Final Flashcards
(134 cards)
1
Q
What kind of graph would this fitness function have (shape)?
Directional selection
A
Directional selection - linear
2
Q
What kind of graph would this fitness function have (shape)?
Stabilizing selection
A
Stabilizing selection - bell curve (highest fitness in the middle) (looks like an upside down U)
3
Q
What kind of graph would this fitness function have (shape)?
Disruptive selection
A
Disruptive selection - two extremes do better than intermediate values (looks an upside bell curve, or a “U” shape)
4
Q
In terms of how strong linear selection (B /beta) is, when would we expect it to be low or 0? 2 conditions.
A
- Environmental conditions are stable
2. Population has experienced those conditions for a long time (many generations)
5
Q
In terms of how strong linear selection (B /beta) is, we would expect it to be low or 0 when…
- Environmental conditions are stable
- Population has experienced those conditions for a long time (many generations)
Why is this?
A
- Strong selection over a long period of time –> get rid of individuals of strong disadvantage
- Individuals in these population will be close to the fitness peak because selection removed unfit phenotypes in earlier generations
Can be thought of as an “unbroken winning streak” - The population has a good genetic strategy for producing a phenotype that does well in the particular environment (if it doesn’t change)
6
Q
In terms of linear selection (B), |B| > 0.5 is considered strong or weak selection?
A
|B| > 0.5 is considered very strong selection
7
Q
Why is possible for the median B (linear selection slope) to be low for survival, but higher for mating?
A
- Selection for survival is stronger than selection for successful mating
o If you don’t survive, you can’t mate!
8
Q
How stable (or variable) is selection in space and time? Answer this question using the example of polemonium plants and their 2 pollinators, moths and hummingbirds.
A
o Variable selection of flowers by pollinators:
- Moths: use recessed stigma (improves transfer of pollen), strongly scented, and light coloured flowers (for night fliers)
• less visits if the stigma is sticking out - Hummingbirds: use exserted stigma (sticking out above the petals), corolla dimensions (width of the opening of the flower)
• Opposite selection gradient slope (B = - #) and more visits if the stigma is sticking out - Polemonium plants → have both types of stigma locations (for both pollinators)
- Continuous variation (encourage both types of pollinators)
- Maximize chance of pollinators (either)
- Environment affects the abundance of pollinators; pollinators affect the abundance of plants in the next generation
9
Q
Fill in the blanks for selection on continuous traits:
- Directional selection is often ___1__
- Selection on mating success is __1__
- ____ and ____ variation exists in selection gradients
1 = strong or weak?
A
- Directional selection is often strong
- Selection on mating success is strong
- Temporal and spatial variation exists in selection gradients
10
Q
Define correlated traits
A
- Many traits influencing fitness are genetically correlated with other traits. Has 2 components =- linkage and pleiotropy.
*not required
o Linkage: Genes responsible for a trait are located near each other on the chromosome, may be associated with each other because of proximity (not functional linkage)
o Pleiotropy: A single genetic locus in which allelic variation affects more than one trait at the same time (ex. Purple flowers also cause purple leaves)
11
Q
Define linkage (part of correlated traits)
A
o Linkage: Genes responsible for a trait are located near each other on the chromosome, may be associated with each other because of proximity (not functional linkage)
12
Q
Define pleiotropy (part of correlated traits)
A
o Pleiotropy: A single genetic locus in which allelic variation affects more than one trait at the same time (ex. Purple flowers also cause purple leaves)
13
Q
In domestication of silver foxes for fur coats, what are direct, and correlated responses?
A
- Direct response: approachability, tail wagging, whimper and permit handling, follow and lick humans
- Correlated response: floppy ears, coat colour variation, curly tail, shorter, thicker tail vertebrae
14
Q
3 long term effects of genetic covariances
A
- Genetic covariances seem to influence evolution over long periods of time (1.3 my in birds)
- May slow evolutionary responses or cause traits to temporarily evolve away from the optimum values
- Mutations with large effects on the phenotype may cause changes in the G matrix
15
Q
Describe fisher’s geometric model of fitness and mutations.
A
- The environment is unchanging but the fitness of the population is changing (fitness peak, adaptive landscape)
- Over many generations, population would be really close to the peak
o If a mutation moves an individual away from peak = decreases fitness
o Beneficial if it moves individual closer to peak = increases fitness
- Large mutations, even if in the right direction, is going to over shoot the fitness peak
o Just as bad (or worse) as moving in opposite direction
Fisher stated that mutations are most likely to be beneficial when they are small
- Moves population in the right direction without over shooting the fitness peak
16
Q
Fisher’s geometric model assumes that populations are close to optimum phenotype, and that small mutations are most beneficial since they’ll bring them closer to the fitness peak without overshooting.
What if the population isn’t close to the fitness peak?
A
- If far from the optimum, the likelihood of a large mutation having a positive effect is higher than if the population is close to the optimum
- Keep in mind – fitness landscapes are not stable, instead are very dynamic (valleys can turn into peaks quickly), so populations may always be chasing a moving fitness peak
- Fisher’s model was a thought experiment up until this point
17
Q
Describe the E. coli experiment (adaptive mutations on phenotypes) that disagreed with Fisher’s geometric model (assumes that populations are close to optimum phenotype, and that small mutations are most beneficial since they’ll bring them closer to the fitness peak without overshooting it).
A
Experimental evolution of E. coli in nutrient poor medium - fitness depends on cell size
o The larger the cell, the higher the SA = more contact it has with the medium and better able to absorb nutrients
o Found 4 different mutations over the generations (3 to make a cell larger and 1 to make the cell smaller)
o The biggest jump came first – when furthest away from the fitness peak
18
Q
Give 2 examples of experimental evidence against fisher’s geometric model (small mutations most beneficial)
A
- Microbes: adaptation to experimental conditions suggest that mutation of large effect may be important
- DNA sequencing: a few nucleotide changes can have large effects on the phenotypes
o Key genes important across many species (important genes repeated over and over again)
19
Q
What’s genetic OTL mapping, and what is it used for (/what can it estimate)?
A
- QTL = quantitative trait loci = physical location on a chromosome that influences a quantitative trait
- Span many nucleotides
- Contains 1 or more of the genes controlling the trait
- Can use genetic linkage maps to estimate:
o Position and number of QTL (genes) controlling quantitative traits
o Size of effect on the phenotype - Can then find linkage (statistical association) between genetic marker and phenotype
20
Q
What is the 2 step mechanism for using QTL mapping?
A
- Generate genetic map using markers (eg. A-F) - test crosses, then map distances between markers on chromosome
- Match phenotypes in segregating (F2) population to marker loci.
Ex.
- Individuals with marker D from species 1 would have a phenotype more similar to species 1.
- Individuals with marker d from species 2 would have a phenotype more similar to species 2.
21
Q
Introgression
A
When 1 individual segment of DNA can be captured by one species, often originating through a hybridization event
22
Q
How was QTL mapping used to learn about the black coat colour gene in wolves?
A
Timber wolves are more likely to have darker pigmentation compared to tundra wolves
- Coat colour benefits them in their habitat (fit in better)
- QTL map to find genetic variation found that an identical allele at the K-locus in domesticated dogs
- Implication that a wolf hybridized with a domesticated dog, and integrated the piece of chromosome that determined coat colour (black) into a wolf population that found the trait advantageous
- Introgression: When 1 individual segment of DNA can be captured by one species, often originating through a hybridization event
23
Q
What’s a LOD score?
A
LOD = logarithm of the odds –> indicates the likelihood that a locus controlling a quantitative trait is at a particular position along the chromosome
24
Q
What would these LOD scores mean?
LOD = 0 LOD = 2.4
A
o LOD = 0 –> Variation is not linked to chromosome
oLOD = 2.4 or above –> Variation is linked to chromosome (2.4 is the threshold, below this it may be sampling error)
25
What does it mean if you have a LOD score graph, with 2 peaks with a valley in between?
2 peaks represent 2 different loci/genes having an independent effect on the trait in question
The dip between them tells us that these genes are located on distant segments of the chromosome
26
Describe how we learned about armoured plates in stickleback fish using QTL.
- Eg. Stickleback (armored fish): 1 locus (A) explains most variation in plate number
o Spines (poke) and amour plates to protect from predation
o “modifier” genes with small effect on phenotype also contribute to variation
- Sticklebacks are marine but have invaded FW habitats, often first fish to recolonize, tolerate FW equally well as SW.
- In the FW habitat – marine sticklebacks survive and there are predictable changes
o Paxton benthic form feeds on bottom – smaller than marine and lose almost all of the amour and spines are reduced (hardly any other fish in the environment so no need for energetically costly plates, and less Ca2+ in FW)
o Pelagic/open water form also exists – even smaller than Paxton form, feed on zooplankton and suspended food particles at surface
- Performed crosses to determine locus responsible for plate number variation
Locus (A) (master gene controlling plate phenotype)
AA – 60-70 armor plates
Aa – 30-62 armor plates
27
What 2 things have we learned from QTL?
| Genetics of adaption
- Most quantitative loci are of small effect
| - But QTL of large effect can be very important ecologically (monkey flower coloring, armor gene)
28
What 2 things have we learned from experimental evolution with microbes?
(Genetics of adaption)
- Mutations of small effect are more likely to be beneficial (don’t want to overshoot peak)
- Mutations that are fixed early have larger fitness effects than those fixed later
29
What 2 things have we learned from DNA sequence analysis?
| Genetics of adaption
- Changes in a few nucleotides can have large effects on the phenotype
- Key genes are important across many species (found over and over in different lineages)
30
Describe the Madagascar orchid and sphinx moth to illustrate adaption.
- Orchid has a long tube (nectar spur) with nectar producing cells at the bottom
- Pollinator moths had a long tongue/proboscis that was able to reach the nectar
o Darwin predicted a single species of moth specialized on it
- Implication: The orchid only wants to provide nectar to its specific pollinator, so it slowly began making the nectar spurs longer so that only it’s specific pollinator could feed from it – moth responded by extending its tongue to keep up with the flower
31
It is difficult to determine the function of a trait in a focal organism. Use the example of a hooked beak on pigeons to show this.
- Eg. Hooks on pigeon beaks reduce parasite loads
o Is the hook on beaks used to stab parasites (food source and removes them)?
- Do similar traits fulfill the same function in multiple species (birds of prey)?
o A lot of birds have hooked beaks, but eagles and hawks use their hooks for predation (killing and shredding prey)
- Did the trait originate for its current function?
o Did an ancestral pigeon use the hook to kill prey in this manner, and then removing parasites become a secondary useful function?
- Is the trait maintained by natural selection or “phylogenetic inertia”?
o It’s possible that this trait was important once but isn’t now (remnant function) that’s maintained by phylogenetic inertia (constraint on future evolution due to previous adaptions)
32
3 types of studies, and 2 levels of studies we can do/use to demonstrate adaption.
What's a goal of these studies?
- Goal: show that trait developed or is maintained through natural selection
o Type of study: experimental, observational, theoretical
o Level of study: population, comparative (among taxa)
33
Describe the example of Wing waving in Tephritid fly to escape jumping spider predation, in terms of adaption.
Include the 3 hypotheses and experimental results.
- These flies have wing bands and can wave their wings in a pattern that appears to mimic jumping spiders (one of their predators), which makes the spiders leave them alone because they are tricked into thinking it’s another spider of the same species
Hypotheses:
1: Waving and wing bands did not mimic jumping spiders
- It’s just a coincidence, perhaps a pheromone is being secreted and the wing flap helps transmit it, which repels the spider
2: Waving and wing bands mimic jumping spiders, and deter other predators
- Jumping spiders have aposematic coloring, so perhaps the flies are trying to fool other species
3: Mimic jumping spiders to deter predation by jumping spiders
Experimental results:
- Jumping spiders attacked flies that were missing either wing bands or waving behavior
o Manipulated flies to only display one at a time, did not prevent predation
- Other predators attacked flies regardless of wing patterns and waving
o Adaption seems to be specific to avoiding jumping spider predation
- Both adaptions are required to avoid predation
34
Describe an observational study that investigated the rock thickness preference for snakes - what were the results, and issues with the study?
Thermoregulation in garter snakes:
- In lab and field they keep body temp the same (28-32 degrees)
- Do snakes make adaptive choices when they choose rocks to hide under at night? (rocks radiated the heat back at night)
Hypotheses:
H1: Snakes choose rocks with the best thermal properties as refuges
H0: Snakes choose rocks at random to use as refuges
Look at thickness of rocks and the distribution of rocks the snakes are hiding under
Thermal properties under rocks:
- Thin rocks – got hot in the day, cold at night
- Thick rocks – underside too cold
- Medium rocks – just right
Compared rocks available to those chosen by snakes as a nocturnal refuge:
Rocks available – almost equally distributed
Rocks chosen – mostly choose medium rocks
- Therefore → reject the null hypothesis
- But we also have behaviors that are not predicted, so we can’t say that rock thickness is the only influence on choice → can’t conclude that H1 is correct
Strengths of study – info about snake preference is known in advance, have multiple hypotheses with distinct predictions (formed prior to experiment)
Confounding factors – often an issue in observational studies, accounted for by measuring prey and moisture content, would they provide a better or more complete explanation of observed patterns.
35
What is a major problem with observational studies?
Cofounding factors - things we haven't even considered or can't test can be at least partly contributing to our results
36
Describe theoretical studies.
- Consider benefits and cost of contrasting phenotypes
- Assign numerical values to benefits and costs, or define the relationship between the trait value and benefit
- Mathematical approaches to predict best phenotype under certain conditions
- Examples of this are in population genetics and life history evolution
37
Describe comparative (interspecific) studies. What is a potential problem?
- Each species is a data point
o Usually observational studies
o Greater generality
o Greater potential for confounding factors
- Widely used to compare associations between a trait and the environment or correlation among traits
Potential problem: species may resemble one another because they are closely related rather than because they experience similar selection pressures
• Can use phylogenetic information to determine this
38
Describe seed size vs habitat (shady or sunny) in a comparative (interspecific) study - what was the problem with this study?
Eg. Are large seeds an adaptation for living in shady habitats? (examined 12 species)
- Limited sunlight, takes longer to produce resources
- Found that 6/12 species had large seeds → all lived in shady habitats
o Appears to support that large seeds are associated with shady conditions
o Creating phylogenic tree revealed that the 6 large-seeded plants came from one lineage, and the small-seeded plants came from a different one
So actually comparing 2 different lineages, not 12
- Then used 6 comparisons between sister species (nearest living relatives), and found that changes in seed size are consistently associated with changes in habitat
o Same result, much stronger support
39
What are 2 ways we can take phenotypic resemblance due to shared ancestry (phylogeny) into account when doing comparative (interspecific) studies?
- Sister species comparison
o Requires many species
o Can be frequent changes in hypothesized causal variable (Ex. Environment, habitat)
o Only involve comparisons of living species
- Independent contrasts
o Compare changes in causal variable with changes in dependent variable
o Often involves estimation of ancestral phenotypes
40
Describe the study looking at testis size in fruit bats and flying foxes - what technique was used?
Ex. Testis size in fruit bats (small) and flying foxes (large)
- Fruit bats live in larger groups – more males (more competition) therefore large testis
- Flying foxes live in small family groups – less competition, less likely to breed multiple times in sequence, no need for large testis → smaller testis
- If the bats are from different lineages, then it’s possible that they evolved in different directions in respect to this trait
o If testis size correlates to group size → can infer the trend and predict what selection was acting on
Was selection acting on group size and resulted in increased testis size, or did testis size come first?
- Phylogenetically independent contrast (PICs):
o Comparison made between each species and its closest relatives
Use data (differences between testis size and group size) to create an evolutionary trajectory from the origin
• Conclusion: Larger group sizes increased testis size
41
Describe: - Phylogenetically independent contrast (PICs):
o Comparison made between each species and its closest relatives
Use data (differences between testis size and group size) to create an evolutionary trajectory from the origin
(Example is testis size in fruit bats vs flying foxes)
42
When should independent contrasts (comparative method) be used, and what is required?
- For discrete or continuous traits
- Implies perfectly known phylogeny, accurate reconstruction of ancestral phenotypes
- Assume similarity among relatives IS NOT maintained by natural selection
o But selection may maintain associations between large seeds and shady environment (similar selection pressures) = “phylogenetic niche conservatism”
43
phylogenetic niche conservatism
Selection maintains features in different species due to experiencing the same selection pressures (ex. environmental conditions)
44
Causes of non-adaptive variation (7):
- Direct effects of the environment (phenotypic plasticity)
- Natural selection is not the only force (Genetic drift)
- Multiple adaptive phenotypes (ex. camouflage in grouse chicks)
- Laws of physics or chemistry - flower colour changes with pH
- Tradeoffs (time and resources)
- Pleiotropy
- Developmental constraints
45
Define: phylogenetics
- Phylogenetics: The study of evolutionary trees
46
Define: phylogeny
- Phylogeny: The evolutionary history of a species or group of species.
o We can only infer evolutionary history using “clues” left behind
47
Why is DNA a document of evolutionary history?
- Most sensitive – each change is recorded in the organism and makes it easier to figure out which taxa are related
o Includes silent mutations that would not result in any phenotypic change
- Observed DNA sequence differences aren’t necessarily basis of phenotypic differences Neutral genetic markers
o Despite being silent or not in the coding sequence, we can use them to figure out which organisms are related
o An independent indicator of common ancestry
48
Define: neutral genetic markers
- Observed DNA sequence differences aren’t necessarily basis of phenotypic differences (ex. silent mutations) = Neutral genetic markers
o Despite being silent or not in the coding sequence, we can use them to figure out which organisms are related
o An independent indicator of common ancestry
49
Genome
the whole hereditary information of an organism (genes and non-coding sequences) encoded in the DNA
50
Nuclear genome (what is it, what are pros and cons of using it for studies?)
o DNA in the nucleus on chromosomes
o Inherited from both parents
Pros:
o Encodes most traits that are very common
Cons:
Nuclear DNA is large and complex in Eukaryotes
Complete genomes are being sequenced but genome annotation (identifying actual gene regions) is far behind sequencing
Gene content varies
Contains large amount of non-coding DNA
Not easy to work with in non-model organisms (sequence genes, interpret results)
51
Chloroplast Genome (where is it, how did it evolve, and what are the benefits of using it for studies)?
- In cytoplasm of plant and protists
- Chloroplast thought to have originated as endosymbiotic cyanobacteria (many similarities)
- Has its own small genome (circular), reduced in size
- Many ‘missing’ genes are now in the chloroplast nucleus
52
Mitochondrial genome (where it Is, where it came from, and how it varies/what it contains).
- in cytoplasm of most eukaryotes
o Derived from endosymbiotic bacteria
- Circular genome with its own ‘machinery’ for protein synthesis (ribosomes, tRNAs)
o Uses different genetic code than nuclear genome
o 16-17 kb in vertebrates but can be bigger and more variable in plants
o Contains very little non-coding DNA
Many genes transferred to nucleus, no longer self-sufficient
- Gene content and gene order of remaining genes highly conserved
- The Mt genome contains:
a) 13 protein coding genes
a. Enzymes involved in oxidative phosphorylation (cytochromes)
b) 22 tRNA
a. Code for RNA that transfers amino acids during translation
b. Not protein coding but not junk DNA
c) 2 rRNAs
a. Small and large subunits of mitochondrial ribosomes (12S and 16S ribosomal RNA)
d) Control region D-loop, origin of replication/transcription
53
Monophyletic group
Monophyletic group: A group that shares a common ancestor that is not included in any other groups.
54
Are fish a monophyletic group? Are wolves and dogs monophyletic?
- Monophyletic group: A group that shares a common ancestor that is not included in any other groups.
o Example: Amphibians, reptiles, mammals
o Fish are not a monophyletic group – they form a lineage including other groups
Eg. Are wolves and dogs monophyletic?
- Wolves were domesticated at least 4 times (4 total lineages)
- This means that neither one of them are monophyletic with respect to one another
55
Character
- Character: structure or feature
| o Black vs grey fur, A vs T at a particular nucleotide position
56
Character states
variant conditions of the character
57
Homologous characters
Alike due to shared ancestry – 2 sisters
58
Analogous/homoplasious characters
Arose independently (through parallel or convergent evolution) – ex. chance mutation in humans causes their DNA to be more similar to chimpanzees, just a random occurrence
can be misleading when inferring relatedness based on morphological characters
59
Characters must be homologous – how can you determine if 2 characters are homologous?
- Same gene
I. Same gene
o Some genes are similar (eg. From the same gene family)
o Especially in taxa with polyploidization in their history
o Conserved primers may not always amplify homologous genes
Might end up comparing heterogeneous sequences by accident
• Cytochrome 2 looks similar to cytochrome 1, when using PCR to amplify genes, the copies can be close enough that you amplify multiple copies at once, sequence version B instead of A, etc.
And sometimes “pseudogenes” Eg. “Numts” (nuclear copies of mitochondrial genes)
60
Characters must be homologous – how can you determine if 2 characters are homologous?
- Same gene position
II. Same gene position
o Must “align” sequence to make sure comparing same position of each genes
Using programs such as ClustalW (maximize the amount of match)
o Due to 3-nucleotide codons, insertions or deletions (Indels = insertion and/or deletion) must be in multiples of 3 to maintain reading frame
Start with a start codon (usually ATG), when there are nucleotide deletions, it tends to be in multiples of 3 (no frame shift mutations)
• Ex. A single A would not be deleted, but the codon AAC might be
o Eg. D-loop – more challenging to align correctly
Includes Indels of any number (therefore more variable)
Good for intraspecific comparison, but sequences among distantly-related taxa can be different, no match looks good
61
Characters must be homologous – how can you determine if 2 characters are homologous?
- Character *state* must be homologous
III. Character state must be homologous
o Same nucleotide at a given position due to descent from common ancestor (or convergent evolution?)
Eg. Independent mutations in divergent lineages just happened to both produce a C or T at a particular site?
o Only 4 character states (nucleotides)
Good chance independent mutations will occur, and multiple substitutions at the same site (ex. T C T C A)
• We only see the final A
• The same thing can happen in another species:
o Ex. Species 1: T C T C A
o Ex. Species 2: G A G A
They seem to be the same
Therefore, we distinguish homology from analogy by “preponderance of evidence” → using as much data as we can get
o Compare large number of characters (sites)
Wouldn’t base conclusions on similarities or differences at only a few sites
62
To make phylogenetic trees, you compare characters. Why do you need to consider the complexity of them?
Consider “complexity” of characters:
- Some mutations are more common than others (= less complex morphological traits)
o Many organisms have converged traits based on where they live (aquatic – dark back and light stomach), MANY lineages birds and fish both have this
Less trustworthy, not strong indication for relationship
63
To make phylogenetic trees, you compare characters. Why are transitions a problem?
o Eg. Transitions → DNA equivalent to a character state change that may be untrustworthy because it occurs over and over again
o Third position mutations also receive less weight since they’re so common
(Consider “complexity” of characters:
- Some mutations are more common than others (= less complex morphological traits)
o Many organisms have converged traits based on where they live (aquatic – dark back and light stomach), MANY lineages birds and fish both have this
Less trustworthy, not strong indication for relationship)
64
To make phylogenetic trees, you compare characters. Describe how purines vs pyrimidines can mutate/switch, and if this results in a mutation or not?
Purines (A, G) and Pyrimidines (C, T):
- Width of nitrogenous base is different
o Width the same when the base pairs come together (purine + pyrimidine)
o Purine + purine = too short
o Pyrimidine + pyrimidine = too long
DNA repair machine can detect this (measure the widths between sugars)
• Hard to detect errors that exchange one purine for another or one pyrimidine for another
65
Transversion
Transversions:
- Purine for a pyrimidine (or vice versa)
- Repaired most of the time (before bring passed on therefore a rare mutation)
66
Third position mutation
Third-position mutations:
| - Transcriptionally silent, often no effect
67
Saturation of transitions vs transversions
Substitutions lose their phylogenetic signal at saturation:
- The longer ago species diverge from one another, the more different those DNA sequences will become
o Used a measure of how long ago they diverged (molecular clock)
- As new mutations get added, there’s nothing to prevent the new mutation from overwriting an old mutation
o Transitions accumulate, then start to diverge from x=y (saturation), peak
• Saturate can’t diverge anymore in terms of percent of change without compromising function
o Transversions saturate much slower (closer to a linear relation) and can trace back further in time
68
Transition
Transition mutation (common point mutation):
- Swaps a purine for a purine (eg. G to A)
- Swaps a pyrimidine for a pyrimidine (eg. C to T)
69
Kimura’s two-parameter model (K2P)
o Corrects for multiple substitutions at the same site (degree of saturation), and differences in frequency of transitions vs transversions
Increases with time since divergence
o Let’s us more accurately estimate time of divergence
70
Phenetics (in tree building)
- Estimates taxonomic affinities from overall similarity
- Compares as many characters as possible
o No weighting or phylogenetic assumptions (regarding homology or polarity of character states)
- Assumes that contribution of analogy to overall similarity should be swamped by degree of homology if enough characters compared
71
Phylogenetic species concept:
- Represents evolutionary history
- Genealogical species concept
- Species are smallest identifiable units that are diagnostic and monophyletic
- More closely related if shared ancestor more recently
- Sister taxa = closest relatives
72
Neighbour joining method (in tree building)
- Using K2P, a distance method
- Represents phenetic approach
- Clusters taxa so that the most similar forms are grouped together
- Many possible trees but the best one minimizes total distance among taxa
73
Cladistics (in tree building)
- Argue that degree of relatedness does not always equal to the degree of similarity
- Classifies organisms according to order that branches arose – tree must be dichotomous and taxa must be monophyletic
74
Synapomorphies
- Each branch point defined by novel characters unique to species on that branch (synapomorphies)
o Shared derived character belonging to a lineage
Eg. Feathers shared derived characters among all birds
75
Plesiomorphy
o Plesiomorphy = ancestral character
| Shared by multiple lineages, eg. Birds have a vertebrae but that’s shared with all vertebrates
76
Apomorphy
o Apomorphy = derived character (different from ancestral conditions)
Can be unique to an organism
Eg. Reptiles have legs but snakes don’t
77
Analyzing enough ____ lets us reconstruct a lineage
Analyzing enough synapomorphies lets us reconstruct a lineage
78
Presence of _____ (rather than retention of ancestral characters) tell us about branch order
Presence of synapomorphies (rather than retention of ancestral characters) tell us about branch order
79
Polytomy
| and what is hard vs soft polytomy?
Polytomy – section of a phylogeny in which the evolutionary relationship cannot be fully resolved to dichotomies (tree has multiple branches off one ancestor)
- Soft Polytomy: unable to resolve due to insufficient info
- Hard Polytomy: an event in which an ancestor gave rise to more than 2 daughter species at the same time
80
Polytomy
Polytomy – section of a phylogeny in which the evolutionary relationship cannot be fully resolved to dichotomies (tree has multiple branches off one ancestor)
81
Neighbor joining tree (phenetic method):
o Counting the number of differences between different species, coming up with proportion and choosing the most similar taxa to cluster together
Distance based
o Only the branch order that is important
82
Parsimony tree (Cladistics model):
o Using the changes in characters to choose the best arrangement of taxa
Only branch order is important
o Simpler explanations preferred, so analysis of synapomorphies determines which phylogeny would require the fewest changes to illustrate evolutionary relationships
Only characters shared by 2 or more taxa are informative:
• Mutations unique to one lineage aren’t useful, it doesn’t allow you to group the lineage with anything else
Only shared, derived characters (synapomorphies) are informative for this approach
83
Polarity
direction of change
84
To identify synapomorphies, we have to know what is ancestral and what is derived. What are some ways this can be done?
- With morphological characters, we may know from:
o Fossil record, embryological studies
- By comparing to character state in an outgroup:
o Outgroup = species that branched off earlier from taxa being compared (= ingroup)
o Finding appropriate outgroups – must clearly be outside of the group
Should be uncontroversial close enough to allow inference yet far enough to be a clear outgroup
85
Bootstrapping, what it is and what it's used for. How does it differ from using phylogenic methods?
Outgroups
- Evaluating outgroups statistically using bootstrapping
o Measure of how confident we are in a particular relationship
(Assessing the amount of confidence we have, using our data)
o Uses data to come up with a distribution of possible trees and looks at how many of those trees contain the particular set of taxa that are united on a branch
o In phylogeny, if we had a 300 nucleotide sequence, we would use all of it to make a tree.
o In bootstrapping – From the 300 bp, randomly select one site and use it as first entry in ‘new’ data set
Place it back into the data set and sample again you may sample the same site multiple times, while not sampling others at all
• Every new sequence is a subset of the original data
You do this over and over and build new trees to assess relationships
Then look at how many trees link 2 species together
o This process tells in what percentage of the trees each particular branch occurred - if results are being biased by a few nucleotide sites, branch values will be low, but when using tons of data (millions), you can assume that the relationships are accurately represented
o Can add number to each node of a tree (range from 0 - 100 = percentage of bootstrap trees that support this relationship):
Strong support = 100
• >70 = grouping is reliable
• 50-70 = suggestive, but not conclusive
• > 50 = not strongly supported by the dataset (prone to error)
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What are molecular clocks (used for)?
- Used to date when and how rapidly major events occurred – like species divergences
o Eg. Radiocarbon dating
o The more distantly related species are, the more different the nucleotide make up between them will be
Attempts to calibrate molecular clock Measure of genetic distance between 2 taxa whose divergence is known
• May use fossil records or geological records
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How much does the mitochondrial genome change every million years?
o Estimated 2% sequence divergence per million years in mammals
Similar ranges in other lineages too (sea urchins, butterflies, geese)
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The mitochondrial genome changes about 2% every million years - what are some exceptions?
o Mutation rate is faster in organisms with short generation times and in warm blooded (vs cold blooded) organisms:
Butterflies with 5 generations per year vs humans who don’t start reproducing until ~20 years Butterfly mutation rate is higher
Warmer body temperature – mutation rates increases with temperate
• It’s believed these 2 often cancel each other out, but doesn’t have to be this way
o Substitutions become fixed at different rates (Transitions faster than Transversions)
o Environmental conditions can cause differences in the genome Bacteria in hot springs have very GC rich bases (vs AT), similar phenomenon at altitudes
o Some genes and gene regions are more conserved than others (coding vs non-coding regions, COI, D-loop)
o Calibration using fossil record of geological events is only an estimate of actual divergence dates
Clocks “tick at different rates”
Ex. Parasites have faster rates of mutation than their hosts (they are smaller, have shorter generation times, and reproduce more)
Ex. Snapping shrimp lineages diverged at different times, based on when their habitat disappeared – deep water species diverged earlier
• Genetic distance between sister species is not identical in all pairs
Ex. Viral replication of genetic material is more error prone than in humans, so higher mutation and divergence rate influenza, HIV
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Distinguish between characters and character states by using an example.
e.g., Character = toe number
Character state = 5 (humans) or 3 (guinea pigs)
e.g., Character = leaf venation
Character state = parallel- or net-veined
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Why is phylogeny important? 2 major points with subpoenas.
1. Useful for classification, for manageability, to covey information
- Species grouped hierarchically
o Higher levels of classification are more inclusive
Lower levels more exclusive
- Cladistic classification requires that taxa at all levels must be monophyletic
- Helps us organize and communicate information about millions of species
- Helps us predict properties of organisms (according to properties of closest relatives)
2. Helps us elucidate mechanisms of evolution:
- Look at evolution of traits in a phylogenetic context
- To see way in which characters change overtime (direction and frequency)
o Parallel/convergent evolution (implicates natural selection)
- Eg. Evolution of viviparity in sharks (live birth) – convergent evolution
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What 3 characters are used in phylogeny reconstruction?
a. Molecular characters (nucleotides)
b. Comparative morphology
- Outer form and inner structure:
o Eg. Number, structure and position of bones in vertebrates
o Number and shape of teeth, presence/absence of feathers, etc.
c. Comparative physiology, histology or ethology (animal behaviour)
- Eg. Body temperature regulation, cellular types and organization, animal social systems
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Homoglous vs analogous characters - how does this matter in phylogeny?
Homologous characters likeness is due to shared ancestry
- Not always obvious, convergence can be misleading, lots of changes in features (obscuring similarities)
- Adaption and modification can obscure homologies
Analogous (homoplasious) characters Resemblance between species from different evolutionary branches
- Must be aware of parallelism (parallel evolution) or reversal of character states (reverted back to older form)
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How can we distinguish between homology and analogy? LIST 3 ways.
1. Compare embryology:
2. Fossil record:
3. Agreement with other phylogenetic hypotheses:
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There are 3 ways we can distinguish between homology and analogy, describe:
- Compare embryology:
o Before extensive modification during subsequent development obscures homologies
Eg. Gill pouches – becomes Eustachian tubes in humans
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There are 3 ways we can distinguish between homology and analogy, describe:
- Fossil record:
o Transitional fossils linking past and present forms help establish ancestry
e.g., Homology between mammalian ear ossicles and jaw elements of reptiles
e.g., Whale fossils with hindlimbs demonstrate that body shape in whales and sharks analogous
o Useful in determining ages of taxa (as old as the oldest fossils)
o Also useful in determining polarity (direction) of character states (i.e. ancestral or derived)
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There are 3 ways we can distinguish between homology and analogy, describe:
- Agreement with other phylogenetic hypotheses
Agreement with other phylogenetic hypotheses:
o If “stronger” evidence indicated groups are not sister taxa
o Analogy (homoplasy) rather than homology
a. Number of features
i. Inconsistent character most likely analogous
ii. Assume that the most parsimonious trees (fewest changes) are most likely to be correct
b. Complexity of features:
i. If 2 similar structures are very complex and match in so many details, it is unlikely that they evolved independently
E.g. skulls of humans and chimps
ii. Complex characters may be given more weight
c. Independent comparison of phylogenies based on anatomical features with those based on molecular characters (or among different molecular characters)
i. E.g. Hominid evolution
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Describe the darwinian demon concept (the organism with the perfect life history). Why don't we see this?
- Reproduce at birth
- Infinite life span
- Infinite reproductive episodes
- Large numbers of viable offspring
Problem: finite time and resource (trade offs), you can't do everything at once.
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Describe the principle of allocation (reproduction vs growth trade off in life history)
- Some of the resources are dedicated to reproduction and some to growth.
- In repro there’s even more subdivision (offspring size, number), etc.
Cost vs benefits - grow bigger and hopefully survive better, and can then produce more offspring. Or you can reproduce quickly in case you get eaten by something bigger. The less you allocate to reproduction, the more you can allocate to growth.
Resource investment in either growth or reproduction reflects: total resources available, trade offs, allocation hierarchy
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Why do organisms age and die? Answer this using the rate of living theory.
•There is a physiological limit to cell & tissue repair
•Short life, high metabolic rate / cell division
vs.
Long life, low metabolic rate / cell division
•Prediction: selection should place populations at physiological limit
•Drosophila studies: artificial selection can increase lifespan without significant changes in metabolic rate
Organisms with a short life have a high metabolic rate and high rate of cell division.
If you look at resting heart rate and body size - larger mammals have slower heart beats (mouse - fast, elephant - slow).
Suggests that organisms should have metabolic rates and rates of cell divisions that are the maximum given how long they live.
But, studies in Drosophila found that specific mutations and artificial selection can increase lifespan up to 3x, same MR.
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Why do organisms age and die? Answer this using the evolutionary theory.
1. Mutations accumulate in populations such that late onset deleterious mutations have negative effects on fitness/reproduction compared to earlier ones (it’s harder to select against late acting mutations, organisms will harbour more late acting mutations since fitness isn’t affected as much).
2. Trade off between reproduction and repair:
•Until recently, most evidence in phenotypic costs of reproduction
•Increased reproduction reduces subsequent growth and survival in many animals and plants.
•e.g., clutch size in birdsseed set in plantsinvestment in ovaries in fish
Birds laying more eggs can have effect on likelihood of individual birds to survive, plants producing more seeds have higher chance of death in the next year.
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In terms of selection on lifespan: what are intrinsic factors?
- Accumulation of late acting deleterious mutations
| - Trade offs between reproduction and repair
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In terms of selection on lifespan: what are extrinsic factors?
Give an few examples, one of them using the Virginia opossum.
- Predation
- Disease
- Resource depletion
Examples:
- Investment in growth can reduce predation (large body size) - elephants, bison
- Large fat stores beneficial if resources are scarce
- Virginia possum: Die quickly on the mainland (2 years) but live 4 years on island. Mainland ones reproduce earlier but reproductive output declines with age (island reproduces later and remains constant). Mainland population ages faster (arthritis - all energy invested in reproduction since they die earlier, likely due to predation). Clear difference in resource allocation.
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Logic of trade-offs applied to many aspects of life history:
* reproductive effort
* mate attraction vs gamete production
* offspring size & number
* reproduction versus defense
Describe predator saturation as in cicadas and plants (agave).
- Cicadas spend 2-3 years as larvae, then shed exoskeleton, become adults, mate, and die. They’re large and noisy, so birds easily pick them off. In N.A., they try to avoid predation by waiting 13-17 years and then emerge in massive numbers - strategy is that if cicadas come out every year, the birds learn to expect the food source, produce more offspring, and consume the cicadas.
Birds can’t anticipate when the next mass of cicadas will come - predator saturation.
- Agave (century plant) flower once in it’s life, about 100 years, and virtually all the agave do this at the same time (same year, no known environmental cues).
The plants store photosynthetic energy in their tissues, waiting for their reproductive time and produce massive numbers of seeds, rodents can’t possibly eat all the seeds, so the opportunity of seeds to survive predation and germinate is maximized. All adults die.
Trees also have mast years. Goal is to starve out predators before you try to reproduce again.
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Apomixis
Apomixis - plant produces seeds but the seeds are produced not by meiosis (can’t get fertilized by pollen), instead produced by mitosis, and so the seeds are genetically identical to the mother plant.
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Parthenogenesis
Parthenogenesis - lizards and fish in which the female parent requires courtship and sometimes even sperm, to reproductive, but none of the male contribution goes to the offspring, offspring is genetically identical to the female parent.
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Cost of males - the paradox of sexual reproduction
Asexual females have a 2 fold transmission advantage (can produce twice as many offspring that can produce their own offspring - no males).
If you are an organism that wants to increase the population size quickly and efficiently, the rate limiting component is almost always the number of females (since they have to invest more into offspring than males), number of females usually determines maximum number of offspring that can be born. If you have a completely female, asexual population, 1 female goes from 2 to 4 to 8 females in a short period of time. In sexual reproduction, you have half as many females (1 female, 1 male born), so you would expect asexuality to predominate since it increases numbers fastest. however, most organisms have some form of sexual reproduction.
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The cost of males theory means asexual females have a 2 fold transmission advantage (can produce twice as many offspring that can produce their own offspring - no males).
What are 2 assumptions made with this?
1) Sexual and asexual females produce same number of offspring
* is not always true, sometimes sexual reproduction creates more offspring. Praying mantis female eats male, so can use the resources stored in male’s body to invest into eggs.
2) Reproductive mode does not affect offspring survival
* Sometimes sexual offspring are laid within spore coat or resting egg stage that may make them more durable in harsh environmental conditions.
* asexual species can be very successful though, like dandelions
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What is the long term advantage of sexual reproduction, and how do we know it's advantageous?
* sex predominant
* most asexual lineages recently evolved
* complete asexuality leads to extinction
* Sex provides variation at the species-level (long-term) advantage
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What are the short term advantages of sex?
Describe this advantage: Temporal fluctuations in selection pressures
Some evidence, many theories. * All theories assume recombination and selection will: increase frequency of superior genotypes and decrease frequency of non-optimal phenotypes.
1. Temporal fluctuations in selection pressures (fluctuating optimum, sex continually generates new phenotypes) -ex. beak depth in Galapagos finches (drought favoured larger beaks for a few years), red queen hypothesis (parasites/pathogens are continually evolving, so host must evolve too).
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What are the short term advantages of sex?
Describe this advantage: Heterogeneous environments (spatial variation in selection pressure)
- what does this say about asexual taxa?
Some evidence, many theories. * All theories assume recombination and selection will: increase frequency of superior genotypes and decrease frequency of non-optimal phenotypes.
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2. Heterogeneous environments (spatial variation in selection pressure):
Lottery model:
–offspring disperse into various patches
–sexual female: many different tickets
–asexual female: many copies of 1 ticket
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Asexual taxa often occur in biotically simple environments.
Sibling Competition–genotypes differ in resource use–diverse offspring compete < identical offspring
Tangled bank hypothesis: the more varied a group of organisms is (individuals within sp. or a group of species in a community), the more likely that you will get additional variation in a particular habitat.
- planting a variety of grass species on a lawn will increase growth and aphid resistance
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What are the short term advantages of sex?
Describe this advantage: Eliminating mutations
Some evidence, many theories. * All theories assume recombination and selection will: increase frequency of superior genotypes and decrease frequency of non-optimal phenotypes.
i) Muller’s ratchet–Forward mutations are much more frequent than reverse mutations.
–Asexual offspring inherit all existing mutations & may experience additional mutations.
–Mildly deleterious mutations accumulate in small clonal populations over time.
–Multiple mutations eventually have a drastic effect on fitness
ii) Mutation threshold:
- Fitness is severely reduced in individuals with more mutations than a threshold number.
- Mutations are most rapidly eliminated when they occur with other mutations.
Before selection, sexual reproduction recombination generates a wider *range* of mutations per individual than does asexual reproduction
- If all asexuals have 8 mutations, sexual repro would have a bell curve where most would be in the middle mutation wise (3-4) and only a few at 8
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List the 3 short term advantages for sexual reproduction.
1. Temporal fluctuations in selection pressures
2. Heterogeneous environments (spatial variation in selection pressure)
3. Eliminating mutations
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Tangled bank hypothesis
- the more varied a group of organisms is (individuals within sp. or a group of species in a community), the more likely that you will get additional variation in a particular habitat.
- A hillside with many different species, all competing for resources, the more organisms doing this, the more room there is for even more differing phenotypes doing the same thing.
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Muller’s ratchet
–Forward mutations are much more frequent than reverse mutations.
–Asexual offspring inherit all existing mutations & may experience additional mutations.
–Mildly deleterious mutations accumulate in small clonal populations over time.
–Multiple mutations eventually have a drastic effect on fitness
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Isogamy vs anisogamy
Isogamy: gametes look the same, different genotypes (Y, X), but are visibly identical. Ex. Fungi (can’t tell what mating type it is with the naked eye). In some lineages, like animals, mutations have occurred that affect gamete size, leading to a functional divergence - anisogamy.
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Why does anisogamy occur? Was the ancestor (for sexual repro) anisogamous?
Large gametes tend to get even larger over time, small gametes tend to get even smaller over time. Once one is less mobile than the other, it makes sense to add additional resources to the one that’s already large (would slow down motile one).
Large gametes always called female but femaleness is not a homologous trait in that the large female gametes have evolved in parallel in multiple lineages.
Common ancestor was isogamous, independent evolution.
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What is sexual selection basically, and how is it related to fitness (gamete size, numbers, survival, etc)
W = offspring number x offspring survival
* Large gametes have higher survival capacity
* Small gametes produced in higher numbers
* Theory predicts association between mating types & gamete types
Sexual Selection = Selection on mating success
* May oppose viability selection, but is still a component of natural selection
* Females & males invest unequally in each offspring
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Batemans principle
Batemans principle
–Male fitness is usually limited by number of mates; therefore males will usually compete for mates.
–Female fitness is usually limited by resources; therefore females will usually be choosy.
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Is the strength of sexual selection stronger than or as strong as viability fitness (fecundity) or survival?
Survival is strongest, since you can't reproduce without surviving.
Sexual selection can be strong but not as strong as the others.
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2 examples of male-male competition?
| Does female choice harm males?
1. Combat (explains size dimorphism, antlers, horns)
2. Sperm competition (increases in group size increases testis size)
* Large, colourful males usually better sexual competitors (invest a lot into this) but can reduce their viability fitness/survival. Birds with cropped tails had 0 mating opportunity (but would survive better), all comes down to female choice.
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What are 3 benefits female get through female choice of mates?
1. Males with better genes
2. Resources (copulation gifts)
3. Sexy sons
122
What are species, in theory? What is the essence of speciation?
In theory, species = smallest evolutionarily independent unit
Essence of speciation is lack of gene flow
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Describe the biological species concept.
- What is the criteria?
- In what ways is it difficult to test/apply?
- Criteria is reproductive isolation (lack of gene flow)
- Legal definition used by endangered species act
But difficult to test and apply:
- In populations that don’t co-occur (must make inferences)
- In fossil forms
- Irrelevant in asexual organisms
- Sometimes hybrids aren't as obvious
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Is demonstrating current reproductive isolation enough to classify 2 species as distinct using the biological species concept?
Sometimes reproductive isolation is transient or localized - After short-term anomaly, gene flow could resume.
Similarly, a breakdown of reproductive isolation is transient or localized due to recent but temporary perturbation.
*this can even be seen in early humans, while living on different continents, humans couldn't interbreed (without air travel), but now we can - still the same species.
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How do hybrids pose a problem for the biological species concept?
- If 2 species can hybridize, then how do we classify them?
- Sometimes hybrids aren't as obvious (well known examples like zorse look distinct, but can we tell the difference between a hybrid insect if the species look similar?).
- Hybrids are more common than previously thought.
- Very common in plants and fish, also seen in some animals.
- Hybridization in the wild often occurs due to anthropogenic change (ex. polar bear + grizzly) - climate change, range shifts, removal of isolating barriers, introduced species.
- Species often lack reproductive isolating mechanisms when not naturally sympatric.
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What is a problem with hybridization, besides sterility (which is common)?
* ** INTROGRESSION***
- Loss of genetic integrity.
- Humans tend to increase hybridization, so much so that species can become extinct by replacing their DNA completely with that of another species. An issue in North America occurs with rainbow trout, in the rockies, they hybridize with other fish and their DNA starts to disappear.
- Species often lack reproductive isolating mechanisms when not naturally sympatric.
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Phylogenetic species concept (newer)
- Represents evolutionary history
- Genealogical species concept
- Species are smallest identifiable units that are diagnostic and monophyletic
- Phylogenetic trees show relative order of branching since common ancestor (nodes)
- Sister taxa = closest relatives
- Shared ancestor more recently than “non-species”
- Single ancestor gave rise to all species in that taxon AND to no species in any other taxon
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Polyphyletic taxa
Members are derived from two or more unrelated lineages
Apparent similarity due to convergent (or parallel) evolution
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Paraphyletic taxa
Members are derived from single lineage
| But group doesn’t include all species derived from this common ancestor
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Why is the PSC easier to test than BSC?
- BSC: would have to do breeding experiments to determine if species were reproductively isolated, but that's not always possible/easy (extinct, fossils) and some species will mate in lab conditions that never would otherwise.
- PSC: detects species that have been evolutionarily independent long enough for diagnostic traits to emerge.
Diagnosable because of reproductive isolation - But also must be monophyletic
More closely-related to each other than to other species
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How can PSC and BSC conflict on the issue of monophyly? Use benthic and limnetic sticklebacks to answer this.
- When parallel evolution occurs, may not recognize incipient species.
- In PSC: each population split and thus is 4 species.
- In BSC: No interbreeding between benthic and limnetic, so only 2 species (even though there's 2 types of limnetic and benthic)
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incipient species
a natural population that can interbreed with another related population but is inhibited from interbreeding in nature by some specific barrier
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cryptic species
Cryptic speciation is a biological process that results in a group of species (which, by definition, cannot interbreed) that contain individuals that are morpholigically identical to each other but belong to different species.
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Morphospecies concept and some problems with it
- Used more than PSC and BSC.
- Assumes reproductively isolated populations will accumulate morphological differences
- But not all differences are species-level differences (eg. sexual dimorphism in peacocks, lifecycle differences (caterpillar and butterfly), environmental effects (pH changes flower petal colour), intraspecific polymorphisms (eye colour) and polyphenisms (queen vs worker ants), and some species are cryptic (tree frogs- but DNA barcoding is uncovering many cryptic species)).
