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# BIOL 108 Introduction to Biological Diversity
## Topic 7: Evolution of Population
> Lecture A2
> Yan-yin Wang
Types Evolutionary Changes
Macroevolution : Evolutionary change above the species level.
Example: phenotypic variations of coat colours.
Populations, and only populations evolve under the pressure of natural selection.
Population is the smallest unit of evolutionary change.
Definition: A group of individuals of the same species
that live in the same area and interbreed, producing fertile offspring.
Microevolution : Evolutionary change below the species level; change in the allele frequencies in a population over generations.
Accounts for evolutionary changes of both phenotypes and genotypes.
> https://evolution.berkeley.edu/evolution-at-different-scales-micro-to-macro/
> # Macro vs micro evolution.
Basic Terminology of Genetics
Chromosome : A cellular structure carrying genetic material.
Gene : A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses).
Genetic studies focus on genes being discrete unit of information.
Molecular studies focus on genes being specific sequences.
Alleles : Alternative versions of a gene that correspond to different combination of nucleotides in each version.
Each sexually reproducing parent give one chromosome to offspring called homologous chromosome.
Each chromosome has one set of allele.
Each allele usually remain separate, the seemingly blended phenotypes are results of incomplete dominance.
> # Structure and location of DNA.
> # Alleles on chromosome.
> https://microbenotes.com/alleles/
Microevolution in Populations
Microevolution : Evolutionary change below the species level; change in the allele frequencies in a population over generations.
Gene pool : The aggregate of all copies of every type of allele at all loci in every individual in a population.
Geographically separated populations of the same species may have distinct gene pool, if interbreeding is not possible.
Individuals within a population share alleles by interbreeding and producing fertile offspring.
The frequencies of alleles in the gene pool are changed in the process.
> Upadhyay, SK, Parihar, RD, Dhiman, U, Developmental Biology & Evolution (2019) Vikas Publishing House
> # Conceptual representation of gene pools.
Genotypic Variations Make Evolution Possible
Variations in heritable traits provide materials for natural selection.
A prerequisite for evolution.
Genotypic variation : The variability in genotypes within a population.
One of the main components of biodiversity.
A given individual has a specific genotype.
From genotypic variation to microevolution:
Interbreeding of individuals with different genotypes.
Increase in different genetic make-up (e.g. alleles) in the gene pool.
Phenotypic variations arise due to alteration of genetic make-up.
> Fukushima, K., & Pollock, D. D. (2023). Detecting macroevolutionary genotypephenotype associations using error-corrected rates of protein convergence. Nature Ecology & Evolution ,7(1), 155-170.
> # Connection between genotype and phenotype.
Selection Factors Influencing Allele Frequencies
Phenotype is a product of both inherited genotypes and environmental influences.
Not all phenotypes can be inherited (e.g. scars).
Not all phenotypes are subjected to natural selection.
Natural selection can only act on variations with a genetic components.
> https://www.sharks.org/blog/2020/6/8/squid-vs-shark
> # Scars on the oceanic whitetip shark, Carcharhinus longimanus .
Source of Genotypic Variation
Mutation, gene duplication, and recombination are sources of new genes and alleles.
Mutations : Random changes in the nucleotide sequence of an organisms genetic make-up (usually DNA sequence).
Characteristics of mutation:
Mutations occur only randomly.
Natural selection does not create the correct mutations.
Mutations can be beneficial, neutral, or deleterious for the current environment.
Mutations create new alleles.
Only mutations in gamete-producing cells (eggs or sperms) are heritable in sexually reproducing taxa.
> Anderson, H., Salonen, M., Toivola, S., Blades, M., Lyons, L. A., Forman, O. P., ... & Lohi, H. (2024). A new Finnish flavor of feline coat coloration,salmiak, is associated with a 95 kb deletion downstream of the KIT gene. Animal Genetics .
# Mutations in genome lead to new allele responsible for the tuxedo coat in feral cats in Finland. Source of Genotypic Variation
Mutations : Changes in the nucleotide sequence of an organisms genetic make-up (usually DNA sequence).
Types of mutations:
Small scale:
Point mutations: A single change in nucleotide base.
Insertions/deletions: Addition or removal of one or small number of nucleotide bases.
Large structural changes: Major alterations (usually damages) in structure of DNA.
Example: UV radiations cause damages to the DNA helix.
> # Sickle cell anemia.
> Khurmi, N., Gorlin, A., & Misra, L. (2017). Perioperative considerations for patients with sickle cell disease: a narrative review. Canadian Journal of Anesthesia ,64 (8), 860.
Source of Genotypic Variation
Mutation creates new alleles, and the accumulation of many mutations can lead to evolutionary changes in both genotypes and phenotypes.
How often do mutations occur?
Rates of mutation are overall low in animals and plants.
Prokaryotes (e.g. bacteria) has much higher rates of mutations compared to eukaryotes (e.g. human).
Example: Approximately 60 to 100 new mutations are accumulated per generation in human.
> # The rate of mutations passed on per generation in 68 species of vertebrate animal.
> Bergeron, L. A., & Zhang, G. (2023). Rate at which mutations are passed to offspring established for various animal species. NATURE.
Source of Genotypic Variation
Mutation, gene duplication, and recombination are sources of new genes and alleles.
Gene duplication : Copies of nucleotide sequence of an organisms genetic make-up.
Types of duplication:
Small segments: Duplication of DNA segments that affects multiple genes
Gene duplication: Copy of the entire gene.
Whole-genome duplication: Doubling of the entire genome.
Supply of new materials for evolution and for increased genome complexity.
> Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., ... & Schartl, M. (2021). Giant lungfish genome elucidates the conquest of land by vertebrates. Nature ,590 (7845), 284-289.
# Phylogeny of major vertebrate branches.
> https://www.science.org/doi/10.1126/sciadv.abj0829
# A lung fish. Source of Genotypic Variation
Mutation, gene duplication, and recombination are sources of new genes and alleles.
Gene recombination: Shuffling of existing alleles into new combinations during sexual reproduction.
Meiosis : a type of cell division in sexually reproducing organisms to produce gametes that contains half the chromosomes as the original cells.
Types of gene recombination:
During meiosis:
Cross-over: The reciprocal exchange of homologous genetic material.
Independent assortment: Different genes are independently separate from one another.
Random Fertilization: Combination of gametes with different versions of chromosomes.
> https://www.genome.gov/genetics-glossary/Crossing-Over
> # Cross over during meiosis.
Source of Genotypic Variation
Mutation, gene duplication, and recombination are sources of new genes and alleles.
Gene recombination: Shuffling of existing alleles into new combinations during sexual reproduction.
Meiosis : a type of cell division in sexually reproducing organisms to produce gametes that contains half the chromosomes as the original cells.
Types of gene recombination:
During meiosis:
Cross-over: The reciprocal exchange of homologous genetic material.
Independent assortment: Different genes are independently separate from one another.
Random Fertilization: Combination of gametes with different versions of chromosomes.
> Rahman, M. (2014). Independent assortment of seed color and hairy leaf genes in Brassica rapa L. Canadian Journal of Plant Science ,94 (4), 615-620.
> # Independent assortment of seed colours and leaf hairiness in Brassica rapa .
Factors Influencing Allele Frequencies
Natural selection, genetic drift, and gene flow are the mechanisms that alter allele frequencies in populations.
Natural selection leads to adaptive evolution.
Adaptation : Inherited characteristics of an organism that enhances its survival and reproduction in a specific environment.
Relative fitness : The contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals in the population.
Genetic drift and gene flow are non-adaptive processes.
Changes in allele frequency that do not increase the populations capacity to adapt to its environment.
> https://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648/#:~:text=Natural%20selection%2C%20genetic%20drift%2C%20and%20gene%20flow% 20are%20the%20mechanisms,Weinberg%20assumptions%2C%20and%20evolution%20occurs.
> #Allele-frequency change under directional selection.
Factors Influencing Allele Frequencies
Natural selection
Only natural selection can lead to adaptation.
Natural selection acts on existing variations (not creating the adapted traits).
Better adapted individuals can generally produce more offsprings and contribute their alleles to the gene pool in greater proportions.
Types of natural selection on populations:
Directional selection
Disruptive/diversifying selection
Stablising selection
> Choudhuri, S. (2014). Bioinformatics for beginners: genes, genomes, molecular evolution, databases and analytical tools . Elsevier.
> Types of natural selection on populations.
Natural Selection: Directional selection
Directional selection : Natural selection in which individuals at one end of the phenotypic range survive or reproduce more successfully than do other individuals.
A response to consistent selection pressure.
Example: global temperature rises steadily.
Under directional selection:
Genotypic variations lead to new phenotype with higher relative fitness.
Frequency distribution of phenotypic variations shifts towards adapted traits.
Theoretically, genotypic variations in a population would be reduced.
> Choudhuri, S. (2014). Bioinformatics for beginners: genes, genomes, molecular evolution, databases and analytical tools . Elsevier.
Types of natural selection on populations.
# Colour variations of the peppered moth, Biston betularia .
> https://butterfly-conservation.org/moths/why-moths-matter/amazing-moths/peppered-moth-and-natural-selection
Natural Selection: Disruptive Selection
Disruptive selection : Natural selection in which individuals at both ends of the phenotypic range survive or reproduce more successfully than do other individuals.
The intermediate phenotypic traits are less adapted than either one of the extremes.
Under disruptive selection:
Genotypic variations lead to more than one new phenotypes with higher relative fitness.
Frequency distribution of phenotypic variations shifts towards multiple adapted traits.
Frequency of the intermediate trait decline over time.
> Choudhuri, S. (2014). Bioinformatics for beginners: genes, genomes, molecular evolution, databases and analytical tools . Elsevier.
Types of natural selection on populations.
# Examples of disruptive selection from the threespine sticklebacks Gasterosteus aculeatus (a) and red crossbills Loxia curvirostra (b) .
> Rueffler, C., Van Dooren, T. J., Leimar, O., & Abrams, P. A. (2006). Disruptive selection and then what?. Trends in Ecology & Evolution ,21 (5), 238-245.
Natural Selection: Stabilising Selection
Stabilising selection : Natural selection in which individuals at intermediate or common variants of the phenotypic range survive or reproduce more successfully than do other individuals.
Under stabilising selection:
Conserve genotypic and phenotypic (often functional) traits and select against the extremes (often deleterious).
Common phenomenon of stabilising selection.
The mean (average) of the trait stays the same, but its variance (spread) is reduced.
> Choudhuri, S. (2014). Bioinformatics for beginners: genes, genomes, molecular evolution, databases and analytical tools . Elsevier.
Types of natural selection on populations.
# Examples of stabilising selection in human birth weight .
> https://digfir-published.macmillanusa.com/pol2e/asset/img_ch15/c15_fig14.html
Genetic Drift
Natural selection, genetic drift, and gene flow are the mechanisms that alter allele frequencies in populations.
Genetic Drift : Random events that change allele frequency in a population.
Characteristics of genetic drift:
Non-adaptive factor.
Allele frequency fluctuate over generations.
Rare alleles may be lost, which could reduce the genotypic diversity.
Genetic drift has greater impacts on smaller populations.
> # Illustration of genetic drift during expansion of a population.
> Excoffier, L., & Ray, N. (2008). Surfing during population expansions promotes genetic revolutions and structuration. Trends in ecology & evolution ,23 (7), 347-351.
Genetic Drift: Theoretical Example
Comparisons on the size of populations.
A meager population with 100 individuals.
A population with 5000 individuals. Genetic Drift: Theoretical Example
Comparisons on the initial allele frequency (i.e. how rare a genotype is).
A population with 2000 individuals, and the initial frequency is 0.5.
A population with 2000 individuals, and the initial frequency is 0.01.
Oh, I want to play that game: https://heavywatal.github.io/driftr.js/ Types of Genetic Drift in Nature
Types of genetic drift:
Bottleneck effect : Population size suddenly decreases due to changes in environment, which alters the allele frequency in the gene pool.
Characteristic of bottleneck effect:
Events take place within the range of natural habitat.
Caused by disastrous events (e.g. earthquake, mass hunting by human).
Initial result is the distinct reduction in population size (e.g. 1000 to 10).
Allele frequency post bottle neck effect is not representative of the original population.
If the population remains small, genetic diversity may continue to decline under the effects of genetic drift.
# Schematic illustration of relative allelic frequencies through 4 generations for 14 microsatellite loci.
> https://www.nature.com/scitable/topicpage/genetic-drift-bottleneck-effect-and-the-case-1118/
# The bearded vulture,
Gypaetus barbatus .
> Gautschi, B., Mller, J. P., Schmid, B., & Shykoff, J. A. (2003). Effective number of breeders and maintenance of genetic diversity in the captive bearded vulture population. Heredity ,91 (1), 9-16.
An Example in Canada
Greater prairie chicken once lived in both Canada and the United States.
They are extirpated in Canada.
Caused by loss of natural habitat, which in turn lead to a bottleneck in gene pool in the population living in the US.
The genetic variation dropped.
# Grouses that still live in Canada.
https://www.wildernesscommittee.org/news/environmentalists-want-ottawa-save-albertas-sage-grouse
The extirpation of Greater prairie chickens.
Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., Jackson, R. B., & Rawle, F. E. (2021). Campbell Biology, Canadian Edition (4th ed.). Pearson Canada.
https://www.thecanadianencyclopedia.ca/en/article/grouse Types of Genetic Drift in Nature
Types of genetic drift:
Founder effect : Selected few individuals of the population become isolated and form a new population, whose gene pool also become distinct.
These selected individuals are called founding individuals.
Characteristic of founder effect:
Events take place by forming a new population.
The founding individuals carry a fraction of the total gene pool from the original population.
The alleles of the founding individuals become dominant in the gene pool of the new population.
The allele frequency in the original population unchanged.
> By Founder_effect.png: User:Qz10derivative work: Zerodamage - This file was derived from: Founder effect.png:, Public Domain, https://commons.wikimedia.org/w/index.php?curid=20570109
> Illustration of founder effect.
Founder Effect in Nature
The silvereye (# Zosterops lateralis ) show distinct make-up in genomes between island populations.
Sendell Price, A. T., Ruegg, K. C., Robertson, B. C., & Clegg, S. M. (2021). An Island hopping bird reveals how founder events shape genome wide divergence. Molecular Ecology , 30 (11), 2495-2510.
# The distribution of silvereyes.
https://birdsoftheworld.org/bow/species/silver3/cur/introduction
# The silvereye, Zosterops lateralis. Lack of Founder Effect
The absence of founder effect can be detrimental to local ecosystems.
Example: The oriental shrimp ( Palaemon macrodactylus )
Lejeusne, C., Saunier, A., Petit, N., Bguer, M., Otani, M., Carlton, J. T., ... & Green, A. J. (2014). High genetic diversity and absence of founder effects in a worldwide aquatic invader. Scientific Reports , 4(1), 5808.
# The oriental shrimp, Palaemon macrodactylus .
https://www.marylandbiodiversity.com/view/18747 Key Points of Genetic Drift
Genetic drift alter the allele frequency in a random fashion.
Genetic drift can lead to loss of genotypic diversity (e.g. a trait becomes fixed or absent).
Genetic drift has larger impact on smaller populations.
Genetic drift can cause deleterious trait to be fixed in small population. Gene Flow
Natural selection, genetic drift, and gene flow are the mechanisms that alter allele frequencies in populations.
Gene flow : The transfer of alleles between populations.
Characteristic of gene flow:
Events take place via movements of fertile individual or gametes (e.g. seed or pollens).
Can introduce new genotypic variations to receiving population.
Work against genetic drift and can slow down adaptation if selection pressure exists.
Gene flow reduces genetic variations between population over time.
Population become similar (i.e. homogenised) over time.
> #Allele-frequency change under directional selection.
> https://evolution.berkeley.edu/evolution-101/mechanisms-the-processes-of-evolution/gene-flow/
> #Seeds of the weed, Galium aparine (Cleavers).
> https://inspection.canada.ca/en/plant-health/seeds/seed-testing-and-grading/seeds-identification/galium-aparine
Example of Gene Flow
Gene flows in black bear population using wildlife corridor in Banff National Park.
# Distribution of bear population in Banff.
Sawaya, M. A., Kalinowski, S. T., & Clevenger, A. P. (2014). Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park. Proceedings of the Royal Society B: Biological Sciences, 281(1780), 20131705.
# Black (left) and grizzly (right) bears.
https://www.basecampgroup.com/blog/banffs-beasts/ Gene Flow and Local Adaptation
Local adaptation : Populations become more adjusted to their local environment, often gain adapted traits that are absent in population from other locations.
Gene flows can reduce the fitness of the receiving population (i.e. how well the population is adapting to the local environment).
Non-adaptive or deleterious traits are introduced (e.g. water snake in Lake Erie).
Gene flow can increase the fitness of the receiving population.
Adaptive traits are introduced.
Example: Alleles related to insecticide resistance can be passed from one population of god-forsaken mosquitos to another.
> Gene flow impacts the camouflage of water snakes in Lake Erie between Ontario and Ohio..
> Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., Jackson, R. B., & Rawle, F. E. (2021). Campbell Biology, Canadian Edition (4th ed.). Pearson Canada.
Evolutionary changes
Three factors that influence allele frequencies in population.
Natural selection is the only factor that leads to adaptive traits.
Genetic drift and gene flow are non-adaptive.
Two more factors that can introduce evolutionary changes.
Extinction : the last individual of a species is dead, or its survival cannot be considered beyond reasonable doubts.
Extirpation : The local extinction of a species in a certain geographical area, but its populations can be found in other locations.
> # The extinct elephant bird, Aepyornis ingens from Madagascar.
> https://www.getaway.co.za/travel-news/new-discovery-elephant-bird-lineage-identified-from-ancient-eggshells/
How Populations Maintain Genotypic Variation
Neutral variation : Genotypic variation that does not provide a selective advantage or disadvantage (i.e. they are neither adaptive nor deleterious).
Example: Blood types in human.
Genotypical variation is maintained by the combination of:
Gaining new alleles (mutation, duplication, and recombination, etc.).
Stabilising selection.
Gene flow.
Balancing selection.
> Human blood type is an example of neutral variation.
> https://www.getaway.co.za/travel-news/new-discovery-elephant-bird-lineage-identified-from-ancient-eggshells/
Balancing Selection
Balancing Selection : A type of natural selection that maintains genetic diversity (i.e. stable allele frequencies) within a population.
Populations that cover a wide range of habitats (or even globally distributed) could promote balancing selection.
Mechanisms of balancing selection
Heterozygote advantage : Individuals with two different alleles of a given gene (heterozygote; e.g. Aa) are more adaptive to the environment compared to individuals with two identical copies of alleles (homozygote; e.g. AA or aa).
Natural selection tends to maintain heterozygotes.
Both stablising and directional selection can lead to heterozygote advantage.
> # Different coat colours in rock pocket mice, Chaetodipus intermedius .
> Nachman, M. W., Hoekstra, H. E., & D'Agostino, S. L. (2003). The genetic basis of adaptive melanism in pocket mice. Proceedings of the National Academy of Sciences ,100 (9), 5268-5273.
Balancing Selection
Mechanisms of balancing selection
Heterozygote advantage .
Frequency-dependent selection : Selection in which
the fitness of a phenotype depends on how common the phenotype is in a population.
Often occur between species (e.g. predation, competition, parasitism) between individuals within population.
Types of frequency-dependent selection:
Positive: fitness of a phenotype increases as it becomes more common in the population.
Example: Cooperative hunting between grouper fish and moray eels.
Negative: fitness of a phenotype decreases as it becomes more common in the population.
> #Atlantic Goliath Grouper, Epinephelus itajara (top) and the moray eels, muraenids. The two can have some jolly cooperations!
> https://www.neaq.org/animal/goliath-grouper/
> https://www.scuba.com/blog/meet-the-morays/
Balancing Selection
Mechanisms of balancing selection
Heterozygote advantage .
Frequency-dependent selection : Selection in which the fitness of a phenotype depends on how common the phenotype is in a population.
Often occur between species (e.g. predation, competition, parasitism) between individuals within population.
Types of frequency-dependent selection:
Positive: fitness of a phenotype increases as it becomes more common in the population.
Example: Cooperative hunting between grouper fish and moray eels.
Negative: fitness of a phenotype decreases as it becomes more common in the population.
Example: The number of lefty and righty in the scale-eating cichlid population would be balanced to equal over time.
> #Jaw morphologies of the scale-eating cichlid,
> Perissodus microlepis .
> Takeuchi, Yuichi; Hori, Michio; Tada, Shinya; Oda, Yoichi (2016). Morphological mouth asymmetry of scale-eating cichlid fish Perissodus microlepis.. PLOS ONE. Figure. https://doi.org/10.1371/journal.pone.0147476.g001
Perfect Trait Does Not Exit in Nature
Purpose of adaptation and genes is to be continuously passed on.
Genotypic and phenotypic traits only need to be good enough.
Natural selection is not random, but it also lack an ultimate goal.
> Individuals adapt to the environment as they struggle to survive, without a predestined path to traverse.
> A blueprint evolving from primitive to advance does not exit.
Natural selection can only act on existing variations.
> Genotypes and phenotypes subjected to natural selection arise randomly.
Existing traits from prior adaptations limits the range that natural selection can operate.
> No do-over in nature (e.g. whales have flippers instead of fish fins).
Environmental changes occur in various way, which can influence natural selection.