96 Questions
What is the main topic of the lecture on February 16th?
Quantitative Trait Loci
Which term describes traits that vary continuously among individuals?
Polygenic trait
What process generates genetic variation by mixing alleles?
Recombination
Which term refers to the occurrence of an allele at one locus being nonrandomly associated with another locus?
Linkage disequilibrium
What is the focus of the lecture on February 14th?
Paleontologist Roundtable
Which term describes the interaction between alleles at different loci?
Epistasis
What best defines quantitative genetics?
Study of genetic mechanisms and evolution of continuous phenotypic traits
What is the main focus of quantitative trait locus (QTL) analysis?
Identifying genomic regions responsible for coat color in mice
How does the degree of linkage between different loci relate to their distance on the same chromosome?
The degree of linkage decreases as the distance between loci increases
What is the main goal of genome-wide association studies (GWAS)?
Identifying variants and genomic regions associated with specific traits
How does linkage disequilibrium in cats reflect their breed history?
Linkage disequilibrium increases with breed history
What does the term 'linkage disequilibrium' refer to in genetics?
Association between specific genetic variants that are inherited together
How does quantitative trait locus (QTL) analysis help in understanding phenotypic traits?
By studying recombination to establish the link between phenotype and genotype
What is the main purpose of detecting linkage disequilibrium?
To understand the relationship between phenotype and genotype
Why are single-nucleotide polymorphisms (SNPs) often used in genetics studies?
To identify genomic regions associated with specific traits
What type of mutations do not change the protein sequence?
Synonymous mutations
What does a faster evolution rate at nonsynonymous sites compared to synonymous sites indicate?
Positive selection
What is the dN/dS ratio used to determine in molecular evolution?
Signature of positive selection
In the context of selection on DNA sequences, what does a slower evolution rate than synonymous sites indicate?
Purifying selection
What phenomenon describes the rapid spread of an adaptive allele through a population?
Selective sweep
How do alleles that are strongly selected leave a signature in neighboring alleles?
Genetic hitchhiking
What does tracking phylogenies back in time lead to in gene trees?
Coalescence nodes representing common ancestry
In the context of phylogenies, what can positive selection cause?
Shallow coalescence
Which type of tree depicts ancestor-descendent relationships of species?
Species tree
What can tracking gene trees help to understand in molecular evolution?
Neutral theory of molecular evolution
Why don't gene trees and species trees always match?
Positive selection on DNA sequences
What term describes the type of trait exhibited by the mutation from G to T?
Synapomorphy
In genetic terms, what do the Gs and Ts represent?
Alleles
What is the main focus of the neutral theory of molecular evolution?
Genetic drift as the main driver of molecular evolution
In the context of molecular evolution, what aspect is being compared when analyzing mutation rate vs. molecular evolution rate?
Rates of synonymous mutations vs. nonsynonymous mutations
Which process is primarily responsible for shaping DNA sequences when considering selection on DNA sequences?
Natural selection
What aspect of DNA sequences is mainly influenced by nonsynonymous mutations?
Protein structure and function
'Homologous' traits in genetic loci refer to traits that are ___.
Unrelated and functionally different
What type of mutation does not alter the amino acid sequence of a protein?
Silent mutation
According to the neutral theory of molecular evolution, what is the main driver of most evolution at the molecular level?
Genetic drift
Which statement accurately describes the rate of molecular evolution compared to the mutation rate?
Different types of DNA segments evolve at different rates.
Which type of mutation is more likely to be subject to selection due to altering the protein sequence?
Nonsynonymous mutation
In the context of DNA sequences, what does the term 'substitution' refer to?
A mutation that becomes fixed in a lineage
What is the primary factor on which selection acts in DNA sequences?
Amino acid sequence
Which process involves the co-option of a particular gene or network for a totally different function due to a mutation?
Gene duplication
What evolutionary event can occur as a result of the reorganization of a preexisting regulatory network?
Gene duplication
Which mechanism is especially likely to lead to new functions if duplicated?
Promiscuous proteins
What process can result in the evolution of complex traits like the ability to consume citrate in E.coli?
Gene duplication
The evolution of snake venoms involved which mechanism?
Gene recruitment
Which term refers to a homologous gene that arises through duplication?
Paralog
'Promiscuous proteins' are capable of carrying out two functions and are especially likely to take on new functions if ___.
Are duplicated
'Horizontal gene transfer' is a source of innovation primarily in which organisms?
Bacteria and archaea (and some eukaryotes)
What is the term for the phenomenon where a gene acquires a new function that it did not have before?
De novo gene formation
Which process involves the creation of new genes by copying a pre-existing gene within the genome?
Gene duplication
In the context of genetic evolution, what term describes the movement of genes between different species?
Horizontal gene transfer
Which term refers to proteins that can interact with multiple partners, potentially leading to the evolution of new functions?
Promiscuous proteins
What process involves the utilization of existing genes for new functions or in different tissues?
Gene recruitment
How does a de novo gene differ from a gene arising from duplication?
De novo genes are formed from non-coding DNA sequences.
What is a common outcome of horizontal gene transfer in bacteria?
Increased genetic diversity
Which statement best describes the role of promiscuous proteins in evolutionary processes?
'Promiscuous' proteins interact with multiple partners, aiding evolutionary flexibility.
What phenomenon can lead to the creation of brand new genes that did not previously exist in a genome?
Gene recruitment
How can horizontal gene transfer contribute to the evolution of new traits or adaptations?
By transferring genes between different species
Which process involves the accidental emergence of new traits due to the promiscuous nature of certain proteins?
Promiscuous proteins
In the context of evolution, what does gene duplication primarily contribute to?
Increasing the number of identical copies of existing genes
Which mechanism is responsible for the creation of paralogs, genes that arise from gene duplication events?
Replication errors
How do duplicated genes provide a platform for evolutionary innovation?
By creating entirely new genes with novel functions
What role does horizontal gene transfer play in the integration of foreign genetic material into a host genome?
Facilitating the acquisition of novel traits from other species
How can promiscuous proteins contribute to evolutionary changes in an organism?
By catalyzing new chemical reactions and functions
What is a common outcome of gene recruitment processes in terms of trait evolution?
Cooption of existing genes for novel functions and adaptations
What is the main focus of artificial selection?
Producing variations in plants and animals
In the context of evolution, what role do humans play in artificial selection?
Agents of selection
How have humans impacted the evolution of domestic dogs?
Creating diverse breeds through artificial selection
What is a direct outcome of pigeon breeding due to artificial selection?
Many breeds and variants
How do pesticides and herbicides act as agents of selection?
Induce resistance in target species
What impact has cod fishing had on Atlantic cod?
Decreased size and age at maturity
Why are herbarium specimens important in the study of evolution?
To document changes in plant morphology over time
What evolutionary change has been observed in male horns due to hunting?
Shortening of male horns
What refers to the reproductive capacity of an individual, such as the number and quality of eggs or sperm?
Fecundity
Which of the following describes a situation where females are limited by the number of mates they can obtain?
Operational sex ratio
What term refers to differential reproductive success resulting from competition for mates?
Sexual selection
Which selection process involves competition between males for access to females?
Intrasexual selection
What type of selection results from females being selective about their choice of mates?
Intersexual selection
Why can sexual dimorphisms result from intrasexual selection?
To compete with other individuals in intrasexual competition
Which factor predicts which sex will experience stronger sexual selection?
Operational sex ratio
What is the phenomenon where females choose mates based on traits that benefit their offspring's fitness?
Good Genes Hypothesis
Which evolutionary concept explains the crazy ornaments seen in males as a result of female preference for these traits?
Fisherian runaway selection
What is the underlying theory suggesting that females choose mates based on indicators of genetic quality, such as health or vigor?
Good Genes model
Which effect makes sexual reproduction beneficial due to the ability to outpace parasites?
Red Queen effect
Based on the text, which hypothesis suggests that female choice can be related to reducing parasite load?
Hamilton-Zuk Hypothesis
What drives the evolution of sexual reproduction according to the evidence presented?
Maximizing reproductive success variance
What phenomenon can lead to more parasite infections correlated with a higher number of males in a population?
"Red Queen" effect
"Arbitrary choice" and "Good genes" are contrasting explanations for what aspect of evolutionary biology?
Female choice in animals
Why might sexual reproduction be considered costly compared to asexual reproduction?
Ploidy
What is a potential drawback of sexual reproduction in terms of genetic mutations?
Masking deleterious mutations
How does sexual reproduction facilitate adaptation to changing environments compared to asexual reproduction?
Allows for faster generation of novel genotypes
What is one of the primary advantages of sexual reproduction in terms of genetic diversity?
Combining beneficial mutations
Which of the following is NOT a consequence of sexual reproduction according to the text?
Multiple advantages over asexual reproduction
What is a major limitation faced by asexual reproduction discussed in the text?
Muller's ratchet accumulation of deleterious mutations
In terms of genetic variation, what does Muller's ratchet in asexual populations primarily result in?
Irreversible accumulation of harmful mutations
What evolutionary factor is affected due to Muller's ratchet in asexual populations over time?
"Burden of accumulated deleterious mutations"
'Search cost' is mentioned as a disadvantage of which type of reproductive mechanism according to the text?
"Asexual reproduction"
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
-
Intrasexual selection (male-male competition)
-
Intersexual selection (female choice)
-
Benefits: direct (e.g. food, protection) and indirect (e.g. better genetic quality)
-
Examples: red-winged blackbird, cherry barb, and golden metallic stag beetle### Evolution of Sexual Reproduction
-
Sexual reproduction evolved as a mechanism to combine beneficial mutations and generate novel genotypes.
-
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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