Podcast
Questions and Answers
What is the main topic of the lecture on February 16th?
What is the main topic of the lecture on February 16th?
- Quantitative Trait Loci (correct)
- Genetic linkage
- Recombination
- Polygenic traits
Which term describes traits that vary continuously among individuals?
Which term describes traits that vary continuously among individuals?
- Recombination
- Linkage equilibrium
- Epistasis
- Polygenic trait (correct)
What process generates genetic variation by mixing alleles?
What process generates genetic variation by mixing alleles?
- Linkage equilibrium
- Linkage disequilibrium
- Recombination (correct)
- Quantitative genetics
Which term refers to the occurrence of an allele at one locus being nonrandomly associated with another locus?
Which term refers to the occurrence of an allele at one locus being nonrandomly associated with another locus?
What is the focus of the lecture on February 14th?
What is the focus of the lecture on February 14th?
Which term describes the interaction between alleles at different loci?
Which term describes the interaction between alleles at different loci?
What best defines quantitative genetics?
What best defines quantitative genetics?
What is the main focus of quantitative trait locus (QTL) analysis?
What is the main focus of quantitative trait locus (QTL) analysis?
How does the degree of linkage between different loci relate to their distance on the same chromosome?
How does the degree of linkage between different loci relate to their distance on the same chromosome?
What is the main goal of genome-wide association studies (GWAS)?
What is the main goal of genome-wide association studies (GWAS)?
How does linkage disequilibrium in cats reflect their breed history?
How does linkage disequilibrium in cats reflect their breed history?
What does the term 'linkage disequilibrium' refer to in genetics?
What does the term 'linkage disequilibrium' refer to in genetics?
How does quantitative trait locus (QTL) analysis help in understanding phenotypic traits?
How does quantitative trait locus (QTL) analysis help in understanding phenotypic traits?
What is the main purpose of detecting linkage disequilibrium?
What is the main purpose of detecting linkage disequilibrium?
Why are single-nucleotide polymorphisms (SNPs) often used in genetics studies?
Why are single-nucleotide polymorphisms (SNPs) often used in genetics studies?
What type of mutations do not change the protein sequence?
What type of mutations do not change the protein sequence?
What does a faster evolution rate at nonsynonymous sites compared to synonymous sites indicate?
What does a faster evolution rate at nonsynonymous sites compared to synonymous sites indicate?
What is the dN/dS ratio used to determine in molecular evolution?
What is the dN/dS ratio used to determine in molecular evolution?
In the context of selection on DNA sequences, what does a slower evolution rate than synonymous sites indicate?
In the context of selection on DNA sequences, what does a slower evolution rate than synonymous sites indicate?
What phenomenon describes the rapid spread of an adaptive allele through a population?
What phenomenon describes the rapid spread of an adaptive allele through a population?
How do alleles that are strongly selected leave a signature in neighboring alleles?
How do alleles that are strongly selected leave a signature in neighboring alleles?
What does tracking phylogenies back in time lead to in gene trees?
What does tracking phylogenies back in time lead to in gene trees?
In the context of phylogenies, what can positive selection cause?
In the context of phylogenies, what can positive selection cause?
Which type of tree depicts ancestor-descendent relationships of species?
Which type of tree depicts ancestor-descendent relationships of species?
What can tracking gene trees help to understand in molecular evolution?
What can tracking gene trees help to understand in molecular evolution?
Why don't gene trees and species trees always match?
Why don't gene trees and species trees always match?
What term describes the type of trait exhibited by the mutation from G to T?
What term describes the type of trait exhibited by the mutation from G to T?
In genetic terms, what do the Gs and Ts represent?
In genetic terms, what do the Gs and Ts represent?
What is the main focus of the neutral theory of molecular evolution?
What is the main focus of the neutral theory of molecular evolution?
In the context of molecular evolution, what aspect is being compared when analyzing mutation rate vs. molecular evolution rate?
In the context of molecular evolution, what aspect is being compared when analyzing mutation rate vs. molecular evolution rate?
Which process is primarily responsible for shaping DNA sequences when considering selection on DNA sequences?
Which process is primarily responsible for shaping DNA sequences when considering selection on DNA sequences?
What aspect of DNA sequences is mainly influenced by nonsynonymous mutations?
What aspect of DNA sequences is mainly influenced by nonsynonymous mutations?
'Homologous' traits in genetic loci refer to traits that are ___.
'Homologous' traits in genetic loci refer to traits that are ___.
What type of mutation does not alter the amino acid sequence of a protein?
What type of mutation does not alter the amino acid sequence of a protein?
According to the neutral theory of molecular evolution, what is the main driver of most evolution at the molecular level?
According to the neutral theory of molecular evolution, what is the main driver of most evolution at the molecular level?
Which statement accurately describes the rate of molecular evolution compared to the mutation rate?
Which statement accurately describes the rate of molecular evolution compared to the mutation rate?
Which type of mutation is more likely to be subject to selection due to altering the protein sequence?
Which type of mutation is more likely to be subject to selection due to altering the protein sequence?
In the context of DNA sequences, what does the term 'substitution' refer to?
In the context of DNA sequences, what does the term 'substitution' refer to?
What is the primary factor on which selection acts in DNA sequences?
What is the primary factor on which selection acts in DNA sequences?
Which process involves the co-option of a particular gene or network for a totally different function due to a mutation?
Which process involves the co-option of a particular gene or network for a totally different function due to a mutation?
What evolutionary event can occur as a result of the reorganization of a preexisting regulatory network?
What evolutionary event can occur as a result of the reorganization of a preexisting regulatory network?
Which mechanism is especially likely to lead to new functions if duplicated?
Which mechanism is especially likely to lead to new functions if duplicated?
What process can result in the evolution of complex traits like the ability to consume citrate in E.coli?
What process can result in the evolution of complex traits like the ability to consume citrate in E.coli?
The evolution of snake venoms involved which mechanism?
The evolution of snake venoms involved which mechanism?
Which term refers to a homologous gene that arises through duplication?
Which term refers to a homologous gene that arises through duplication?
'Promiscuous proteins' are capable of carrying out two functions and are especially likely to take on new functions if ___.
'Promiscuous proteins' are capable of carrying out two functions and are especially likely to take on new functions if ___.
'Horizontal gene transfer' is a source of innovation primarily in which organisms?
'Horizontal gene transfer' is a source of innovation primarily in which organisms?
What is the term for the phenomenon where a gene acquires a new function that it did not have before?
What is the term for the phenomenon where a gene acquires a new function that it did not have before?
Which process involves the creation of new genes by copying a pre-existing gene within the genome?
Which process involves the creation of new genes by copying a pre-existing gene within the genome?
In the context of genetic evolution, what term describes the movement of genes between different species?
In the context of genetic evolution, what term describes the movement of genes between different species?
Which term refers to proteins that can interact with multiple partners, potentially leading to the evolution of new functions?
Which term refers to proteins that can interact with multiple partners, potentially leading to the evolution of new functions?
What process involves the utilization of existing genes for new functions or in different tissues?
What process involves the utilization of existing genes for new functions or in different tissues?
How does a de novo gene differ from a gene arising from duplication?
How does a de novo gene differ from a gene arising from duplication?
What is a common outcome of horizontal gene transfer in bacteria?
What is a common outcome of horizontal gene transfer in bacteria?
Which statement best describes the role of promiscuous proteins in evolutionary processes?
Which statement best describes the role of promiscuous proteins in evolutionary processes?
What phenomenon can lead to the creation of brand new genes that did not previously exist in a genome?
What phenomenon can lead to the creation of brand new genes that did not previously exist in a genome?
How can horizontal gene transfer contribute to the evolution of new traits or adaptations?
How can horizontal gene transfer contribute to the evolution of new traits or adaptations?
Which process involves the accidental emergence of new traits due to the promiscuous nature of certain proteins?
Which process involves the accidental emergence of new traits due to the promiscuous nature of certain proteins?
In the context of evolution, what does gene duplication primarily contribute to?
In the context of evolution, what does gene duplication primarily contribute to?
Which mechanism is responsible for the creation of paralogs, genes that arise from gene duplication events?
Which mechanism is responsible for the creation of paralogs, genes that arise from gene duplication events?
How do duplicated genes provide a platform for evolutionary innovation?
How do duplicated genes provide a platform for evolutionary innovation?
What role does horizontal gene transfer play in the integration of foreign genetic material into a host genome?
What role does horizontal gene transfer play in the integration of foreign genetic material into a host genome?
How can promiscuous proteins contribute to evolutionary changes in an organism?
How can promiscuous proteins contribute to evolutionary changes in an organism?
What is a common outcome of gene recruitment processes in terms of trait evolution?
What is a common outcome of gene recruitment processes in terms of trait evolution?
What is the main focus of artificial selection?
What is the main focus of artificial selection?
In the context of evolution, what role do humans play in artificial selection?
In the context of evolution, what role do humans play in artificial selection?
How have humans impacted the evolution of domestic dogs?
How have humans impacted the evolution of domestic dogs?
What is a direct outcome of pigeon breeding due to artificial selection?
What is a direct outcome of pigeon breeding due to artificial selection?
How do pesticides and herbicides act as agents of selection?
How do pesticides and herbicides act as agents of selection?
What impact has cod fishing had on Atlantic cod?
What impact has cod fishing had on Atlantic cod?
Why are herbarium specimens important in the study of evolution?
Why are herbarium specimens important in the study of evolution?
What evolutionary change has been observed in male horns due to hunting?
What evolutionary change has been observed in male horns due to hunting?
What refers to the reproductive capacity of an individual, such as the number and quality of eggs or sperm?
What refers to the reproductive capacity of an individual, such as the number and quality of eggs or sperm?
Which of the following describes a situation where females are limited by the number of mates they can obtain?
Which of the following describes a situation where females are limited by the number of mates they can obtain?
What term refers to differential reproductive success resulting from competition for mates?
What term refers to differential reproductive success resulting from competition for mates?
Which selection process involves competition between males for access to females?
Which selection process involves competition between males for access to females?
What type of selection results from females being selective about their choice of mates?
What type of selection results from females being selective about their choice of mates?
Why can sexual dimorphisms result from intrasexual selection?
Why can sexual dimorphisms result from intrasexual selection?
Which factor predicts which sex will experience stronger sexual selection?
Which factor predicts which sex will experience stronger sexual selection?
What is the phenomenon where females choose mates based on traits that benefit their offspring's fitness?
What is the phenomenon where females choose mates based on traits that benefit their offspring's fitness?
Which evolutionary concept explains the crazy ornaments seen in males as a result of female preference for these traits?
Which evolutionary concept explains the crazy ornaments seen in males as a result of female preference for these traits?
What is the underlying theory suggesting that females choose mates based on indicators of genetic quality, such as health or vigor?
What is the underlying theory suggesting that females choose mates based on indicators of genetic quality, such as health or vigor?
Which effect makes sexual reproduction beneficial due to the ability to outpace parasites?
Which effect makes sexual reproduction beneficial due to the ability to outpace parasites?
Based on the text, which hypothesis suggests that female choice can be related to reducing parasite load?
Based on the text, which hypothesis suggests that female choice can be related to reducing parasite load?
What drives the evolution of sexual reproduction according to the evidence presented?
What drives the evolution of sexual reproduction according to the evidence presented?
What phenomenon can lead to more parasite infections correlated with a higher number of males in a population?
What phenomenon can lead to more parasite infections correlated with a higher number of males in a population?
"Arbitrary choice" and "Good genes" are contrasting explanations for what aspect of evolutionary biology?
"Arbitrary choice" and "Good genes" are contrasting explanations for what aspect of evolutionary biology?
Why might sexual reproduction be considered costly compared to asexual reproduction?
Why might sexual reproduction be considered costly compared to asexual reproduction?
What is a potential drawback of sexual reproduction in terms of genetic mutations?
What is a potential drawback of sexual reproduction in terms of genetic mutations?
How does sexual reproduction facilitate adaptation to changing environments compared to asexual reproduction?
How does sexual reproduction facilitate adaptation to changing environments compared to asexual reproduction?
What is one of the primary advantages of sexual reproduction in terms of genetic diversity?
What is one of the primary advantages of sexual reproduction in terms of genetic diversity?
Which of the following is NOT a consequence of sexual reproduction according to the text?
Which of the following is NOT a consequence of sexual reproduction according to the text?
What is a major limitation faced by asexual reproduction discussed in the text?
What is a major limitation faced by asexual reproduction discussed in the text?
In terms of genetic variation, what does Muller's ratchet in asexual populations primarily result in?
In terms of genetic variation, what does Muller's ratchet in asexual populations primarily result in?
What evolutionary factor is affected due to Muller's ratchet in asexual populations over time?
What evolutionary factor is affected due to Muller's ratchet in asexual populations over time?
'Search cost' is mentioned as a disadvantage of which type of reproductive mechanism according to the text?
'Search cost' is mentioned as a disadvantage of which type of reproductive mechanism according to the text?
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Study Notes
Quantitative Traits and Genetics
- Quantitative traits vary continuously among individuals and have a complex genetic basis
- Polygenic traits are influenced by many genetic loci and can interact with environment (phenotypic plasticity)
- Quantitative genetics is the study of the genetic mechanisms and evolution of continuous phenotypic traits
- Linkage: mixing and matching alleles; recombination generates genetic variation by mixing alleles
- Linkage disequilibrium: nonrandom association of alleles at different loci, often due to close proximity on the same chromosome
Detecting Linkage Disequilibrium
- Map of linkage disequilibrium can be used to identify regions of the genome associated with particular traits
- Example: Alhaddad et al. (2013) found linkage disequilibrium in cats reflects breed history
Quantitative Trait Locus (QTL) Analysis
- Links traits with genes using recombination to understand the link between phenotype and genotype
- Often uses single-nucleotide polymorphisms (SNPs)
- Example: Hopi Hoekstra found QTL analysis identifies genomic regions responsible for coat color in mice
Genome-Wide Association Studies (GWAS)
- Identifies variants and genomic regions associated with particular traits
- Example: Palmer and Kronforst (2020) found GWAS identified genes involved in mimicry in swallowtail butterflies
Selective Sweeps and Genetic Hitchhiking
- Selective sweeps: adaptive allele spreads through a population more quickly than recombination acts to separate it from neighboring alleles
- Genetic hitchhiking: strongly selected alleles are frequently found in a population surrounded by the same set of alleles at neighboring locations
- Example: Tian et al. (2009) found selective sweeps and genetic hitchhiking in maize
Evolution of Genome Size
- Genome size varies tremendously across species
- Bacterial genome size dependent mainly on number of genes
- Eukaryotic genomes vary more in size due to noncoding DNA
- Example: Lynch (2010) found evolution of genome size seems connected to mutation rate
Phylogenetic Trees and Gene Trees
- Phylogenetic trees: hypothesizes of the evolutionary relationships among different taxa
- Gene trees: phylogenetic trees of DNA sequences at a particular locus
- Gene trees do not always match species trees
- Example: Hebert et al. (2004) and Jarvis et al. (2014) found gene trees do not always match species trees
Artificial Selection
- Definition: selection of traits by humans
- Related to natural selection
- Examples: domestication of plants and animals, breeding of pigeons, and pesticide resistance in houseflies
Evolution of Complex Traits
- Complex traits evolve through gene duplication and co-option
- Example: evolution of eyespots in butterflies
- Networks that result in complex traits are rooted in ancient genetic toolkits
Constraints on Evolution
- Limitations to asexual reproduction (Muller's ratchet and genetic load)
- Asymmetrical parental care alters the operational sex ratio
- Sexual selection: differential reproductive success resulting from competition for mates
Sexual Selection
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Intrasexual selection (male-male competition)
-
Intersexual selection (female choice)
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Benefits: direct (e.g. food, protection) and indirect (e.g. better genetic quality)
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Examples: red-winged blackbird, cherry barb, and golden metallic stag beetle### Evolution of Sexual Reproduction
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Sexual reproduction evolved as a mechanism to combine beneficial mutations and generate novel genotypes.
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Asexual reproduction can lead to faster multiplication of lineages, but sexual reproduction provides advantages.
Costs of Sexual Reproduction
- Twofold cost of sex: sexual reproduction is costly due to limited number of reproducing individuals and search costs.
- Disadvantages of sexual reproduction include reduced relatedness, risk of sexually transmitted infections, and ploidy issues.
Advantages of Sexual Reproduction
- Combining beneficial mutations enables faster evolution and clearance of deleterious mutations.
- Sexual reproduction allows organisms in finite populations to better adapt to changing environments.
Limitations of Asexual Reproduction
- Muller's ratchet: asexual populations accumulate irreversible, deleterious mutations over generations, leading to genetic load.
- Genetic load: the burden of accumulated deleterious mutations increases over time, limiting asexual reproduction.
Key Concepts
- Hermaphrodite: an organism that produces both sperm and eggs.
- Parthenogenesis: a type of asexual reproduction where offspring are produced without fertilization.
- Ploidy: the number of sets of chromosomes in an organism's cells.
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