8.5 Coalescent Theory: Gene Trees and Genealogies

What is the primary focus of coalescent theory?

How do gene trees differ from species trees or population trees?

In the context of coalescent theory, what does the term 'coalescent point' refer to?

Consider a population of diploid organisms. According to coalescent theory, what happens when tracing the ancestry of gene copies backward in time?

What is a major advantage of the coalescent approach in population genetics?

What is the approximate probability that any particular pair of gene copies shares a common ancestor in the previous generation in a Wright-Fisher population of N diploid individuals?

In a neutral coalescent model for a diploid Wright-Fisher population of size N, what is the average time to coalescence for a randomly chosen pair of gene copies?

In the coalescent process for a neutral locus, where do most of the coalescent events between pairs of gene copies occur?

How does population size affect coalescent times?

What does the 'bugs-in-a-box' metaphor represent in the context of coalescent theory?

In the 'bugs-in-a-box' metaphor, what does the act of one bug eating another represent?

Consider a neutral locus in a population. How do allelic differences arise among a set of gene copies?

If all the gene copies in a population coalesce recently, what can be inferred about the total amount of genetic variation in the population?

For a neutral locus, what two separate processes determine the distribution of variation?

How does the strength of genetic drift relate to the coalescent time at a neutral locus?

If two randomly selected alleles are separated by an average of 4N generations and the mutation rate is μ per locus per generation, how many mutations are expected to differentiate the alleles on average?

What can researchers infer from coalescent times obtained from patterns of genetic variation?

How does positive selection influence the coalescent time of a new allele?

Why do alleles under balancing selection often have coalescent points further in the past compared to neutral or positively selected alleles?

Consider a population where a new allele arises and is subject to positive selection. What is the expected effect on neutral variation at the locus under selection?

In a population experiencing balancing selection at a particular locus, what is the expected long-term outcome regarding the alleles under selection?

Which of the following scenarios will most likely lead to a gene genealogy with a coalescent point far from the present?

If a researcher observes a locus with significantly less neutral variation than expected under neutrality, what evolutionary force is most likely acting on that locus?

How can researchers use coalescent models to learn about the demographic history of a population?

Which of the following statements best describes the relationship between gene trees and species trees?

In the context of coalescent theory, what is the significance of the shape of the coalescent tree?

Suppose a population of lizards on an isolated island has 250 diploid individuals. According to coalescent theory, approximately how many generations would it take, on average, for two randomly chosen gene copies at a neutral locus to coalesce?

Consider a locus in a population of birds. Researchers find evidence that a particular allele at this locus is under balancing selection. How would this affect their interpretation of the locus's gene genealogy?

In a theoretical population that perfectly fits the Wright-Fisher model, a scientist samples 10 gene copies from a large population (N) of diploid individuals. The probability that any particular pair of these gene copies shares a common ancestor in the immediate previous generation is approximately 1/(2N). Given this, which one of the following accurately describes the likelihood of multiple coalescent events occurring simultaneously?

Suppose a scientist is studying two populations of fish. Population A has a constant size of 1,000 diploid individuals, while population B has a constant size of 500 diploid individuals. According to coalescent theory, what differences would the scientist expect to observe in the coalescent trees of these two populations?

Imagine a population of beetles where a new allele arises that confers resistance to a common pesticide. This allele quickly spreads through the population due to strong positive selection. According to coalescent theory, what would you expect to observe at the locus of this resistance allele, compared to a neutral locus in the same population?

Scientists are studying a gene in wild tomatoes. They find that two distinct alleles at this gene have persisted in the population for a very long time, with neither allele reaching fixation. Which evolutionary force is most likely responsible for this pattern, and how would it affect the gene genealogy at this locus?

Researchers are investigating a newly discovered population of butterflies. They analyze the genetic variation at several neutral loci and use coalescent models to estimate the historical population size. Based on this analysis, they conclude that the population experienced a severe bottleneck event in the past. What would be the most likely signature of this bottleneck in the coalescent trees of these loci?

In applying coalescent theory to analyze the genetic history of a population, what critical assumption must be met to effectively separate the genealogical process from the mutational process at a given locus?

Consider a scenario where a researcher aims to use coalescent theory to infer past demographic changes in a population of migratory birds, focusing on a set of neutral loci. However, gene flow between this population and a neighboring one is suspected but not well quantified. How might unmodeled gene flow influence the accuracy of coalescent-based demographic inferences?

Two research groups are studying the same population of penguins, but analyze different sets of genetic markers. Group A focuses on microsatellites, which have a high mutation rate, while Group B examines single nucleotide polymorphisms (SNPs), with a much lower mutation rate. How might this difference in marker choice affect their coalescent-based analyses of the penguin population's history?

What is the primary application of gene trees in the context of coalescent theory?

In coalescent theory, what does tracing the ancestry of gene copies backward in time reveal?

What does a coalescent tree represent?

In a mathematical model of the coalescent process for a neutral locus, what does the model primarily predict?

Consider a neutral locus in a large Wright-Fisher population of N diploid individuals. What is the chance that any particular pair of gene copies shares a common ancestor in the previous generation?

In the coalescent process for a neutral locus, where do most of the coalescent events between pairs of gene copies occur relative to the present?

How does population size affect coalescent times, assuming a Wright-Fisher population of constant size?

In the 'bugs-in-a-box' metaphor, what does a coalescent event correspond to?

According to coalescent theory, how do allelic differences arise among a set of gene copies at the same locus?

Researchers can infer coalescent times from patterns of genetic variation and thereby estimate which historical demographic parameters?

How does positive selection influence the coalescent time of a new allele compared to a neutral allele?

What does the randomness associated with the particular genealogical history and the randomness associated with where mutations arise along this coalescent tree contribute to?

In a population that perfectly fits the Wright-Fisher model, a scientist is studying two neutral loci, Locus A and Locus B. Locus A exhibits a higher level of genetic diversity than Locus B. According to coalescent theory, what inference can be made regarding the effective population size experienced at these loci?