Fundamentals of Evolutionary Biology Flashcards
What is population genetics?
Evolution as change of allele and genotype frequencies in populations over time
Understanding what drives changes
What is an allele?
Variant of a gene/locus
What is a genotype?
Allelic composition of gene/set of genes/whole genome
What is a Zygote?
Diploid product of fertilisation
What is a Phenotype?
Physical realisation of genotype
What is a Gamete?
Haploid product of meiosis - sex cells
What does homozygous mean?
Same alleles at locus
What is an Gene pool?
Sum of alleles at all loci within population
What is a polymorphism?
More than one allele present at given loci within a single population
What are the assumptions of the Hardy-Weinberg Equilibrium?
Mating is random
Population size is infinite
No mutation
No migration
No natural selection
What is the closest to the Hardy-Weinberg assumptions you can get in practice?
Salmon eggs and milt mixed in fisheries closest to these assumptions
When the population is made up of homozygotes how many generations does it take to reach HWE?
1 generation
What is assortative mating?
Choice of mates based on phenotype
Does not affect all loci - only encoding phenotype
What is positive assortative mating?
Like mates with like - increases the number of homozygotes
Eg. tall people mating with tall people
May contribute to speciation
What is an example of positive assortative mating?
Reproduction of like with like.
Genus burmeistera bats
- more efficient at pollinating wide flowers
Hummingbirds
- more efficient at pollinating narrow flowers
So pollination occurs between wide flowers by bats and between narrow flowers by hummingbirds
- Low fitness for intermediate flowers
What is an example of negative assortative mating?
Oxalis alpina - monoecious - male and female reproductive parts on the same flower
There are two floral morphs (phenotypes)
- Thrum flowers (long male reproductive part)
- Pin flowers (long female reproductive part)
If a bee goes from thrum to thrum, the location of the pollen on the bee prevents pollination (due to the location of the organs)
If a bee goes from thrum to pin, the flower structure and the location of the pollen allow transfer and pollination to occur.
What is inbreeding?
Mating of related individuals
Don’t affect allele frequencies
Affects all loci in the genome
Describe the inbreeding coefficient?
0 < F < 1
F = 0, random mating
F = 1, eg. self fertilization
Why does inbreeding increase the number of homozygotes?
- Increases the likelihood that they will share the same alleles (versions of genes) inherited from their common ancestor
Are most wildtype alleles dominant or recessive?
Most wildtype alleles are dominant.
Are most mutations dominant or recessive?
Most mutations are recessive and deleterious
Why can recessive deleterious alleles persist at low frequency?
they incur no reduction in fitness in heterozygotes.
How does inbreeding expose deleterious recessive alleles to selection?
increasing the frequency of homozygotes in a population.
What is inbreeding depression?
the reduction in mean population fitness that occurs as a result of inbreeding.
What is an example of inbreeding in pedigree dogs?
The gene pool of 10,000 pugs is only made up of 50 individuals, leading to high levels of inbreeding.
What is an example of inbreeding in humans?
The Hapsburg Jaw and polydactyly
- Examples of inbreeding in European royals
How does positive assortative mating modify genotype frequencies at specific loci?
Increased homozygosity
- Preferential mating with individuals with similar characteristics
- Increased likelihood that offspring receive identical alleles from both parents at these loci.
Change in Allele Frequencies
- Can lead to the development of subpopulations.
Are mutations more likely to occur in somatic or germline cells?
somatic cells.
What can mutations in early development cause?
Mosaicism and tumors
What is the ultimate source of all heritable variation in evolution?
Germline cell mutations
Are mutations a random or deterministic process?
Mutations are a random process
- Influenced by environmental effects but still ultimately random
What are some causes of mutations?
- DNA polymerase infidelity
- Base substitutions
- Chromosomal abnormalities
- Errors in repairing double-strand breaks in DNA.
Why are missense mutations primarily studied?
Have the potential to change the amino acid sequence of a protein
- Have a more significant impact on the organism
Luria and Delbrucks experiments - What does the Poisson distribution support?
Poisson distribution suggests mutations arise independently
Luria and Delbrucks experiments - What did the experiment show?
Supports the idea that mutations are random
- Results show mutations not directed by external factors
Is mutation a strong or weak force to change allele frequencies in evolution?
Weak
- While mutation is not the main driver of evolution, it provides the raw material on which evolution can act
What are the forms of recombination?
Mixing of non-homologous chromosomes occurs.
- Independent assortment.
Mixing of homologous chromosomes occurs.
- Crossing over.
What does independent assortment achieve?
Results in the random segregation of maternal and paternal chromosomes into gametes.
- During meiosis
What is crossing over?
Homologous chromosomes pair up and exchange segments of DNA
- Forming chiasmata (point at which paired chromosomes remain in contact during the first metaphase of meiosis)
What are the benefits of crossing over?
- Leads to the production of recombinant chromosomes and increasing genetic diversity
Are there variations in the results produced by genetic drift simulations?
Outcome different each time - stochastic
- Can drift in any direction by chance
Genetic drift in a larger population =
More stable allele frequency (less effect).
Does genetic drift produce more or less genetic diversity?
Reduces genetic diversity
- Sooner or later due to random sampling, alleles will be lost from the population
What is the effect of a smaller population size on the effects of genetic drift?
Much more severe between generations in small populations
What are key features of genetic drift?
Caused by variation in random sampling of gametes in finite populations
- Leads to loss of variation
Random process (Stochastic)
- cannot predict allele freq change with certainty
- Unlike natural selection/mutation pressure
What is effective population size?
- Number of individuals in a population who contribute offspring to the next generation
- Reflects the genetic diversity of a population.
Often differs from the actual population size due to factors such as:
- Unequal sex ratios
- Variation in offspring number
- Population structure.
What is census population size (N)
The total number of individuals in a population
- not all individuals contribute equally to the gene pool
What is the concept of ideal population?
Theoretical population in which Mating is random
- All individuals equally likely to have offspring
- Number of offspring doesn’t vary more than by chance
- Number of breeding individuals remains same each generation
- Equal numbers of males and females involved in breeding
Most population do not conform to census population size. They act as if they are far ____
Smaller
- This is where the effective population size (Ne) comes in
What is effective population size (Ne)?
Effective population size (Ne) is the size of an idealized population that would experience the same rate of genetic drift as the actual population
- not all individuals in a population contribute equally to the gene pool
- provides a more accurate estimate of the potential for genetic drift to occur
Humans N = 7B, Ne = 10k
Why is the human effective population size so small?
Reflects historical small population
Why is N>Ne?
Not all individuals in a population contribute equally to the gene pool
- leading to a difference between N and Ne
Factors
- variation in reproductive success
- fluctuations in population size
- differences in male and female contribution to the next generation affect Ne
What is the contribution of variation in reproductive success to N>Ne?
- Can lead to an uneven contribution to the gene pool
Some individuals may have more offspring than others
- leading to a larger genetic contribution
How does randomness affect N>Ne?
- Random fluctuations in the number of offspring can lead to deviations from the idealized population assumptions used to calculate Ne.
What is the contribution of fluctuations in population size to N>Ne?
- Population bottlenecks, expansions, or fluctuations can cause changes in Ne.
- Historical population events can have long-term effects on Ne
Populations that fluctuate consistently
- Will have a low Ne
How do differences in male and female contribution affect N>Ne?
When male and female contribution to the next generation is not equal
- effective population size (Ne) can be much smaller than census population size (N)
- leading to a greater impact of genetic drift and reducing genetic diversity.
What is the contribution of overlapping generations to N>Ne?
Individuals of different ages can have different contributions to the gene pool
- Age-structured populations can have a larger difference between N and Ne
Why is free mating not usually allowed in zoo populations?
Ensure more equal male contribution to the next generation
- Unequal male and female contribution can have a negative impact on genetic diversity and effective population size
- By controlling mating, zoos can increase genetic diversity and maintain a healthy population
What is a population bottleneck?
Population is severely reduced in size, resulting in a loss of genetic diversity
- Can occur naturally or as a result of human impacts, such as habitat destruction or overhunting
- Population bottlenecks can have significant long-term consequences for genetic diversity and the viability of a population
What is a good example of a population bottleneck?
Cheetahs experienced a population bottleneck around 10,000 years ago at the end of the last glaciation period
- This bottleneck severely reduced their population size and genetic diversity
- Today, cheetah populations still have low genetic diversity due to this historical event, as well as recent human impacts
How can a few generations of low population size impact genetic diversity?
Can have massive consequences for genetic diversity
- Genetic drift can have a greater impact on a small population
- Reduced genetic diversity can take thousands of generations to restore.
How does the effective population size (Ne) differ between a population bottleneck and a population expansion?
Ne is closer to the pre-expansion population size during a population expansion
What is an example of a population bottleneck caused by human hunting?
Northern elephant seals experienced a population bottleneck due to human hunting in the 1890s
- Drastically reduced their genetic diversity.
What is the Founder Effect?
Loss of genetic diversity that occurs when a new small population is formed from a larger population
How does the Founder Effect occur?
Small population is extracted from a larger population
- Results in a random sample that may be skewed
- Can lead to a loss of genetic diversity and vulnerability to genetic drift in the small population
What is an example of the Founder Effect?
Amish population
- The Amish people were founded by ~200 German colonists
- Genetically isolated
- Founders had a recessive deleterious autosomal allele underlying a form of dwarfism, and polydactyl of the hands, short stature, and congenital heart malformation
- 12.3% of the Amish population are now heterozygotes for this gene
What is genetic population structure?
- pattern of variation of genetic traits within and between populations
How can genetic population structure be detected?
Analyzing the genetic makeup of individuals within populations and how they cluster with closely related individuals
What is gene flow in genetic population structure and what are its benefits?
Gene flow is the transfer of genetic information from one population to another
- can counteract the effect of random genetic drift
- homogenizing allele frequencies between populations and reducing genetic differentiation
What is the fixation index F?
Measure of the extent of genetic population structure
- Based on the inbreeding coefficient f
What is the inbreeding coefficient f?
The probability of identity by descent of two alleles drawn from a population
What does FST compare?
FST compares the probability of identity by descent of two alleles drawn from a subpopulation
- to drawing two alleles from a total population comprised of multiple subpopulations.
What is observed heterozygosity (Ho)?
Proportion of individuals that are heterozygous
What is expected heterozygosity (HE)?
Proportion of individuals that are expected to be heterozygous based on Hardy-Weinberg (i.e. 2pq).
What does F measure in an inbreeding population?
The fractional reduction in heterozygosity of an inbreeding population relative to a randomly mating population with the same allele frequencies
What is Fis and what does it measure?
Fis is often used to refer to F, where I represents individual and S represents subpopulation
- measures the proportionate reduction of heterozygosity due to mating of related individuals within a subpopulation.
What is the meaning of ST and IT in the context of proportionate reduction in heterozygosity of subpopulations and inbred organisms?
ST - represents the proportionate reduction in heterozygosity of subpopulations relative to the heterozygosity of the total combined population
IT - represents the proportionate reduction in heterozygosity of inbred organisms relative to the total population.
What is the difference between Fst and Fit in measuring inbreeding?
Fst
- used measure in population genetics to quantify genetic differentiation between populations
Fit
- inclusive measure of inbreeding and represents the proportionate reduction in heterozygosity of inbred organisms relative to the total population
What does a high Fst value indicate in population genetics?
High Fst value indicates that allele frequencies are different between populations
- there is significant genetic differentiation between populations
What factors affect FST?
- Gene flow, or movement of individuals between populations, tends to decrease FST
- size and distance between populations can also affect FST, with smaller and closer populations having lower values.
Allozymes:
Genetic markers used to determine genetic population structure
- Variation in enzymes encoded by different alleles detected through electrophoresis
- Often used in the past, but now being replaced by more powerful DNA-based markers
What are some genetic markers used to determine genetic population structure?
- Sequence data
- Mitochondrial DNA
- Autosomal markers
- Microsatellites
- Allozymes
What are microsatellites?
Microsatellites are simple sequence repeats that are often used to estimate genetic diversity
- Scored based on the length of repeated units
How do microsatellites arise?
- Arise because of a DNA slippage mechanism in replication
- Easily misalign, leading to an increase or decrease in the number of repeats
What is mitochondrial DNA?
- Mitochondrial DNA is a type of genetic marker that is maternally inherited
- often used to study population genetics and evolutionary biology
What is whole/partial genome sequencing?
a method of determining the genetic makeup of an organism by analyzing its entire or a portion of its DNA sequence
What are allozymes?
Allozymes are variant forms of enzymes that are used as genetic markers
What is autosomal DNA?
- DNA located on the autosomes
- Non-sex chromosomes in the genome
What are the characteristics of microsatellites as genetic markers?
- Very variable with high mutation rate
- Easy to amplify even from small amounts of degraded DNA
- Suitable for use with a wide range of organisms, including museum specimens
What are Single Nucleotide Polymorphisms (SNPs)?
Genetic markers that represent a single base change in DNA sequence that occurs at a specific position in the genome
What are the implications of biogeography of human populations for ‘race’ and medicine?
Human populations are not that genetically diverse
- Findings suggest that the concept of ‘race’ is not a valid biological concept, and has no scientific basis
- Suggests that personalized medicine based on individual genetic differences is a more reliable than medicine based on racial or ethnic categories
What is the island model of population structure?
Assumes a set of populations
- each with infinite size and no genetic drift
- connected by gene flow with migrants at the same rate (m) regardless of distance
Why do species not behave as panmictic with purely random breeding?
Most species have some geographic structure and are composed of many sub-populations (demes)
- in which genetic drift and natural selection can operate differently
- leading to non-random breeding patterns
What is the effect of gene flow on genetic diversity?
Increases genetic diversity
- by introducing new alleles
- can decrease genetic differentiation between populations by homogenising allele frequencies through migration
What are demes?
Species often have many sub-populations
What happens to demes over time in the island model?
Demes tend toward the total population average over time
- gene flow homogenizes allele frequencies across populations
What is FST?
FST is a measure of population differentiation due to genetic drift
How do migration and genetic drift affect FST?
Migration homogenizes allele frequencies, thus reducing FST, while genetic drift skews allele frequencies, thus increasing FST.
What is Nem?
Parameter used to estimate the number of migrants per generation in a population
- product of the effective population size (Ne) and the migration rate (m)
- represents the number of individuals per generation that move between populations due to migration
- May not be true for wild populations
Name two opposing evolutionary forces
Interplay between genetic drift and mutation
In larger populations_____ heterozygosity is expected
Higher
What is adaptation?
Evolutionary process where organism becomes better able to survive in an environment
- From natural selection acting on heritable characteristics
What is phenotypic plasticity?
Ability of one genotype to produce more than one phenotype
- Response to different environmental conditions
Daphnia - water fleas
Genetically identical - one exposed to chemical cues of predator becomes much more armoured
What is this an example of?
Phenotypic plasticity
Why is there lots of phenotypic plasticity in plants?
Immobile
- high need to meet environment
What are the four components of natural selection?
- High rate of population growth
- Heritable traits
- Variation in these traits among individuals of species
- Some of these traits must affect fitness
What is directional selection and when does it occur?
Individuals with one extreme of a trait have higher fitness than individuals with the other extreme
- It can occur when environmental conditions change, or when a new predator or prey is introduced
What is stabilizing selection and when does it occur?
Individuals with intermediate values of a trait have higher fitness than those with extreme values
- Can occur when environmental conditions are stable or when extremes are disadvantageous.
What is disruptive (diversifying) selection and when does it occur?
Individuals with extreme traits have higher fitness than those with similar traits
- It can occur when environmental conditions are variable or when there are different niches to be filled
What are polymorphisms?
Variations in DNA sequences that occur within a population
What is homozygote advantage?
Individuals with two copies of the same allele have higher fitness than those with two different alleles
What is a heterozygote advantage?
Individuals with two different alleles have higher fitness than those with two copies of the same allele
How does homozygosity for the Hb-S allele affect fitness (malaria)?
Homozygotes for the Hb-S allele have a severe form of sickle cell anemia, which can be life-threatening.
How does heterozygosity for the Hb-S allele affect fitness?
Heterozygotes for the Hb-S allele have some protection against malaria and do not develop sickle cell anemia
What is the sickle cell allele (Hb-S)?
Provides some protection against malaria
- mutation in the beta-globin gene that codes for hemoglobin
What is balancing selection and how is it maintained?
Mode of natural selection in which multiple alleles are maintained in a population due to
- Heterozygote advantage
- Frequency-dependent selection
Absolute fitness:
Number of offspring an individual produces
Relative fitness:
Absolute fitness of a genotype divided by the absolute fitness of the genotype with the fitness
Term: Selection coefficient (s)
Amount by which the fitness of a genotype differs from that of a reference genotype
Does a greater selection differential increase or decrease evolutionary rate
Increase
What are selection experiments?
Manipulate environment or apply selective pressures
- Study how natural selection affects the frequency of alleles or genotypes in a population
What is the effect of selection on genotype frequencies under Hardy-Weinberg equilibrium?
Drives genotype frequencies away from Hardy-Weinberg equilibrium
Why was there a lag in the increase of recessive Boston betularia (peppered moth) form after the pollution decreased?
- process of forming homozygous individuals carrying two copies of the recessive carbonaria allele is slow
Overdominance/heterozygote superiority and what does this cause?
Heterozygous genotype has a higher fitness than either of the homozygous genotypes
- Maintains genetic diversity in a population
What is underdominance?
Heterozygous genotype has a lower fitness than either of the homozygous genotypes
- can lead to an unstable equilibrium, depending on where the equilibrium lies
What is Fixation?
Fixation is the process in population genetics by which a particular allele reaches a frequency of 100% and becomes the only allele present at a given locus in the population
- means that all individuals in the population are homozygous for that allele
What is quantitative genetics?
study of how quantitative traits are inherited and evolve
What are quantitative traits?
Vary continuously
- Height, blood pressure, plumage colour, wing length
- Many sexual selection traits
- Not usually single gene
What are some entirely environmental traits? - Use human and flamingo as example
Language
- Genetic capacity to learn language but entirely dependent on environment
Flamingo colour
- Genetic capacity to pick up colour
What is phenotypic plasticity?
Capacity of an organism (genotype) to develop any of several phenotypic states depending on the environment
- Can be morphological, behavioural, life history (investment in early or late reproduction)
- Some traits more plastic than other
Give an example of Daphnea phenotypic plasticity?
Reared in presence of predators gain defensive structures
Describe the phenotypic plasticity shown by Crucian carp?
Shallow vs deep phenotypes
Deep - larger and rounder
Shallow - more streamlined
How does the presence of predators affect the phenotype displayed but Crucian carp?
Deep body phenotype
- Provides them with a fitness advantage in high predation environments
- More adaptive escape response
- Attain higher swimming speed, acceleration, and turning rates
- Less vulnerable to predation by pike
How does the absence of predators affect the phenotype displayed but Crucian carp?
Shallow and streamlined body shape phenotype
- phenotype allows them to more efficiently
- provides fitness advantage by enhancing their competitive ability
- compete for limited resources
- food and breeding sites
How does gape size of pike affect phenotypic plasticity of Crucian carp?
Gape size of pike limits their ability to eat deep phenotype crucian carp
- smaller pike cannot prey on these fish
- advantage for deep phenotype
Give an example of directional selection
Ground finch Geospiza fortis - Not actually a finch
Major drought 1977
- Only large seeds available
- Only birds with large beaks could survive
- Large beaks were selected for
Give an example of diversifying/disruptive selection
Crossbills
- Seeds from hemlock or lodgepole - small or big
- Small bill depth can access hemlock, large can access lodgepole
- Intermediate doesn’t get shit
Give an example of stabilising selection
Birthweight in human infants
- Favours individuals with trait values near population mean
- Lowest infant mortality around norm
Describe a study on correlational selection on garter snakes
Study of different traits at same time
Stripedness - camo
Reversal - escape behaviour
- High striping and few reversals led to high survival rates due to effective camouflage
- High stripey individuals with many reversals had low survival rates - poor camouflage
- Low strip snakes with many reversals had high survival rates, effective escape behaviour can compensate for a less effective camouflage strategy
Describe a positive selection gradient in orange guppies
Orange guppies
- more vulnerable to predation
- more attractive to females (because if they survive while very orange they are more attractive?)
A positive selection gradient would indicate that males with more intense orange coloration have higher reproductive success
- Guppies would become more orange
Do larger population evolve faster or slower than small populations?
Faster
Strong selection on one trait often has ________ consequences for other traits. Give an example
Selection for milk production in cows lead to decreased fecundity
- ability to produce offspring or reproductive cells
What are genetic correlations?
Certain traits are correlated at the genetic level
- Same regions of the genome are associated with variation in multiple traits
- Eg. long arms with long legs
- Partially heritable
Traits can evolve while not under direct selection
- Natural selection operating on one trait can affect another
What is pleiotropy?
Single locus affects more than one trait
- This can result in seemingly unrelated traits being genetically correlated because they are both affected by the same gene
What is Linkage disequilibrium?
Non-random association between alleles at different loci
- can result in seemingly unrelated traits being genetically correlated
- both affected by loci that are physically close to each other on the genome
Describe pleiotropy seen in Mexican cave tetra
No light - Lost eyes
- Sensory cells now respond to vibrations
Pax6 gene
- Controls eyesight, enhanced senses and other genetic factors
- Genetic correlations
What is cosmopolitan distribution of organisms?
Species or group of organisms that is distributed worldwide
- occurring in many different geographic regions
What is endemic distribution of organisms?
Species or group of organisms that is restricted to a particular geographic region or habitat and is not naturally found anywhere else
What is Disjunct distribution of organisms?
Species or group of organisms that has non-continuous distribution
- isolated populations that are separated by large geographic distances.
What is vicariance?
Distribution in which a formerly continuous population
- becomes separated by a physical or environmental barrier
- mountain range, river, or sea
- leading to the development of distinct, geographically isolated populations
What is wallace’s line?
Separates two distinct distinct modern terrestrial faunas
- Corresponds to a deepwater separation between continental plates
- Same latitude, similar geology, area of coast line etc
- very similar general environments
- Two completely different communities of fauna
What divides the neartic and neo-tropical biogeographic realms?
Mexican plateau and tropical low-lands
- geographical barrier of the Isthmus of Panama
What separates paleartic and oriental biogeographic realms
Himalayan Mountains
What separates paleartic and ethiopian biogeographic realms?
Sahara and Arabian desert
What are some cosmopolitan species?
- Fruit flies
- Brown rat
- Common rock dove
- House dust mite
- Commensal organisms (follow humans)
What are some endemic species?
Fossa and lemurs (Madagascar)
What are some disjunct species?
- Marsupials (Australasia and the Americas)
- Alligators (North America and China)
- Araucaria pine (South America and Australasia)
What did zoogeographic realms - 2013 Outline?
Looked at more than vertebrates
- Mostly corroborated Wallace’s realms
- Finer separation
- Australasian realm split into Australian and Oceanian
What are forms of dispersal?
- Range expansion through favourable habitat
- Jump dispersal across unfavourable habitat
What is a filter route?
Corridors only certain organisms can cross
What is waif dispersal?
- Passive
- sweepstakes
- eg. rafting, Wind, storms
What is an example of a dispersal corridor?
- Isthmus of Panama
- Links central and South American
- Land bridge
Describe how the Krakatoa eruption is a good example of dispersal?
1883 Krakatoa eruption killed all life
- 50 years later repopulated forest from Java and Sumatra
What are air currents involved in the dispersal of?
Seeds, spores, small animals
- Prevailing winds will disperse organisms in particular directions
What are ocean currents involved in the dispersal of?
Seeds, plankton, larvae etc
What is a common cause of disjunct populations?
- Extinction
- Does not occur at same time in all places
What does vicariance cause?
Leads to divergence and speciation
What is a relict population?
A taxon that persists as a remnant of what was once a diverse and widespread population
What produces relict populations?
Past environmental changes
- Climate fluctuations, geological events, or human activities that have created isolated or marginal habitats
- Subset of population is confined to available hospitable area
- broader population either shrinks or evolves divergently
What were the competing theories surrounding lemur evolution?
Previously thought lemurs arose by vicariance
- Split from Gondwana
Molecular phylogenies
- Many species too young to have arisen by vicariance
- Waif dispersal from Africa
The isolation of South America from other continents was a vicariance event. What did it produce?
There was no exchange of organisms in or out after the first 10 million years
- Caenozoic
- Isolation led to the evolution of unique and diverse mammalian faunas in South America
How were the unique mammalian faunas found in Antarctica and Australia produced?
Dispersal events of Marsupials, xenarthrans, and native ungulates
- From South America
- During Caenozoic
What caused the extinction of the SA megafauna and in what period did it occur?
- Human hunting and climate change
- End of Pleistocene
What caused the extinction of the Marsupial, native ungulates and Xenarthrans extinct in Antarctica?
Climate change
Give the Ranks of Linnaean Classification
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
King Phillip Came Over For Good Spaghetti
Thank me later
What is cladistics?
Hypothesising relationships among organisms based on uniquely shared characters/traits
What are the assumptions of cladistics?
Assumptions:
- (Inherited) characters change/are acquired over time
- Any group of organisms related by common descent
- Character similarities/differences reflect evolutionary history
What are some advantages and disadvantages of using morphological characters in phylogenetics?
Advantages
- useful for understanding evolutionary relationships among extinct taxa
- many features to choose from
Disadvantage
- can introduce biases based on subjective decisions about what features to include
- some traits may be more susceptible to convergent evolution than others
What is homology?
Shared trait because of common descent - useful character
What is homoplasy and what problems does it cause?
Similarity of traits not due to common ancestry
- Arises through convergent evolution, parallel evolution, or evolutionary reversal
- makes it difficult to reconstruct accurate evolutionary relationships among different taxa
What is parallel evolution?
Occurs when two or more closely related lineages independently evolve similar traits or features
- Similar to convergent evolution
What is evolutionary reversal (reversion)?
A trait or feature that was lost in an ancestor is subsequently regained in a descendant lineage
What are the considerations of both molecular and morphological phylogenies ?
Molecular
Data very abundant (10s thousands characters)
- Objective (?) – computer algorithms
Accessibility
- Expensive (becoming cheaper)
Morphological
Data
- hundreds of characters
Subjective
- human interpretation
Accessibility
- Labour intensive
Why are fossils still essential for phylogenies?
Molecular fossil data unusable beyond 5mya
What is a rooted phylogenetic tree?
Rooted
- one taxon acts as outgroup to all others
- single common ancestor considered
- length of each branch indicating the amount of evolutionary change that has occurred
What is a phylogram?
Branch lengths represent the amount of evolutionary change that has occured
What is an ultrametric tree?
All tips equidistant from root
- Branch lengths represent absolute time or some other measure of evolutionary time
- assume a constant rate of evolution over time
What is an unrooted phylogenetic tree
Unrooted
- no assumptions about ancestry
- does not have a root node
- branching pattern represents only the relative similarities and differences among the organisms
- not used for evolutionary history
What is a homolog?
Genes from same ancestor
What are orthologs?
Genes separated by speciation events
What are paralogs?
Genes separated by gene duplication
What leads to whole gene duplication events?
Misalignment and unequal crossing over
What can cause species and gene trees to look different?
Duplication followed by loss of genes
How can homologs and paralogs be difficult to differentiate?
Paralogs can independently acquire mutations after gene duplication
To help understand
For example, imagine a gene duplication event that produces two paralogs, A and B. Over time, mutations accumulate in each paralog independently, resulting in differences in their DNA sequences. If we compare the sequences of paralog A from two different species, we might conclude that they are orthologs (i.e. genes that diverged through speciation events). However, if we compare the sequences of paralogs A and B within the same species, we will see that they are more similar to each other than to the A orthologs from other species.
I still dont understand
What is horizontal gene transfer?
The movement of genetic material between different species or clades
What is the impact of horizontal gene transfer for phylogenies?
Makes evolutionary relationships between organisms more complex
- resulting in network instead of a simple tree
Where does most horizontal gene transfer occur?
Mostly between closely related bacteria but can be in eukaryotes and distant clades
What is incomplete lineage sorting?
Ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events
What is coalescence?
All copies of the gene present in the current population are derived from a single ancestral copy that existed in the past
What causes incomplete lineage sorting?
When a speciation event occurs, the ancestral population splits into two or more daughter populations
- each may carry a slightly different set of gene copies.
- Over time, the genes in each population will diverge due to mutation and drift, and new alleles will arise.
- As a result, the gene tree may not match the species tree, because of the differences in the sorting of alleles between populations. NOIDEA WHATHISMEANSSO CONFUSED SEND HELP IF YOU CAN
What is parsimony in phylogenetic inference?
- Seeks to find the simplest explanation requiring the fewest assumptions.
- It suggests that the tree topology that requires the fewest character changes should be preferred
What is the problem with using parsimony in phylogenetic inference?
Often loads of possible trees that can be supported through this method
- Especially when dealing with many taxa
- For example, with just six taxa, there can be 945 possible trees to support through parsimony
What is the goal of phylogenetic inference methods?
Measure characters and use them to infer the relationships among organisms
- ultimately resulting in a phylogeny
What are heuristic tree searches in phylogenetic inference?
Find the best-fitting phylogenetic tree
- involve sub-sampling and applying algorithms to obtain an approximate answer to phylogenetic inference
- algorithm always climbs up and looks for local optima in the imaginary tree-length landscape
- aim is to hit the biggest peak, through random start points and comparing optima
- samples trees randomly to find most likely to be optimal
- Possible to get multiple most parsimonious trees
Why are heuristic trees used?
Used to overcome the limitations of computationally intensive methods such as exhaustive search algorithms
- which are not practical for large datasets
What can be be done if a Heuristic tree search gives you multiple ‘most parsimonious trees’?
Summarise multiple trees as a consensus tree
- shows the uncertainty of the contested divergences
What is maximum likelihood in phylogenetic inference?
Inferring phylogenetic trees based on the principle of finding the tree that maximizes the probability of the observed data given an evolutionary model
How does maximum likelihood differ from parsimony?
Maximum likelihood, like parsimony, aims to find the tree with the fewest evolutionary changes.
- Maximum likelihood uses evolutionary models to guide toward the most probable tree
- Parsimony only counts the number of changes
What factors does maximum likelihood take into account?
Mutation rates and differences in rates between sites and genes
How is certainty calculated in maximum likelihood?
- Bootstrap analysis
- Run maximum likelihood analysis on each dataset
- Construct consensus tree from the resulting trees to determine the support for each branch
What does the bootstrap analysis show?
Shows if and which species have a disproportionate influence on the tree
- provides a measure of statistical support for each branch of the tree
What is Bayesian Inference?
Method for inferring the probability of a hypothesis tree given the data
- Calculating the posterior probability of the hypothesis tree given the data
- the prior probability of the tree
- the probability of data given the tree
Why is Bayesian Inference useful?
Allows incorporation of a prior knowledge and provides a way to calibrate certainty
- often used in combination with other methods for more accurate results
What is the problem of long branch attraction in phylogenetic analysis?
Distant taxa may appear to be closely related due to the high number of mutations they have accumulated
- Leading to incorrect placement on the tree
How can likelihood account for long branch attraction in phylogenetic analysis?
By looking for homology
- Likelihood can help distinguish true relationships from artificial ones caused by long branches
What is a molecular clock?
Estimate the time of divergence between two species based on the assumption that mutations accumulate in DNA sequences at a relatively constant rate
- May be different between molecules
How is the molecular clock calibrated?
Comparing the amount of sequence divergence between closely related species whose divergence times are known from the fossil record
What are some confounding problems with molecular clock estimation?
- Variation in mutation rates among genes and lineages
What is a sibling species? Give an example
Morphologically (almost) identical but are incapable of producing fertile hybrids
- can only be identified by genetic, behavioral, or ecological factors
Examples
- Eg. mosquitos - 6 species but only some transmit malaria
- Eg yeast - budding yeast identical but you can only use S. cerevisiae to bake bread
What are the problems with the biological species concept?
Only applicable to sexually reproducing organisms
Asexual organisms given binomial names
- considered taxonomic species but not biological species
Does not apply to fossils
Intermediate cases
- Reproductive barrier incomplete
Give an example of hybrid zone species
- Eg hybridisation zone of carrion and hooded crows
- Eg broad sympatric hybridisation of gray oak and gambel’s oak
Why might the Biological species concept be difficult to use on geographically isolated populations?
Difficult to determine if they are capable of interbreeding due to physical barriers
What is the phylogenetic species concept
Based on evolutionary history
- descended from a common ancestor and who all possess a combination of certain defining, or derived, traits
What are the two version of the phylogenetic species concept?
A basal cluster of organisms that is diagnosable distinct from other such clusters and within which there is a parental pattern of ancestry and descent (PSC1)
The smallest exclusive monophyletic group of common ancestry (PSC2)
What types of pre-mating barriers are there
- Behavioural isolation
- Ecological Isolation
Describe differential sex pheromones as a pre-mating barrier to gene flow
Give an example
Serve to identify individual of same species
- Vary in chemical structures, chirality and ratios
Eg European Corn Borer (Moth)
- Females from different races produce different blends of the cis and trans isomers of the same pheromones
What type of organisms are sex pheromones used?
Mainly mammals and insects
Describe differential courtship as a behavioural pre-mating barrier to gene flow
Give two examples
Differences in the behaviour of individuals of different species during courtship and mate selection
Variation in secondary sexual characters
- Eg. Such as the brightly coloured plumage of male hummingbirds
- used to attract mates of the same species while repelling potential mates of different species
Use of different acoustic signals in green lacewings
- Distinguish between members of different species during courtship
What is ecological isolation as a barrier for gene flow?
Inability of a species to use another species’ environment
Describe microspacial isolation as an ecological pre-mating barrier to gene flow
Give an example
Occupy same space but reproductively isolated due to different niches
Eg. Goldenrod plants
- Adapted to specific soil moisture
Describe macrospacial isolation as an ecological pre-mating barrier to gene flow
Species adapted to two largely allopatric habitats
What are types temporal isolation as an ecological pre-mating barrier to gene flow
Mating seasons
Mating time and activity (morning vs evening)
What type of ecological isolation do North American periodical cicadas exhibit?
Temporal isolation
- Different life cycle lengths
- Living in same area
- 13 year vs 17 year
- Alternate species opportunity to mate once every 221 years
What type of ecological isolation do ladybirds exhibit?
Microspatial
- Host specific insects
- They mate where they feed
- Different species different host
What type of ecological isolation do field crickets exhibit?
Macro-spatial
- one species prefers loamy soils
- other prefers sandy soils
Temporal
- reach sexual maturity in autumn
- spring field crickets reach sexual maturity in spring
What type of ecological isolation does drosophila exhibit?
Temporal
- One species of drosophila breeds in the morning, another in the evening
Describe pollination isolation as an ecological pre-mating barrier to gene flow
Give as examples
Morphological disparity adapted for different pollinators
Eg. figs and fig wasps
- Nearly all 750 fig species pollinated by different wasps
Eg bees vs hummingbirds
- flowers shaped for ease of their pollinators
What are examples pre-zygotic barriers
- Mechanical isolation
- Copulatory behavioural isolation
- Gametic isolation
What is mechanical isolation as a pre-zygotic barrier to gene flow?
Structural incompatibility of reproductive organs between two species
- Not very common among animals
Give an example of mechanical isolation
Eg. Japanese Carabid beetles
Males from other species with different shape and size genitalia
- Can cause tearing of female reproductive organs
- Sometimes fatal
Creates a strong selective pressure for females to only mate with males of the same species
Where is mechanical prezygotic isolation common?
Give an example
More common in plants
Flowers have specific shapes
- incompatible with some pollinators
Some flowers have deep floral tubes
- can only be reached by pollinators with long proboscises
What is copulatory behavioural isolation as a pre-zygotic barrier to gene flow?
Behaviour of individual during copulation insufficient to allow normal fertilisation
- Failure of sperm transfer despite compatibility between genitals
Give an example of copulatory behavioural isolation?
Eg drosophila
- Females terminate copulation before transfer if tactile stimulation incorrect
What is gametic isolation as a pre-zygotic barrier to gene flow?
- prevents the fusion of gametes from alternate species
- prevent fertilization between individuals
What is non-competitive gametic isolation?
Caused by intrinsic factors such as differences in gamete size or shape
What is competitive gametic isolation?
Involves active selection of conspecific (same species) gametes over heterospecific (different) gametes
Describe competitive gametic isolation in drosophila
Females inseminated by both conspecific and heterospecific sperm
Produce few hybrid offspring
- Conspecific gametes were favoured
- some progeny were hybrids
What are examples of post-zygotic barriers?
If hybrid zygote formed
- Hybrid inviability
- Hybrid sterility
What is hybrid inviability?
Zygote dies due to genetic incompatibilities
What is hybrid sterility?
Zygote survives, unable to produce viable progeny
- Very wasteful evolutionarily
What is an extrinsic post-zygotic barrier to gene flow?
Use Heliconius butterflies as an example
Hybrid does not find appropriate niche
Heliconius butterflies
- exhibit a range of mimicry rings
- which serve as a defense against predators
Hybridization between different mimicry rings
- results in non-mimetic hybrids
- these have lower fitness due to increased predator mortality
What type of gene flow barrier do sagebrush experience?
Ecological Post-zygotic barrier
- hybrids of two species outcompeted
Two taxons - mountain and basin
- Hybrid hopeless in basin (out competed by both mountain and basin taxons)
- Hybrid fitness in mountain is alright but outcompeted by mountain taxon
What is behavioural post-zygotic barrier? Give an example
Cannot obtain mates
Eg. lacewing
- Courtship song
- Hybrid has intermediate song
- discriminated against by females of both species
Are ecological post-zygotic gene flow barriers fixed and insurmountable? Give example
Can appear/disappear as environmental conditions change
Eg. Sagebrush hybrid outcompetes parent species in specific soils
What is an example of difficulty distinguishing between intrinsic and extrinsic post-zygotic barriers?
Eg Mus musculus musculus and M.m. domesticus (mouse sub species)
- Hybrid more prone to parasites (extrinsic) due to reduced genetic resistance (intrinsic)
What is Haldane’s rule?
When reproductive isolation is incomplete
- the heterogametic sex (the sex with different sex chromosomes) shows the strongest degree of reproductive isolation (most likely to be unviable)
What type of organisms does Haldane’s rule apply to?
Rule applies when the sex chromosomes are different between the two species
- such as in mammals (where females are XX and males are XY)
- Lepidoptera (where females are ZW and males are ZZ)
- birds (where females are also ZW and males are ZZ)
Describe dominance theory in Haldane’s rule
When two different species interbreed, the genes on their chromosomes may be incompatible
- fitness of hybrid offspring on one allele is dominant over the other
For example - consider two genes A and B, with two alleles each (A1, A2, B1, and B2)
A1 is incompatible with B2
B2 is dominant over B1.
In this case - heterozygous individuals with A2B2 will be fit because they have one compatible allele and one dominant B2 allele.
Heterozygous individuals with A1B2 will be affected because they have one incompatible A1 allele and one dominant B2 allele.
How does Haldane’s rule determine which species will be affected?
Whether males or females are more affected by the incompatibilities depends on which sex is heterogametic (has different sex chromosomes) and which allele is dominant
In birds and Lepidoptera
- where the XY is the female, an incompatible gene on the X chromosome will affect heterogametic males (XY) more than homogametic females (XX).
In mammals, where the XY is the male
- an incompatible gene on the X chromosome will affect heterogametic females (XX) more than homogametic males (XY).
What are the effects of Haldane’s Rule?
- heterogametic sex has a greater proportion of genes that are unique to its sex chromosome
- makes it more susceptible to the negative effects of genetic incompatibilities.
What is sequence divergence and how is it a barrier to gene flow ?
Refers to the accumulation of genetic differences over time between populations or species
- Lack of recombination/problems in meiosis due to differences in the sequence of homologous chromosomes
- Can make it difficult for them to match up during fertilization
- Strength of isolation increases with genetic distance
What is structural divergence and how is it a barrier to gene flow?
Refers to chromosomal rearrangements
- Prevents annealing of parental homologues in meiosis
What are some example of potential chromosomal rearrangements?
translocations, fissions, inversions, deletions, and duplications leading aneuploidy
What are disharmonious interactions and how do they act as barriers to gene flow?
- Negative epistatic interactions (improper binding) between two or more genes that can result in reduced fitness or sterility in hybrids
- Incompatibilities between genomes that lead to disharmonious interactions
- Causing reduced fitness or sterility in the hybrid offspring
What is Dobzhansky-Muller incompatibility (D-M incompatibility)
Arises if one population evolves the A1B0 genotype and the other evolves the A0B1 genotype
- allowing formation of unfit A1B1 hybrids if the populations were to come into contact
Why is prezygotic isolation stronger in sympatric than allopatric taxon pairs? Prezygotic isolation is high in sympatric even when genetic distance is low.
Two species live in the same geographic range, there is a higher probability of encountering and attempting to mate with each other
- evolved stronger prezygotic isolation mechanisms to prevent hybridization and maintain genetic differentiation
What is character displacement?
- When two similar species that coexist in the same geographic area
- evolve different traits that allow them to use different resources or occupy different ecological niches
What is reinforcement?
- Natural selection strengthens reproductive barriers between two closely related species
- Reduces chance of interbreeding and the production of hybrid offspring
What is the expected consequence of reinforcement?
Evolution of traits that further promote the divergence between two sympatric species
Explain the theory of pied flycatcher male colour morphs - black & white as well as brown
- When the two species are sympatric
- Brown morphs are more prevalent and preferred by females
- Reducing chance of hybridisation
Describe allopatric speciation
Reduction of gene flow to 0
- physical (geographic) barrier extrinsic to the organism
- due do geological or climate events
- divergence without hybridisation events
What is vicariance?
- Divergence of large populations
- Allopatrically
What is an example of a vicariance event leading to allopatric speciation?
Emergence of the Isthmus of Panama in Pliocene
- Divided snapping shrimp populations to pacific and Caribbean
- Now in labs only 1% interspecific pairs can mate
What occurs if isolation is not complete when geographic barrier lifts?
- Secondary hybrid zone forms
- Hybrids with low fitness
What mechanisms contribute to reproductive isolation?
Natural selection
- ecological selection
- sexual selection
Dobzhansky-Muller incompatibilities
Genetic drift
Use leaf beetles as an example of ecological speciation
Georgia and New York populations feed on maple
Ontario population feeds on Willow
- Greater RI between Ontario and New York despite close geographic proximity
- Sexual isolation more pronounced between ecologically divergent population
Use three-spined sticklebacks as an example of ecological speciation
Two ecomorphs
- benthic (large, big mouth, big prey)
- limnetic (small, feeds on plankton)
Found in different Canadian lakes
- Females preferentially mate same ecomorph, whether from same or different lake
- reproductive isolation has evolved between the two morphs
How does sexual selection produce reproductive isolation? Give an example of an animal
Isolation by female preference for phenotypic traits of conspecific males
- Eg. birds of paradise, hummingbirds
What is a typical example of a population that undergoes genetic drift?
Bottlenecked population that has experienced severe reduction in size
What happens during a bottleneck event?
Small subset of individuals survives and reproduces
- Reduction in genetic diversity
- Increase in the frequency of certain alleles
What is peripatric isolation and what evolutionary force acts quickly in this case?
Divergence of small population from large ancestral population
- Founder effect
- Genetic drift acts strongly on small populations
Invasion of novel habitat
- strong selection
What is an example of peripatric speciation?
Eg. paradise kingfisher variation in New Guinea
- Several different species on small islands
What is parapatric speciation?
Divergence of spatially distinct population
- some gene flow (0<m<0.5)
Give an example of parapatric speciation.4
Eg A. odoratum - grass species
- Grass evolved to tolerate heavy metals near mines
- Populations under strong selection pressure for metal tolerance diverged from neighbouring populations growing on uncontaminated toil
- Increased self fertilisation to avoid dilution of tolerance genes
What is sympatric speciation?
Divergence between a single, initially randomly mating, population (m=0.5)
- Speciation despite high gene flow
When might insect sympatric speciation occur?
Insect sympatric speciation when shifting host/adapting to new plant host
- Same species but beginning to develop new niche
What causes sympatric speciation?
- Host/Habitat-shift speciation
- Polyploid/Hybrid speciation
Describe Host/Habitat-shift speciation as a force for sympatric speciation
- Powerful disruptive selection imposed by two ecological niches
- Association between ecological niche and mate choice
- Leads to the development of reproductive isolation
Describe Rhagoletis (fly) sympatric speciation - what was observed to cause reductions in gene flow?
Sibling species each inhabits different host
Apple vs Hawthorne - choice of host
Conclusions
- Host preference must have genetic basis
- Genetic based trade-off in fitness associated with colonising and adapting to new plant host (alleles suitable for one host may be selected against in the other)
- The two plants have different fruiting time (favouring alleles optimising time for mating)
Describe Palm (Howea forsteriana (Kentia plant) and Howea belmoreana (Curly palm) on Howae Island sympatric speciation?
Occurred due to divergent selection pressures imposed by differences in soil preference
- Resulted in differences in the timing of reproduction and flowering season between the two species
- Over time, this reproductive isolation occurred
Despite no lack of physical barrier
Describe Polyploid/Hybrid sympatric speciation
Cytological change (cellular change brings reproductive barrier)
Polyploids are post-zygotically isolated from their diploid progenitors
- Ie. 4n breeding with 2n gives 3n
- unpaired chromosome
- unviable
Instantaneous speciation by a single genetic event (autopolyploidy and allopolyploidy)
What does autopolyploid mean?
Fusion of two 2n gametes of same species
What does allopolyploid mean?
Fusion of two 2n gametes from two closely related species
What is hybrid speciation in plants? Give an example
Some recombinant offspring produced by hybrids of two species are fertile but reproductively isolated from parent species
Eg Helianthus
- Hybridisation between H. petiolaris and H. annus gave 3 other Helianthus species
What is Time for Speciation (TFS)?
- Time required for complete RI (Reproductive Isolation) from start of process
What is biological speciation interval?
Time between origin of new species and when that species specialises again (TFS + waiting time until next TFS)
What causes rapid rates of speciation?
- Polyploid speciation (instantaneous)
- Hybrid speciation
- Adaptive Radiation (rapid speciation and phenotypic adaptation to exploit unoccupied niches)
Sympatric speciation is ______, however it happens ______!
Sympatric speciation is fast (Rapid TFS), however it happens rarely (long BSI)!
When is allopatric speciation involving genetic drift fast?
Smaller population (founder-effect) - under genetic drift and selection
- can have rapid TFS
What is phylogenetic niche conservatism?
Current and ancestral taxa are likely to occupy similar niches
- Better adapted than, and outcompete, other taxa
- Eg. if a woodland niche becomes vacated, it’s easier for terrestrial mammals and plants to move in than fish
What are phylogenetic time lags and what is the difficulty they produce?
Traits are not lost immediately
- Can make it difficult to determine whether the trait is truly adaptive or not
- Comparison with other taxa can reveal former use
When a selection pressure is removed why aren’t the traits to deal with it removed immediately?
- Neutral or negative selection pressure replaces positive selection
- The trait may persist for some time still (especially if neutral)
- Removal may have no positive effect, or even a more deleterious side effect
What is a human example of a trait that has lost its adaptive function of humans and what was it used for?
Human vermiform appendix
- Used to be for fermentation
- Still is in other organisms
What is a mammalian developmental constraint that really bothers giraffes?
7 cervical vertebrae (few mammals deviate)
- Hard to change as vertebrae development occurs early
- Would allow increased flexibility and length
What is the cichlid (a fish) jaw an example?
Mutation removing constraints allows for adaptive radiation
- allowed radiation into new niches
What is an example of irreversible evolution in marine mammals and birds?
Heart chambers are completely separated
- Whales, seals, penguins don’t breath under water
- No point sending blood to lungs
- But they must
Crocodiles, marine iguanas can divert blood away from lungs (due to design of the heart)
What does homology mean?
Similar due to common descent
What does analogy mean?
Similar due to common selection pressures (convergent evolution)
What is an example of analogy in animals?
Dolphins resemble ichthyosaurs
- due to convergence
- adapted to swimming
What is the difference in reptilian and mammalian movement? What are the constraints produced this difference?
Reptiles
- lateral undulations
- movement pattern limited by constraint of anatomy
Mammals
- vertebrae articulate around the transverse plane
allows for up-and-down movement - due to suckling and breathing constraints
What is a common issue found with areas that trace fossils are preserved?
Usually not good for bone fossils
What is the problem with fossils for understanding organisms of the past?
Many features not preserved
- Anatomy
- Physiology
- Behaviour
- Colouration
- Fur/feathers
- Only really get bone
What is Occam’s razor? Explain in evolutionary terms
If we have many plausible explanations/hypotheses, accept the simplest until proven wrong
- In evolutionary terms, this means the explanation requiring the least amount of evolutionary changes
What is the definition of a plesiomorphy?
Ancestral shared state
- eg fingers in limbs of tetrapods (present in last common ancestor)
What is an autapomorphy?
Modification or change to a plesiomorphy
What is a crown group?
Monophyletic clade that contains all the descendants (extinct and extant) of the last common ancestor of two or more extant taxa
What is a stem group?
Paraphyletic group that contains the extinct taxa that are more closely related to one crown group than another
Why are crown groups important?
Allow us to infer similarities and differences between extant organisms
- Traits seen in multiple extant taxa likely plesiomorphies, or ancestral traits, which can help us reconstruct the traits of the last common ancestor of the crown group
Why are stem taxa useful?
Represent extinct organisms that are closely related to a crown group
- Provide information about the characteristics of the last common ancestor of a crown group
- Allow for the inference of the polarity (direction of evolutionary change) of traits that are uncertain in the crown group
What are the two clades that make up Dinosauria?
Saurischia and Ornithischia.
What are the two sister taxa in Saurischia?
Theropoda and Sauropodomorpha
What is the common feature of extant dinosaurs?
Common feature of extant dinosaurs is that they are all bipedal (birds)
Were all therapoda quadrupedal?
No, many including T-Rex, were bipedal
- quadrupedal was evolved later in the group
Were all ornithischians quadrupeds?
No, especially basal (early) ones, were also bipedal.
Describe the bipediality and quadrupediality of sauropodomorpha
Basal sauropodamorpha may have been facultative bipeds
- later ones were more likely obligate quadrupeds
What is interesting about the forelimb anatomy of Saturnalia?
It is close to the transition from bipediality to quadrupediality
- Indicating a possible facultative bipedal stance
How do we determine if a trait in Saturnalia is ancestral to archosaurs?
Look unique traits present in crocodiles and birds
- If found, the most parsimonious explanation is that it is plesiomorphic and present in the last common ancestor of archosauria and therefore in Saturnalia
What is the common ancestor of aves and crocodilia?
Saturnalia tupiniquim
What are the crown groups defining Archosauria?
Crocodiles and Birds
What are the crown groups defining Amniota?
Reptiles and mammals
What causes development of traits that are not adaptations?
Consequence of physical/chemical restraints
- Eg. blood being red
- This is just the colour of haemoglobin
Consequence of genetic drift
Associated with adaptive trait
- Eg. genetically linked through pleiotropy
- Could be under neutral selection or even maladaptive, but linked to adaptive trait
What is a preadaptation (exaptation)? Give an example
Traits that evolve for one function (due to one set of selection pressures) but by chance are later suitable for performing a novel role
- Eg Primate (human) grasping
Primarily used in eating and locomotion
Exaptative uses
- Tool use
- Became useful for technology
What is the primary palate?
Separates the respiratory tract from the first stage of the digestive tract
What is the function of the primary palate?
Prevent food from entering the respiratory tract during feeding
What is the secondary palate?
Structure that extends from the primary palate to the back of the oral cavity
What is the function of the secondary palate?
Separate the nasal cavity from the oral cavity
- Allowing mammals to breathe while chewing
When did the secondary palate evolve?
Early mammals
- after the divergence from non-mammalian synapsids (adaptation not present in reptiles)
What are some potential reasons for the evolution of the secondary palate in mammals?
- Allows infants to suckle while breathing
Affects vocal resonance
- Forming sounds/articulation
What is the reason for suckling and speech not being considered primary evolutionary reasons for development of the secondary palate?
Other animals like crocodiles and dicynodonts that also have a secondary palate
- Do not suckle or use speech
What is DNA polymerase infidelity?
Inherent ability of DNA polymerases to occasionally make errors while copying DNA during replication
- Leading to mutations in the DNA sequence
What are base substitutions?
Most common type of mutation
- Single nucleotide is replaced by another nucleotide
What are INDELs (insertions or deletions)?
Result from errors during replication, recombination, or repair
- Particularly in repetitive regions of the DNA sequence
- Leading to frameshift mutations and potentially disrupting protein function
What can chemical instability of purine and pyrimidine bases cause?
Spontaneous damage or loss of these bases from DNA
- Leading to single-strand breaks, crosslinks, or potentially more severe damage if left unrepaired
What can chromosomal abnormalities that result from errors in cell division?
- Aneuploidy (an abnormal number of chromosomes)
- Structural changes (such as translocations, inversions, or deletions)
What can Errors in repairing double strand breaks in DNA cause?
Chromosomal rearrangements
- such as deletions, inversions, or translocations, potentially altering gene expression or disrupting critical gene function
How do the phalanges in beams contribute to the structure’s stiffness in construction?
Both upper and lower on I-beams and lower on L-beams
- increase the stiffness of the overall structure
- making it less likely to bend
How does the intermediate phalange contribute to the strength of an organism’s upper jaw?
Makes the upper jaw stronger, providing a fitness benefit
- Particularly important for organisms that handle live prey
- Pose a risk of breaking the upper jaw
The potential selection pressure for the evolution of the palette based on skull model experiments.
Complete palette is much stronger than none at all
- intermediate phases also increased strength
- selection pressure for the evolution of the palette
What is the ancestral form of the facial muscles in humans and how has it evolved?
Constrictor colli
- Over time, it migrated out and formed the facial muscles we have today.
What is the function of the Buccinator muscle and why is it important?
Forms the cheeks
- Crucial role during chewing
- Prevents food from falling outside of the teeth by keeping it in
The role and potential evolutionary pressures for the development of the Orbicularis oris muscle.
Orbicularis oris muscle forms the lips and plays a role in keeping food in and suckling
- primary selective pressures were likely mastication and suckling rather than facial expressions
How does co-evolution differ from ‘regular’ evolution?
Co-evolution involves mutual responses between species
- Not just adaptation to an environment
- Promotes a diversity of adaptations, with reciprocal responses often being unique and specific to the interacting species
What are some modes of antagonistic co-evolution?
Co-evolution can take the form of predation
- Predator exerts strong selection pressure on prey
Herbivory
- plants develop defences against vegetarian predation
- competition between two different species (interspecific)
What is the Red Queen hypothesis in the context of co-evolution?
- Species are evolving reciprocally but cannot evolve away from each other
- Ongoing evolutionary arms race
What are the potential outcomes of antagonistic co-evolution?
- Indefinite unending escalation (an evolutionary arms race)
- Stable genetic equilibrium (such as when plants evolve defenses to reduce, but not completely stop, herbivory)
- Cycles/fluctuations in the genetics of both species (common in parasitism)
- Possible extinction of both species
What are the conditions necessary for coevolution?
- Genetic variation for relevant traits in both the enemy and victim species
- Reciprocal effects of these traits on the fitness of individuals
- Outcome of enemy-victim interactions being dependent on the characteristics of the involved traits
Describe a example of co-evolution where a predator develops improved vigilance
Predator detecting prey first places selective pressure on vigilance
- prompting the prey to develop better detection avoidance techniques
- such as camouflage
Describe the evolutionary arms race between cheetahs and gazelles
Gazelles evolve longer legs for speed
Cheetah evolves lower bone density to increase its speed
These adaptations may reach a constraint where the costs outweigh the benefits
- such as the potential speed detriment from having too low a bone density
How does the Passiflora plant demonstrate co-evolution with the Heliconius butterfly?
Passiflora plant takes advantage of the Heliconius butterfly’s avoidance of leaves with eggs already on them
- Plant produces egg-like buds
- mimic the appearance of butterfly eggs
- Deters female butterflies from laying their eggs on the plant
- Larvae are highly carnivorous and pose a threat to the plant.
What does the term “lag” refer to in the context of studying co-evolutionary dynamics?
Delay in reciprocal response between two co-evolving species
- response to an adaptation in one species is not immediate in the other, which can complicate the study of these dynamics
What does ‘diffuse’ co-evolution involve? Give example
Involves multiple species, with their effects not being independent
- For example, a pollinator may interact with multiple plant species, causing changes in all involved species
What is ‘escape-and-radiate’ co-evolution? give an example
A species evolves a radical new defense, escaping its enemy
- For example, a plant could evolve a chemical defense that makes it inedible to a particular herbivore
- Often leads to diversification of the victim species and introduction of new or different enemies, which then diversify in response
What is the co-evolutionary relationship between rough-skinned newts and garter snakes?
Rough-skinned newts have evolved a potent toxin, tetrodotoxin (TTX), as a defense mechanism
- When threatened, they exhibit aposematism, an honest signal of toxicity, by exposing their yellow underbelly
- Garter snakes, a predator of these newts, have been observed to develop resistance to this toxin, resulting in an ongoing co-evolutionary arms race
What is aposematism?
Warning signal used by certain poisonous or dangerous animals
- involves a conspicuous display
- bright coloration or distinctive patterns
What is ‘spedific’ co-evolution?
a change in one species leads to a shift in another species
- often leads to an evolutionary arms race where each species responds to adaptations in the other.
What is the tradeoff in TTX production for the rough-skinned newt?
- Producing more TTX reduces the likelihood of being eaten
- but energy and resources required for this high TTX production could result in fewer offspring
What is the tradeoff in TTX resistance for the garter snake?
Developing too much TTX resistance allows them to eat toxic newts
- but physiological adaptations required for this resistance may reduce their crawling speed
How does the monarch butterfly caterpillar respond to milkweed’s defenses?
Evolved a tolerance to the milkweed’s chemical defenses
- Also developed a strategy to notch the milkweed leaf
- Which reduces the plant’s latex production
How does the monarch butterfly benefit from consuming milkweed?
Acquire the plant’s toxins and become toxic themselves
- Deters predators
- Increases butterflies fitness
What is Mullerian mimicry in relation to the monarch and viceroy butterflies?
two or more harmful or distasteful species that share common predators evolve to resemble each other
- resemblance enhances their mutual protection
- the viceroy butterfly, which is also distasteful, has evolved to mimic the appearance of the toxic monarch butterfly, enhancing the protective effect of their shared warning coloration
Why is the relationship between viceroy and monarch butterflies not necessarily considered co-evolution?
viceroy butterflies have evolved to mimic the appearance of monarch butterflies
- it’s not necessarily considered co-evolution because the evolution of one species (viceroy) does not seem to be causing reciprocal changes in the other species (monarch).
- If the monarch butterflies were evolving in response to the viceroys (for instance, to look more dissimilar), it would be a clear case of co-evolution.
What is mutualism in the context of co-evolution?
Mutualism is a type of beneficial interaction in co-evolution where both species involved benefit from their interactions. Examples include pollination, clownfish and anemones, and acacia plants and acacia ants.
How do acacia plants and acacia ants benefit from their mutualistic relationship?
Acacia plants provide accommodation in the form of domatia (hollow thorns) and food bodies for acacia ants. In return, the ants protect the acacia plants from vines, herbivores, and pathogens.
What is the relationship between the Darwin Hawk Moth and Darwin’s Orchid?
Darwin Hawk Moth and Darwin’s Orchid have a tightly coupled mutualistic relationship in pollination. The moth is a specific pollinator of the orchid, and the orchid provides nectar as food for the moth. This relationship is so specific that each has evolved particular traits to facilitate this interaction.
What is commensalism in co-evolution?
Commensalism is a type of interaction in co-evolution where one species benefits from the relationship and the other species is unaffected or experiences very negligible costs.
- Examples include birds nesting in trees and pilot fish foraging on the scraps left by sharks.
How does the commensal relationship between birds and trees work?
Birds benefit from the relationship by having a place to build their nests and live. The trees are largely unaffected by this, although there might be a very minor cost due to the added weight of the nest, but this cost is typically negligible and does not harm the tree
What is adaptation in the context of evolution?
enhances the survival or reproduction of an organism relative to its ancestral state. Essentially, it’s a trait that increases an organism’s Darwinian fitness.
How does coadaptation work in evolutionary terms? what is a good example of this?
- complex characteristics in an organism undergoing mutually inter-dependent adjustments in response to the same natural selection pressures
The eye
- complex organ that has undergone numerous changes and developments over time due to natural selection pressures.
What is an extended phenotype? Give an example
Effects that a gene has on its environment, outside of the individual organism’s body
- An example is a beaver’s lodge
- Though the lodge is not a part of the beaver’s body, it is a product of the beaver’s genes and can impact its fitness.
How does mimicry demonstrate coadaptation?
For the mimicker, resembling a dangerous or unpalatable species can deter predators, increasing their survival.
- Can be a fitness cost for the mimicked organism if predators learn that organisms resembling their warning signals can sometimes be harmless or tasty.
What does the concept of ‘Spandrels of San Marco and the Panglossian Paradigm’ illustrate in evolutionary biology?
Idea that some traits may appear to be adaptive
- but are actually by-products of other structural or developmental constraints
What is Morphodynamics in evolutionary biology?
- Interaction between the environment, functional morphology, developmental constraints, historical constraints, phylogeny, and time
- Investigates how these factors collectively influence the evolution of an organism’s form and structure
What are phylogenetic constraints? Give an example
Limitations on evolutionary change that are imposed by the characteristics of the ancestral species
- For example, the panda’s “thumb” is a modified wrist bone because development can’t just add an extra finger
What are some examples of imperfections in evolution?
Nerves in vertebrate eyes
- sit on top of the photo sensors, creating a blind spot
Whales have a vestigial pelvic girdle
Recurrent laryngeal nerve in mammals
- loops around the heart to get from the throat to the thorax
- was the most efficient path in fish, the ancestors of terrestrial vertebrates
What are functional constraints in evolution? Give two examples of this
Functional constraints refer to the hard limits imposed by physics and chemistry
- organisms have difficulty producing metals because it requires high temperatures
Eg limits in oxygen diffusion
- Eggs can’t get any bigger
- Insects can’t get bigger - tracheal system
Eg mechanical limits to size
- Bones highly conserved in vertebrates - no strength innovations
- Neural transmission speed - too slow if your foot is too far from your CNS
What are fabricational constraints in evolution?
Limitations on evolutionary change imposed by the properties of biological materials and the processes that produce them
- For instance, bone, while versatile, is not as strong as carbon fiber
What is Macroevolution in comparison to Microevolution?
Macroevolution
- changes that occur at or above the level of species, such as adaptive radiation, rates of diversification and change, and mass extinctions.
Microevolution
- on the other hand, involves smaller-scale changes within a population due to mechanisms like mutation, migration, genetic drift, and natural selection.
What are evolutionary trends?
Evolutionary trends are sustained tendencies for evolutionary change in a particular direction
- example of such a trend is Cope’s rule, which suggests that organisms tend to get larger over time
How can we measure evolutionary trends?
Measured using fossils, which can provide evidence for physical changes in species over time
- Such as horn swelling in brontotheres or mammalian brain size
- Additionally, we can produce phylogenetic trees from the genetics of extant organisms and use these trees to extrapolate back in time
- Predicting historical evolutionary events like the onset of bipedal locomotion
What are the limitations of predicting evolutionary trends?
Involves reconstructing past events based on current evidence
- Extrapolating from existing animal behavior, genotype, and phenotype against their relatedness
- Relies on assumptions and can lead to inaccuracies
What is a molecular clock in the context of evolution?
Mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged
Explain: Variable rates of change in molecular clocks
Rates of molecular change can vary between different organisms and even between different gene loci within the same organism
- These variations can be due to differences in life history traits, mutation rates, and selection pressures.
What is the need for calibration in molecular clocks?
Required to convert genetic differences into absolute time
- often done by relating the genetic divergence to independently known dates such as fossil records or known geological events
Describe: Node dating in molecular clocks
Method used to estimate the age of a species or group of species in phylogenetics
- uses known divergence points of species (nodes) to calibrate the molecular clock
- nodes often come from the fossil record or paleogeographic events
The concept of Relaxed Molecular Clocks
A relaxed molecular clock model allows rates of molecular evolution to vary among lineages
- more realistic model than strict molecular clock models because it accounts for natural variability in mutation rates and selection pressures
What is Tip dating in the context of molecular clocks?
Method that uses both node data and genomic phylogeny of modern animals, along with morphological phylogeny of fossils
- allows for simultaneous analysis of extinct and extant taxa using genetic sequence data and morphological character data, with defined fossil dates
The role of selection pressure in molecular clocks
Can distort molecular clocks as it influences the rate of change in genetic material
- Areas of the genome that are under strong selection pressure may evolve at different rates compared to areas that are under weak or no selection pressure
Why are fossils necessary in the study of phylogeny?
Unique deep-time perspective
- Aid in reducing long branch attraction by breaking up long branches
- Show the sequence of morphological change
- Provide a timescale for evolutionary events
- Assist in rooting trees
The challenge of measuring biodiversity trends using fossils
Fossil records are not complete
- Don’t have perfect identification methods
- Fossil biodiversity might appear artificially low
What is meant by post-mass extinction shifts?
Refer to changes in biodiversity following a mass extinction event
Competitive displacement
- Where a species is outcompeted by another
Incumbitive replacement
- where a species becomes extinct due to bad luck rather than any particular disadvantage
What are some examples of organisms exhibiting slow evolutionary rates?
- Coelocanth, a fish with a highly conserved phenotype
- Maple leaves
- Bivalves
Display a very slow accumulation of apomorphies
Describe: The concept of Ephemeral local divergence
Unobservable or short-lived changes in organisms that may not be apparent in the phenotype
- These changes may have arisen and gone extinct with poor preservation
- Thus not leaving substantial evidence in the fossil record
The impact of Phylogenetic, Functional, and Fabricational constraints on evolution
Phylogenetic constraints
- Adaptation of a wrist bone instead of developing an extra finger in pandas
- Limit evolutionary possibilities based on the organism’s evolutionary history
Functional constraints
- Hard limits posed by physics and chemistry
- Limits to size due to oxygen diffusion and mechanical strength
Fabricational constraints
- Limitations of biological materials
- For example, bone not being as strong as carbon fibre
What is Gradualism in evolution? Give an example.
Gradualism is the theory in evolution that suggests changes occur steadily over time, with no sudden leaps
- An example of this is the trilobites, which show a gradual and contemporaneous increase in the number of ribs
The concept of Saltation in evolutionary theory
Idea of rapid evolutionary changes or leaps
- An example of this can be seen in horses, which remained around 80/90kg for a long period
- Before undergoing a rapid increase in body size and hypsodonty (larger teeth)
Explain: The principle of Punctuated Equilibrium
Once species appear in the fossil record, they will become stable, showing little net evolutionary change for most of their geological history
- This ‘stasis’ is punctuated by rare instances of branching evolution
What is an Adaptive Radiation? Give an example.
Divergent evolution of numerous related lineages within a short period of time to occupy different ecological niches
- An example of this is the evolution of Darwin’s finches
- Underwent rapid diversification to occupy different niches in the Galapagos islands after a gap in the niches was created
Give an example of Cope’s Rule
Clades should generally increase in body size over evolutionary time due to advantages that larger size confers in competition and survival
Evolution of horses
- Maintained stable weight for a long period, suddenly experienced a rapid increase in body size
The pattern of Adaptive Radiation observed in Cichlid fish
In the separate freshwater lakes of Africa, Cichlid fish have undergone a unique adaptive radiation
- Due to the complete gene isolation in each lake, every species in each lake belongs to a single diverse monophyletic clade per lake
- Each group has diversified into a similar range of species morphologies
- compelling case of adaptive radiation under similar environments and complete isolation
Explain: Dioecious species
Individual organisms are distinctly male or female
- Each individual produces only one type of gamete
- Either sperm or eggs
Describe: Parthenogenesis
Form of asexual reproduction in which development of a new individual occurs from an unfertilised egg
- It’s observed in various animal species including Komodo dragons, aphids, and daphnia
How does sex contribute to genetic diversity?
Recombination
- Allows for the shuffling and mixing of parental chromosome pairs from generation to generation
- Can introduce new gene combinations
- Can be beneficial for the survival and adaptation of a species
Gynogenesis
Form of asexual reproduction, specifically a type of sperm-dependent parthenogenesis.
- Copulation occurs and sperm triggers embryogenesis
- Does not contribute any genetic material
- This is observed in some species of fish
What is adventitious embryony in plants?
Asexual reproduction in plants
- where a new individual develops from a somatic (non-sexual) cell
Hermaphroditic species
Individuals produce both male and female gametes
- Some species may be one sex when young and mature to the other
- Others may be both at the same time
- Some can self-fertilise
What is the primary function of sexual reproduction, if not for reproduction itself?
Recombination
- Allows for shuffling of parental chromosome pairs
- Promoting genetic diversity from generation to generation
What is the two-fold cost of sex or ‘cost of males’?
First
- Producing males is costly and they don’t really contribute to population growth as only females can bear offspring
Second
- In sexual reproduction, only 50% of an organism’s genes are passed onto offspring
- Compared to asexual reproduction where 100% of the genome is passed on
Explain: The evolution of recombination and sex
Recombination, a process used in DNA repair, is believed to have evolved around 3 billion years ago.
- Sex, which involves recombination to create genetic diversity, likely evolved 1-2 billion years ago
- The exact reasons for the evolution of sex are still a subject of research and debate
Describe: The cost of finding a mate in sexual reproduction
Includes the energy and resources expended in locating a mate and competing with others for the chance to reproduce
- Can involve physical contests, display behaviors, or the risk of predation during the search
Why would asexuality outcompete sexuality if it evolved in a population?
Rapid population growth
- Every individual can bear offspring
Asexual reproduction allows for the passing on of 100% of an individual’s genome to their offspring
- Ensuring a higher degree of genetic continuity
When did recombination and sex evolve according to estimates?
- Recombination is believed to have evolved approximately 3 billion years ago
- Sex probably evolved 1-2 billion years ago
What are the costs of sexual reproduction?
- Energy and time spent finding a mate
- Risk of not finding a mate
- Potential disease transmission during mating
- Increased predation risk during copulation
- Higher energy requirements at the cellular level, as meiotic division is more costly than mitosis.
- Recombination in sexual reproduction can break up favourable combinations of alleles
Describe: Muller’s Ratchet
Genomes of an asexual population accumulate deleterious mutations in an irreversible manner
- Concept highlights the advantage of sexual reproduction
- Recombination can shuffle mutations and reinstate the fittest class, effectively ‘turning back’ the ratchet.
How does sex accelerate adaptive evolution compared to parthenogenesis?
Allowing for the combination of beneficial alleles from different lineages
- In sexual reproduction, two favourable mutations do not need to arise in the same lineage
- They can come from two different parents and be combined in their offspring
- Makes adaptation faster in sexually reproducing species compared to asexually reproducing ones
- Where each favourable mutation has to occur in the same lineage
What are the long-term benefits of sexual reproduction?
Faster adaptive evolution
Prevention of accumulation of deleterious mutations
Maintains variety of genetic combinations
- Lead to greater diversity and resilience in a population
Why is asexual reproduction not as successful in the long term, despite its short-term benefits?
- Accumulation of harmful mutations (Muller’s Ratchet)
- Slower pace of adaptive evolution
Most asexually reproducing species are relatively short-lived on an evolutionary timescale
What are the short-term benefits of sexual reproduction?
Generates greater number of different genotypes that can adapt to a wider range of conditions
- In unpredictable environments, sexual reproduction can supply genetic diversity and result in more resilient offspring
What does it mean for an organism to be facultatively sexual?
Switch between sexual and asexual reproduction depending on environmental conditions
Favourable, predictable conditions
- Asexual reproduction dominates to quickly produce many offspring
Unpredictable Conditions
- Sexual reproduction is favoured as it provides genetic diversity
- Increasing the chance of survival in varying conditions
How do strawberries adapt their reproduction strategy according to environmental conditions?
Facultative sexual strategy
- Shifting between asexual and sexual reproduction based on environmental conditions
Reproduce asexually
- Near the parent plant, where the environment is predictable and matches the mother’s environment.
For seed dispersal
- Offspring’s environment may require different adaptations, strawberries reproduce sexually
- Ensures variety of genotypes that can potentially adapt to different conditions
How do aphids demonstrate facultative sexuality?
Typically reproduce asexually for rapid population growth
- switch to sexual reproduction in response to unfavorable or unpredictable conditions
- ensure genetic diversity
What is the Red Queen hypothesis and how does it relate to sexual reproduction?
In the context of sexual reproduction
- making it harder for parasites to adapt to their host
- If offspring were clones (asexual reproduction)
- parasite perfecting its strategy against one member of the species would then be equipped to overcome any member of the species
Through sexual reproduction
- offspring have a mix of genes
- thus a parasite adapted to infect the parent might not be as successful with the offspring
What is the Frozen Niche Variation model?
Explains why sexual reproduction is favored over asexual reproduction
- individuals of the same species may inhabit slightly different niches due to individual genetic differences, essentially expanding the ecological “space” a species can occupy
- On the other hand, identical clones would have identical niches
- limiting the population’s adaptability to diverse environments and conditions
- suggests that sexual reproduction is beneficial because it can generate a variety of genotypes that can exploit a range of environmental niches.
What are the potential short and long term benefits of sexual reproduction?
What is positive frequency-dependant selection?
Fitness of a trait increases as it becomes rarer
Can produce a cycle
- trait increases until it becomes common enough to cause a reduction in fitness
- trait frequency decreases
What is negative frequency-dependant selection?
Fitness of a trait increases as it becomes more common
- think this is the wrong way round
What is an example of negative frequency-dependant selection?
Color polymorphisms Cepaea nemoralis snails by negative frequency-dependent selection
- predators, the song thrush
- forms a search image for the most common morph
- resulting in much greater predation pressure on the common than the rare morph
How does negative assortative mating modify genotype frequencies at specific loci?
Increased heterozygosity
- When individuals of dissimilar characteristics.
- There is an increased likelihood of offspring with heterozygous genotypes as the relevant loci.
- Maintains population genetic diversity.
In what order and in what contexts do crossing over and independent assortment occur?
Crossing Over: Occurs first - during prophase I of meiosis.
- homologous chromosomes pair up and exchange segments of DNA.
- chromosomes then contain genetic (alleles) material from both parents
Independent Assortment: Later - during metaphase I of meiosis
- chromosomes line up at the cell’s equator.
- homologous pairs of chromosomes (tetrads) align randomly
- creates a mix of maternal and paternal chromosomes distributed into gametes.
