Molecular Ecology: Population Genetics, Hybridization, and Phylogeography

What is isolation by distance (IBD)?

A phenomenon where gene flow between populations is inversely proportional to the geographic distances between them.

How is isolation by distance commonly assessed?

By regressing log-transformed estimates of gene flow against log-transformed geographic distances.

What statistical test is used to assess the significance of the correlation between genetic and geographic distances?

The Mantel test.

What relationship was found between pairwise FST and geographic distances in the 'Baru' populations?

A strong relationship with a correlation coefficient of r = 0.499.

What is a classic example of a species with very low dispersal?

Cepaea nemoralis, a land snail that typically moves only a few meters in its lifetime.

What is the significance of brooding corals and sea anemones in dispersal studies?

They do not release planktonic larvae, limiting their dispersal capabilities.

What is myrmecochory?

A form of seed dispersal where seeds are dispersed by ants, typically over short distances (<2 m per generation).

What did the study of neotropical rain forest birds reveal about genetic differentiation?

Canopy species had lower levels of genetic differentiation compared to understory species.

What are direct methods to measure dispersal?

Mark-recapture, radio tracking, and parentage studies.

What is the main limitation of mark-recapture methods?

They are time-consuming and often yield limited returns.

What advantage does radio tracking provide in dispersal studies?

It provides data on all movements of monitored individuals.

What do parentage studies compare to determine dispersal distances?

The genotypes of offspring and potential parents.

What is Nem in the context of gene flow?

The number of breeding adults that are migrants between populations.

What assumptions does the calculation of Nem make?

It assumes no selection or mutation and that populations are in migration-drift equilibrium.

What are the advantages of dispersal?

Avoiding inbreeding, locating new sites with fewer competitors, and escaping pathogens or predators.

What are some disadvantages of dispersal?

Lack of suitable new sites or mates and potential predation during the process.

What was observed in the damselfly Calopteryx splendens regarding immigrant females?

Males discriminated against immigrant females, affecting gene flow.

What is hybridization in the context of genetics?

The integration of DNA from different species through interbreeding.

What role does landscape genetics play in studying dispersal?

It examines how landscape features influence genetic variation and gene flow.

What is the Mantel test used for in genetic studies?

To assess the correlation between genetic and geographic distances without assuming independence.

What is the significance of studying isolation by distance in conservation?

It helps understand genetic diversity and population structure, informing conservation strategies.

How does genetic drift affect populations?

It decreases genetic variation within populations and increases genetic distance between them.

What is the relationship between genetic divergence (FST) and gene flow?

FST is inversely related to the amount of gene flow between populations.

What are three natural barriers to species dispersal?

Water bodies, mountain ranges, and dry land.

How do mountain ranges affect species distribution?

They limit the distribution of many ground-dwelling species.

What is an example of a barrier to gene flow for eastern chipmunks?

Major rivers serve as important barriers to gene flow.

What does landscape genetics combine?

Population genetics, spatial statistics, and landscape ecology.

What is the aim of landscape genetics?

To understand the relationship between habitats and gene flow.

What does a homogeneous landscape imply about population structure?

It suggests no population structure (panmixia) due to random mating.

What is the difference between landscape genetics and phylogeography?

Landscape genetics focuses on recent gene flow, while phylogeography examines historical gene flow over evolutionary time scales.

What types of data are commonly used in landscape genetics?

Highly variable markers like microsatellites and SNPs, along with environmental data.

What is introgression in the context of genetics?

The integration of segments of DNA through hybridization and backcrossing between species.

How does hybridization contribute to genetic diversity?

It generates genetic diversity and provides new pathways for adaptive evolution.

What is the estimated frequency of interspecific hybridization in vascular plants?

Approximately 25%.

Name two well-known cases of introgression.

Heliconius butterflies and Helianthus sunflowers.

What happens during an initial hybridization event?

An F1 hybrid is produced from two distinct species.

What is the outcome of backcrossing an F1 hybrid into one of the parent species?

It results in the introgression of the other species' DNA into the genome.

What is the effect of introgression in neutral regions of the genome?

Introgressed segments will be broken into smaller pieces by recombination over time.

What is the significance of Mantel tests in landscape genetics?

They compare genetic distances to geographic or environmental distances to identify patterns of isolation-by-distance.

What happens to introgressed segments if they are maladaptive in a region of the genome?

They are likely purged from the population.

Under what condition will introgressed segments containing an adaptive allele increase in frequency?

If the allele provides an ecological advantage.

What is population differentiation?

The process by which isolated populations become genetically distinct due to mutations and genetic drift.

What is the equation that describes the relationship between gene flow and population differentiation?

Nem = estimated number of breeding adults that are migrants; Ne is effective population size and m is the migration rate (or # of immigrants). Populations are maximally divergent when Nem = 0.

How does small increases in gene flow affect population differentiation?

Small increases in gene flow markedly reduce population differentiation (FST).

What does a Nem value of 0.25 indicate about population differentiation?

It leads to FST = 0.5.

What does a Nem value of 1 indicate about population differentiation?

It leads to FST = 0.20.

How does gene flow affect genetic diversity?

Gene flow increases genetic diversity.

What is the relationship between adaptation and gene flow?

Adaptation can occur even with high gene flow if natural selection is stronger than gene flow.

What is the fitness value (w) of a phenotype that leaves the largest number of viable descendants?

The fitness value is considered to be 1.

How is the selection coefficient (s) calculated?

s = 1 - w.

What is the selection coefficient against genotype aa if its fitness is 0.75?

s = 1 - 0.75 = 0.25.

What does a selection coefficient of 0.32 indicate in the context of the peppered moth?

Light-colored moths had a survival chance approximately 32% lower than dark-colored moths.

How do drift and selection interact in light of gene flow?

If selection is strong relative to population size, drift effects are negligible; if selection is weak, drift predominates.

What does incomplete lineage sorting (ILS) refer to?

A scenario where ancestral alleles coexist in a population, leading to shared alleles among descendant populations without introgression.

What is the ABBA-BABA test used for?

To distinguish between introgression and incomplete lineage sorting.

What does Configuration 1 (BBAA) in the ABBA-BABA test suggest?

It suggests a mutation in the common ancestors of populations 1 and 2.

What does Configuration 2 (ABBA) in the ABBA-BABA test indicate?

It suggests a mutation in lineage 3 followed by introgression from 3 to 2.

What is the significance of the Neandertal genome sequencing in 2010?

It indicated that Neandertals shared more genetic variants with present-day humans in Eurasia than with those in sub-Saharan Africa.

What does the ABBA configuration represent in the context of the ABBA-BABA test?

The ABBA configuration involves allele A being present in populations 1 and 2, and allele B in population 3.

What does the BABA configuration indicate in the ABBA-BABA test?

The BABA configuration involves allele B being present in populations 1 and 3, and allele A in population 2.

What are the implications of observing both ABBA and BABA at similar frequencies?

It suggests that only incomplete lineage sorting occurred, without introgression.

What happens to the frequencies of ABBA and BABA if introgression occurs?

The frequencies of ABBA and BABA should be statistically different.

What is the significance of Darwin's finches in evolutionary biology?

They are known for their remarkable diversity in beak form and function, rapid population changes, and unclear patterns of speciation and hybridization.

What methods were used in the genome sequencing of Darwin's finches?

Whole genome sequencing of 120 individuals from 15 Geospiza species and 2 outgroup species, creating a reference genome from G. fortis.

What does the Fst scan method detect in the study of beak morphology?

It detects regions with extreme differentiation among populations, indicating potential adaptive traits.

What is a haplotype?

A haplotype is a group of alleles inherited together from a single parent.

What role does the ALX1 gene play in beak morphology?

ALX1 is crucial for craniofacial development and is associated with variations in beak morphology.

What is the purpose of quantitative trait loci (QTL) analysis?

QTL analysis links phenotypic data with genotypic data to explain the genetic basis of variation in complex traits.

What are the requirements for conducting a QTL analysis?

Two or more genetically different strains regarding the trait of interest and genetic markers that distinguish between these parental lines.

What is the difference between quantitative traits and qualitative traits?

Quantitative traits vary along a gradient and are often regulated by multiple genes, while qualitative traits are discrete and typically influenced by a single gene.

What are SNPs in the context of QTL analysis?

Single nucleotide polymorphisms (SNPs) are the prominent type of genetic markers used in QTL analysis.

What does the term 'adaptive radiation' refer to?

Adaptive radiation refers to the rapid evolution of diversely adapted species from a common ancestor in response to environmental changes.

What is the significance of introgression in evolutionary studies?

Introgression can lead to the transfer of alleles between species, affecting genetic diversity and adaptation.

What is the role of environmental pressures in the evolution of Darwin's finches?

Environmental pressures drive rapid changes in beak phenotype, influencing survival and reproductive success.

What does the term 'incomplete lineage sorting' (ILS) mean?

ILS refers to the phenomenon where ancestral genetic variation is retained in descendant lineages, leading to non-tree-like patterns of genetic variation.

What is the predicted outcome when both ABBA and BABA configurations are observed?

It predicts that if only ILS occurred, ABBA and BABA should be found at similar frequencies due to stochastic processes.

What does the term 'ecologically important traits' refer to?

Traits that determine the relationship between organisms and their environments, often involved in adaptation.

What is the primary goal of molecular ecology?

To understand the genetic basis of ecologically important traits and how organisms adapt to their environments.

What is the significance of the branching order of Darwin's finches?

It helps to understand their evolutionary relationships and whether they exhibit introgression or hybridization.

What does 'genome-wide ABBA-BABA test' reveal about populations?

It reveals the frequency of ABBA and BABA configurations, indicating levels of introgression between populations.

What does the term 'patchworks of alleles' imply in the context of finch genomes?

It suggests that the genomes of some finches contain genetic contributions from multiple ancestral lineages.

What are SNPs in the context of QTL mapping?

SNPs (Single Nucleotide Polymorphisms) are the prominent type of genetic markers used in QTL mapping.

What is the purpose of QTL mapping?

QTL mapping aims to identify the genetic basis of phenotypic traits by associating specific genetic markers with quantitative traits.

What are the two main types of QTL mapping?

1) Linkage mapping, which relies on families or segregating progeny; 2) Association mapping, which relies on unrelated individuals from the same population.

What is the process of creating F1 individuals in QTL mapping?

Parental lines are crossed to create F1 individuals, followed by crosses among F1s or backcrosses with one parental line.

What is the significance of statistical techniques in QTL mapping?

Statistical techniques evaluate the probability that a marker or an interval between markers is associated with a QTL affecting the trait.

What does linkage mapping focus on?

Linkage mapping focuses on individuals with known relationships to identify segregating genetic markers that predict organismal phenotypes.

How does association mapping differ from linkage mapping?

Association mapping is based on historical recombination events over generations, while linkage mapping relies on known relationships among individuals.

What is a centiMorgan (cM)?

A centiMorgan is a unit of recombinant frequency used to measure genetic distance, indicating a 1% chance of separation between two markers due to crossing over.

Why is a high density of genetic markers critical in QTL mapping?

A high density of markers is essential to accurately identify individual genes responsible for traits, as it allows for finer mapping of causal loci.

What are haplotypes in the context of association mapping?

Haplotypes are regions inherited as blocks with no recombination, which can be shuffled together over generations in association mapping.

What is the role of predictive markers in linkage mapping?

Predictive markers are genetic markers that are near causal loci and tend to segregate together, helping to predict phenotypic outcomes.

What does the horizontal line in QTL mapping plots represent?

The horizontal line marks the significance threshold for determining whether a marker is significantly associated with a QTL.

What is the significance of scoring in QTL mapping?

Scoring assesses the presence or absence of markers in relation to phenotypes to identify associations between genotype classes and traits.

What does a 5% recombination rate between loci indicate?

A 5% recombination rate suggests that the loci are likely in the same linkage group, as it is much lower than the 50% expected for loci on different chromosomes.

What is the implication of detecting a marker-trait association?

If a marker-trait association is detected, the marker is considered linked to the QTL, indicating a potential genetic influence on the trait.

What is the goal of interpreting QTL mapping results?

The goal is to identify candidate genes for future experimental studies to verify their role in the phenotype.

What does the term 'segregating progeny' refer to?

Segregating progeny refers to offspring from parents with different traits that are genetically controlled, allowing for the study of allele segregation.

What is the relationship between recombination events and QTL mapping?

Recombination events are utilized in QTL mapping to identify alleles with quantitative effects on phenotypes, enhancing the mapping accuracy.

How do linkage groups relate to chromosomes?

Linkage groups are formed by markers that are often found together on the same chromosomes, approximating the physical structure of chromosomes.