modified to make quantitative predictions
2) Directional selection can rapidly eliminate genetic variation
3) There are many types of non-directional selection, most maintain variation within populations, a few reduce variation within populations but may maintain variation within species
4) Many forces act on a population, a balance of many evolutionary forces
85
Types of non-random mating: Negative assortative mating
- opposites attract
- maintains polymorphisms at relevant loci
- ex) in humans = MHC or multiple histocompatibility complex, attracted to MHC different from their own, not many homozygotes in the population
86
Types of non-random mating: Positive assortative mating
- like with like
- increasing homozygosity at relevant loci
- overlaps with frequency dependent selection
- ex) flowering period in plants, populations tend to become homozygous at specific loci
87
Types of non-random mating: Inbreeding
- mating among relatives
- increasing homozygosity across entire genome
- ex) selfing populations of plants
- frequency of heterozygotes decreases by 50% in every generation until they disappear entirely
88
Inbreeding coefficient (f)
- probability that an individual has alleles that are identical by descent (IBD)
- calculating how inbred an individual is
- ex) cystic fibrosis (CF) in humans
89
Inbreeding depression
- loss in fitness due to inbreeding
- inbreeding increases expression of deleterious, recessive alleles
- inbreeding depression = 1 - (w inbred / w outbread)
90
Inbreeding depression - King Tut
- Pharaoh of Egypt
- Seen god-like
- Wanted to keep blood of gods in the family so close relatives having children not uncommon
- Wife died after having second child
- Had miscarriages
- Died in mid 20s
- 2 closely related matings, resulting in end of lineage
91
Inbreeding depression - People of Pakistani descent in Bardford, England
- marriage between first cousins common
- 13 500 births from 2007-2011
- marriage to a blood relative responsible for 31% of all birth defects in this population
- overall incidence of birth defects 3% in this population
- incidence of birth defects doubles to 6% in offspring of first cousins
92
Variation in inbreeding depression
`-more severe late in life (older)
- may be more severe under stress
- Later a mutant phenotype has a negative effect on individual, harder it is for selection to remove that genetic variation
- Natural selection has an easier time to remove that defect from the population if the offspring dies early in life (did not produce offspring for next generation, By 60 years old, you’ve already produced all the offspring you were to produce in your lifetime)
- ex) Hydrophyllum (biennial)=first year of growth and second year of growth results in reproduction, In second year, coefficient of inbreeding depression increases dramatically=effects of greater magnitude on second year
93
Sustained inbreeding
- deleterious recessive alleles should be "purged" from the population
- used on plants for agriculture to keep genetics of the plant (all the right traits)
- self-fertilization of gardens=crop breeding
- choose to propagate families that have traits that you want = artificial selection, and eliminate families (purge) that don't possess those traits
- line breeding in cattle and maintain populations for conservation of other animals
- may get genetically weaker by inbreeding
94
Genetic drift
- variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce
- random changes in allele frequency due to sampling error
- drift is random, no allele or genotype favoured
- strongest when sample size is small
* allele frequency in one generation affects gamete pool for the next generation
- leads to loss of heterozygosity and fixation for a single allele
- promotes differentiation among populations
- effects are most dramatic in small populations
- rare alleles tend to be under-sampled
- alleles are sampled to form zygotes during random mating
- adults are a sample of the zygote pool
- each generation is a sample of the previous generation
- genetic drift occurs before and after gametes (adult gen 1 to gametes to zygotes to adult gen 2)
- When you take a sample, by random chance, high representation of genetic variation and low representation of genetic variation
- Smaller the population or sample, the greater the opportunity for rare coincidences to have a major effect on the outcome of the system
- Rare alleles more likely to be lost in the sample
- By random chance, you lose heterozygosity = rare alleles
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Genetic drift in a population of 4 vs 400
population of 4:
- High frequency of allele where A=a
- Fix for A allele and a allele
- Do this for 20 generations
- Fixation becomes the norm, loss of heterozygosity
population of 400:
-General trend after 100 generations is slowly decreasing but still has not reached fixation of one allele or another
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Effects of genetic drift
-loss of heterozygosity when population is small, fixation for 1 allele, population size too small to prevent genetic drift from occurring
-heterozygosity won't change if population is large
Hg+1 = Hg [1 - 1/2N]
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Population differentiation: Fst vs Gst
Fst=single locus measure of population differentiation
| Gst= multilocus equivalent
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Population differentiation: Fst
- Fst= fraction of genetic variation found between subpopulations and the total of all subpopulations
- Fst = variance (p) / [mean (p) * (1 - mean (p)]
- low differentiation: Fst=0
- high differentiation: Fst=1
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Genetic drift vs selection. What happens when an allele is at low to moderate frequency in a small population?
- drift leads to random loss of alleles, whereas selection maintains one or more alleles
- combined effects depend on population size (N), strength of selection (s) and allele frequency
- drift overrides selection when s<< 1/4N
- selection overrides drift when s>> 1/4N
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Purging
- may be effective when increased inbreeding is gradual and population size is not small
- small populations experience both drift and inbreeding
- mildly deleterious alleles are more likely to be fixed when N is small (s<< 1/4N)
- this may increase inbreeding depression, reduce population size, fixation of additional deleterious or disadvantageous alleles
- extinction vortex = load of disadvantageous alleles where population threatened with extinction
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Bottleneck population
a sharp reduction in the size of a population due to environmental events (such as famines, earthquakes, floods, fires, disease, or droughts) or human activities (such as genocide)
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How low can you go? Minimum population size to avoid extinction vortex?
- study of New Zealand native and introduced birds
- measured hatching failure and analyzed as a function of past "bottleneck" (minimum population size recorded)
- Birds driven to extinction due to hunting
- Humans, pigs and rats caused species to go extinct upon introduction into New Zealand
- Europeans brought other mammals which further changed dynamics of ecosystem
- Bottleneck: populations were large and then collapsed, after conservation into effect, some populations reexpanded again
- Large populations=hatching rates remained good
- Small populations=hatching failure rates increase
- Direct effect of drift with inbreeding causing an increase in deleterious alleles causing developmental failure in the birds
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Migration
- causes gene flow
| - the jekyll and hyde of evolution (good vs evil)
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Gene flow
- the movement of alleles from one population to another
| - 2 components: gene movement, gene establishment
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Migration models: Island model
- island model=large -population has large effects on migration towards little islands
- gene flow in only one direction
- from one big continent to small islands
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Migration models: Stepping stone model
- Organisms hop from one island to the next
| - Allows for gene flow in both directions
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Migration models: Isolation by distance model
- Diffusion process from end to the other
- One big continent
- No islands
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Migration models: Metapopulation model
- Mathematically the most challenging
- 2D space
- Each population has some degree of proximity to all other populations
- Proximity affects flow
- Subpopulations can be different in size
- Most realistic and best model
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Migration and population differentiation
Fst= 1/ [4Nm+1] when m<0.01
N=effective population size
m=migration rate = proportion migrants/generation
Nm=# of actual migrants between 2 populations per generation
Nm= [1/Fst -1] /4
-1 migrant/generation has a large effect (Nm=1, Fst=0.2)
-neutral genetic markers can be used to estimate Nm
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Migration and allele frequency
p' = psink (1-m) + psource (m)
-p'=freq(A) after correcting for migration
-psink= freq(A) in recipient/resident population
-psource= freq(A) in source of migrants population
-m= migration rate
q' = qsink (1-m) + qsource (m)
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Benefits in migration (Jeckyll effect) in Prairie Chickens
- hunting pressure, agriculture uses destroying their habitats
- protection and habitat restoration since 1960s
- 1970-1990s populations in decline
- down to 2 males in the lech in 1993
- artificial migration increases effective N (rescue through migration)
- brought more males from a different population in Nebraska and were returned after mating
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Extinction vortex (mutational meltdown)
- term used to describe the process that declining populations undergo when”a mutual reinforcement occurs among biotic and abiotic processes that drives population size downward to extinction
- s<1/4N
- concern for fixation
- load of disadvantageous alleles where population threatened with extinction
- deleterious alleles fixed
- further reduction in N, more drift, more inbreeding
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Extinction vortex (mutational meltdown): Woolly mammoth
- mammoths of Wrangel Island, a small isolated population of about 300 individuals that went extinct 3700 years ago
- continental mammoth populations went extinct about 10 000 years ago=small relict population
- Went extinct when great pyramid of Egypt was being built
- This population was not affected by humans
- specific mutations cause loss of olfactory receptors for detecting smells reduced the number/variety of urinary proteins =genomic meltdown during extinction vortex
- Coats were no longer insulative
- Weather event like rain over snow may also have caused extinction
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Costs of migration (Hyde effects)
- may prevent or reduce local adaptation by bringing in deleterious alleles
- equilibrium allele frequencies depend on the strength of selection relative to the rate of migration
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Allele frequency after one generation of s (selection) and m (migration): Lake Erie water snakes
- banded allele from mainland detrimental on island
- banded allele is present on island due to migration
- mainland= Lots of vegetation above the scour line, Lots of places to hide, Bands are cryptic, not to match colours of surroundings, just harder for birds to see them when in vegetation, On mainland, 100% banded, most are AA since no unbanded snakes on island
- island= Island was lowland, scoured by ice, only cobbles, no vegetation, Needed to blend in with rocks, Primary predators are hawks and seagulls, selection reduces frequency (A) But migration from the mainland brings in new A alleles, Equilibrium of island is such that: q= f(a) = 0.93, it would be q= 1 without migration (if mainland population were to be removed)
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Equilibrium allele frequency
- within any population, reflect balance between selection and migration
- across wide range=isolation by distance model effect
- neutral alleles in combination should steady change (adjacent areas most similar)
- selected alleles should show sharper gradients (gradient where selection at one end or the other, intermediate frequency of alleles that show steady changes from one end to the other
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Migration overall
- homogenizes allele frequencies across populations (reduces Fst)
- Fst=reduces genetic distinctiveness
- may alleviate effects of drift and inbreeding = Jekyll effect
- may prevent adaptation to local conditions by bringing unsuitable alleles = Hyde effect or “migration load”
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Evolutionary synthesis
Evolution results from changes in frequency of Mendelian genes
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Wright and Fisher disagreed on relative importance of natural selection, drift and migration. What were their beliefs?
Fisher:
Central problem=refining existing adaptations
Major processes= selection and mutation
Ecological context= large, panmictic populations
Genetic basis= additive gene effects
Wright:
Central problem=origin of adaptive novelty
Major processes= selection+drift+gene flow
Ecological context= small, subdivided sub populations
Genetic basis= epistasis and pleiotropy
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Adaptive landscapes (Wright)
- a visual aid for non-mathematical biologists
- appealing to organismal and molecular biologists
- complex fitness landscapes are analogous to topographic maps
- “elevation lines” represent population mean fitness for given allele frequency
- peaks of mountains= + (represent a local maximum fitness of a population)
- pit or valley = -
- selection takes a population and pushes it upward until it reaches the peak
- organisms occupy different peaks
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Shifting Balance Theory (Wright)
- populations occupy a position on “adaptive landscapes”
- changes in allele frequency correspond to changes in phenotype and changes in population mean fitness
- populations cross “fitness valleys”
- Ultimate goal, reaching the global optimum
- Doing well at global optimum, sends migrants in all directions
- Population at higher peak is recruiting other populations to join in at the global optimum by individuals migrating out to share alleles with the other population
- inspired many studies
- empirical evidence often supports one + phases but never all three
- chromosomal evolution (underdominance), Mullerian mimicry in butterflies (alternative equilibria ), mating systems in plants (alternative equilibria)
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Shifting Balance Theory (Wright): Phases
1) drift drives a population across a fitness valley
2) selection drives the population to a new optimum which is a global optimum (or at least higher than the original optimum)
3) the population at the global optimum grows large and sends out many migrants to neighbouring populations
4) the migrants change allele frequency in recipient populations enough to allow them to cross the fitness valley, a new species or phenotype arises
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Shifting Balance Theory (Wright): Water Hyacinth in Brazil
- most populations large and outbreeding with three mating types
- small populations in marginal habitats lose mating types as a result of drift
- many of these populations evolve self pollination and small less showy flowers
- changes in environment likely change fitness landscapes
- populations occupying former peaks may now occupy valleys
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Shifting Balance Theory (Wright): Commercial fisheries
- the largest mature fish are being removed preferentially
- intensive selective pressure for rapid maturation at smaller body size
- could be shifting fish populations to a new fitness peak
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Polygenic traits
- phenotype is influenced by more than one gene
- apparent blending inheritance
- Mendel’s laws can be extended to multiple loci
- follow a bell-shaped curve distribution due to continuous variation
- continuous variation also reflects the environment
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Additive polygenic model
- by increasing the number of genes controlling a trait, the number of phenotype combinations also increase
- forms a bell-shaped curve distribution
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Quantitative genetics
-statistics method of partitioning variation in polygenic traits
-plant and animal breeding
-powerful, describes inheritance, predicts selection response
-theory based on additive polygenic model
-VP = VG + VE + (VGxE)
V=variation
P=phenotype
G=genotype
E=environment
GxE=genetic x environment interaction *don’t need to worry about
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Epistasis
-the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another
129
Heritability
- heritability estimates resemblance between relatives
- h^2 = VA/VP (additive genetic variation / total phenotypic variation)
- slope=h^2
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Heritability: Galapagos finches
- h^2 > 0.9
- perfect heritability where VA=VP and VA/P =1
- parental phenotype predicts offspring phenotype
- variation in beak depth is heritable
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Response to artificial selection
- depends on strength of selection and heritability (additive genetic variation / total phenotypic variation or VA/VP)
- the more heritable a trait is, the faster it will respond under a regime of selection
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Selection response or Breeder’s equation
```
R = delta z bar = h^2 S
S= delta X
R= delta Y
```
R= response to selection
Z bar = change in average trait value
H^2= heritability
S=strength of selection
Delta X = difference in z bar between parental generation and the members of parental generation that reproduce
Delta Y = difference in z bar between parental generation and offspring generation
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Selection response or Breeder’s equation: No selection for trait Z
- z bar o = z bar p
- z bar R = z bar p
- R = delta z bar = h^2 S
- S = z bar R - z bar p = 0
- R = h^2 * 0 = 0
- o=offspring
- p=parental
- R=reproductive
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Selection response or Breeder’s equation: Selection for trait Z
-z bar o and z bar p = different
-z bar R and z bar p = different
-R = delta z bar = h^2 S
-delta z = z bar o - z bar p
-S = z bar R - z bar p
-R = h^2 *(z bar R - z bar p)
z bar R > z bar p ... S>0 ... R>0
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Realized heritability
Realized h^2 = total R / cumulative S
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Realized heritability: 6-week weight in mice
- 10 generations, 6 replicates in each direction
- upward and downward selection
- generation to generation fluctuations
- straight line = predicted trajectory based on rate of change in that trait in the first generation
- lower limit of 6-week body weight below which the mice are not as healthy or vigorous, females have trouble reproducing = biological barrier
137
Realized heritability: Zea mays selection
- seed protein and seed oil amounts selected for
- selection response sustained in high and reverse lines
- selection response less in low lines
- Upward selective line=increase in seed protein and oil
- Downward selective line=decrease in seed protein and oil
- Below a certain point, no further decrease in protein since kernels need it to feed the embryo
- Below it would no longer be viable
- Upward selecting line bred to now be downwards and vice versa
- Selection can be recreated
- Removing all lipids from kernel = decimation of downward line population
- Removing energy storage =then are inviable
- Plasma membranes of corn kernels dependent on lipid bilayer = cellular inviability
- = Biological limit
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Artificial selection summary
1) most traits respond quickly to selection
2) mutation provides genetic variation for indefinite divergence
3) natural selection may oppose artificial selection
4) selection most efficient in large populations
