ECCB 400 exam 2

Why are DNA repair systems important?

They maintain DNA functionality and correct damage before it leads to mutations.

What is the primary ecological significance of sticklebacks?

They adapt their skeletons when moving from ocean to freshwater environments.

What is the scientific name of the threespine stickleback?

Gasterosteus aculeatus

How quickly can evolutionary changes occur in sticklebacks?

In some cases, changes can occur in as little as 10 years.

What genetic change is associated with increased teeth in freshwater sticklebacks?

A mutant allele in a regulatory region of the gene Bmp6.

What was the first analysis of Neanderthal DNA published?

It was mtDNA extracted from the first Neanderthal fossil discovered in 1997.

How do human and Neanderthal mtDNA sequences compare?

They differ by approximately 27.2 substitutions.

What does the mtDNA information suggest about the common ancestor of Neanderthals and modern humans?

It dates back to approximately 550,000 to 690,000 years ago.

What are molecular markers used for in ecological studies?

They infer genetic relationships and predict DNA behavior under ecological scenarios.

What are the two types of uniparentally inherited organelle genomes?

Mitochondria (mtDNA) and plastids (cpDNA).

What are some shared features of organelles?

They typically contain circular chromosomes, have smaller genomes than nuclear DNA, and are located outside the cell nucleus.

What is the primary function of animal mitochondrial DNA?

It is responsible for cellular respiration.

What is the typical length of animal mtDNA?

About 16-18 kb long.

Why is mtDNA popular in ecological studies?

It is easy to work with, has a high mutation rate, lacks recombination, is haploid, and tends to evolve neutrally.

What is the difference between alleles and polymorphisms?

Alleles are specific DNA versions at a locus, while polymorphisms refer to the presence of two or more alleles at a locus in a population.

What is a haplotype?

A group of DNA variants or genes inherited together from a single parent.

How does mtDNA inheritance differ from nuclear DNA?

mtDNA is haploid and uniparentally inherited, making it more sensitive to demographic events.

What happens to mtDNA haplotypes during population bottlenecks?

Fewer mtDNA haplotypes survive compared to nuclear haplotypes.

What is the relative size of mitochondrial DNA (mtDNA) compared to nuclear genome?

mtDNA population size is approximately ¼ of nuclear genome population size.

How is mtDNA inherited?

mtDNA is haploid and maternally inherited.

What types of substitutions accumulate on animal mtDNA?

Deleterious substitutions are rare, beneficial substitutions are probably rare, and neutral substitutions are common.

What are the differences between mutations and substitutions?

Mutations are genetic changes within species, while substitutions are genetic changes between species.

What is a unique feature of plant mitochondrial DNA?

Plant mtDNA regularly undergoes recombination, leading to gene rearrangements and duplications.

How does the rate of nucleotide substitutions in plant mtDNA compare to animal mtDNA?

Nucleotide substitutions in plant mtDNA are up to 100 times slower than those in animal mitochondria.

What is the typical size range of plant mitochondrial DNA?

Plant mtDNA size varies from 40 to 2,500 Mbp.

What is the typical size of animal mitochondrial DNA?

Animal mtDNA is approximately 16 kb to 253 kb.

What is chloroplast DNA (cpDNA) and its typical size?

cpDNA is often used as a molecular marker in plants and is around 120-220 kbp.

How is cpDNA inherited in most angiosperms?

cpDNA is maternally inherited.

What are the advantages of using cpDNA as a molecular marker?

cpDNA is uniparentally inherited, structurally stable, and contains microsatellites that evolve faster.

What is the Park Grass Experiment (PGE)?

The PGE is the oldest running ecological experiment, begun in 1856, studying the effects of nutrient variation on plant populations.

What selective mechanism was proposed by Alfred Russell Wallace?

The Wallace effect, which suggests that low fitness of hybrids selects for reproductive isolation between diverging populations.

What is the significance of the sweet vernal grass (Anthoxanthum odoratum) in the PGE?

It was studied to observe reinforcement of reproductive isolation based on cpDNA inheritance.

What are the two types of chromosomes found in the nucleus of most animals?

Sex chromosomes and autosomes.

What is a unique feature of the mammalian Y chromosome?

It is inherited patrilineally and is the only effectively haploid mammalian chromosome.

What is the mutation rate of Y chromosomes compared to other chromosomes?

The mutation rate of Y chromosomes is higher than that of other chromosomes.

What are pseudoautosomal regions (PARs) in the Y chromosome?

PARs are small regions at the tips of the Y chromosome where recombination occurs with the X chromosome.

What is the role of PAR1 regions in the Y chromosome?

PAR1 regions are required for appropriate segregation of the Y chromosome during mitosis and meiosis.

Where does recombination occur on the Y chromosome?

Recombination occurs only in two small pseudoautosomal regions (PARs) at the tips of the chromosome.

What is required for the Y chromosome to segregate properly during cell division?

The PAR1 regions of X and Y chromosomes are required for proper segregation.

What is the function of the SRY gene?

The SRY gene (sex-determining region Y) effectively converts an embryo into a male.

How can hybrids be identified from their DNA?

Hybrids can be identified because hybridization results in individuals that contain a mixture of alleles from both parental species.

What happens to nuclear markers over time in hybrids?

Nuclear markers will be eroded over time if hybrids continually back-cross to their parental species.

What is introgression in the context of hybridization?

Introgression is the movement of genes from one species into the gene pool of another, usually through repeated backcrossing of hybrids with one of its parent species.

What does a phylogeny of nuclear DNA markers suggest about the tree frogs of the genus Hyla?

It suggests that the two species are separated and there is no evidence of hybridization.

What does mtDNA analysis reveal about the relationship between H. arenicolor and H. wrightorum?

Some haplotypes of H. arenicolor are more similar to haplotypes of H. wrightorum, suggesting historical hybridization.

What would indicate no introgression from H. wrightorum to H. arenicolor?

If mtDNA from H. wrightorum specimens clustered with H. arenicolor mtDNA.

What is a molecular marker?

A molecular marker is a specific DNA sequence within an organism's genome used to identify and distinguish between individuals or populations.

What are co-dominant markers?

Co-dominant markers allow identification of all alleles present at a locus, distinguishing between homozygous and heterozygous individuals.

What is the significance of allele frequency in a population?

Allele frequency indicates how common a particular allele is in a population.

What are microsatellites?

Microsatellites, also known as simple sequence repeats (SSRs), are stretches of DNA consisting of tandem repeats of 1-6 base pairs.

How do microsatellites mutate compared to point mutations?

Microsatellites mutate much more rapidly, usually between 10^-2 and 10^-6 mutations per allele per generation, compared to point mutations at around 10^-9 to 10^-10.

What technique is used in DNA fingerprinting?

DNA fingerprinting is done using the polymerase chain reaction (PCR) to amplify microsatellites.

What was discovered by Alec Jeffreys regarding human DNA?

Alec Jeffreys discovered that certain human repeats are particularly variable in length between individuals, leading to the invention of DNA fingerprinting.

What does the presence of co-dominant markers allow researchers to do?

It allows researchers to calculate allele frequencies for populations.

What is the relationship between the number of alleles and the number of individuals in a diploid population?

In a diploid population, the total number of alleles at any autosomal locus is twice the number of individuals.

What is the expected number of alleles at an X chromosome locus in a diploid population with both males and females?

The expected number of alleles at an X chromosome locus is the sum of alleles from females (2 per female) and males (1 per male).

How do dominant markers differ from co-dominant markers?

Dominant markers reveal only a single dominant allele, while co-dominant markers identify all alleles present.

What is the role of multiple co-dominant markers in research?

They are used to generate data from different loci to avoid conclusions based on a single atypical locus.

What technique is used for DNA fingerprinting?

Polymerase chain reaction (PCR) amplifies microsatellites and analyzes individuals based on repetitive sequences.

What are single nucleotide polymorphisms (SNPs)?

SNPs are single base pair positions along a DNA sequence that vary between individuals, often biallelic.

What is the significance of SNPs compared to microsatellites?

SNPs are more numerous, found more often within or near genes, and provide more genetic variation.

What is the definition of adaptive radiation?

A rapid increase in the number of species descending from a common ancestor, characterized by ecological and morphological diversity.

How many species have been generated by cichlid adaptive radiations in East African lakes?

Between 250 (Tanganyika) and 500 (Malawi and Victoria) species per lake.

What are the four modes of speciation?

Allopatric, peripatric, parapatric, and sympatric.

What is allopatric speciation?

New species formed from geographically isolated populations.

What is peripatric speciation?

New species formed from a small population isolated at the edge of a larger population.

What is parapatric speciation?

New species formed from a continuously distributed population.

What is sympatric speciation?

New species formed within the range of the ancestral population.

Why are beetles considered a good example of speciation?

They are the most diverse and species-rich insect group, with over 380,000 described species.

What is the impact of genetic diversity on populations?

Genetic diversity is essential for evolution and adaptation, and low diversity can lead to inbreeding and reduced fitness.

How does genetic diversity affect ecosystems?

It influences the survival of species and populations, and genetically diverse plant communities support more diverse animal communities.

What is the relationship between genetic diversity and resilience to disturbance?

Genetically diverse communities are more resistant to disturbances.

What is the role of genetic analyses in conservation biology?

They help assess genetic diversity, which is crucial for the long-term viability of populations.

What is the significance of the cichlid adaptive radiation in Lake Victoria?

It involved hybrid ancestry and rapid speciation, with many species evolving or recolonizing after a dramatic desiccation event.

What is the purpose of population assignment tests in genetic studies?

To assign genetic markers to specific populations or species based on genetic data.

What is the estimated timeframe for cichlid radiations in Lake Victoria?

Less than 15,000 to 100,000 years for Victoria and less than 5 million years for Malawi.

What is the importance of analyzing genetic diversity in single populations?

It provides foundational data for comparing multiple populations and understanding their viability.

What is the relationship between genetically diverse plant communities and animal communities?

Genetically diverse plant communities support more diverse animal communities and are more resistant to disturbance.

What are the two measures of genetic diversity?

Allele frequencies and genotype frequencies.

What is Hardy-Weinberg equilibrium (HWE)?

A state where genotype frequencies within a population follow a predictable pattern under certain conditions.

What are the allele frequencies for a locus with alleles A (dominant) and a (recessive)?

Frequency of A is p and frequency of a is q, where p + q = 1.

What is the formula for genotype frequencies in Hardy-Weinberg equilibrium?

p² + 2pq + q² = 1.

What assumptions must be met for a population to be in Hardy-Weinberg equilibrium?

Random mating, no selection, negligible migration or mutation, effectively infinite population size, and normal Mendelian inheritance.

How is the frequency of homozygous dominant (AA) genotypes calculated under HWE?

The probability is p², where p is the frequency of the dominant allele.

How is the frequency of homozygous recessive (aa) genotypes calculated under HWE?

The probability is q², where q is the frequency of the recessive allele.

How is the frequency of heterozygous (Aa) genotypes calculated under HWE?

The probability is 2pq, as there are two ways to obtain a heterozygote.

What is observed heterozygosity (Ho)?

The number of heterozygotes at a locus divided by the total number of sampled individuals.

What is gene diversity (h)?

The probability that two alleles randomly chosen from the population will be different, calculated from allele frequencies.

What does it imply if observed heterozygosity (Ho) is less than expected heterozygosity (He)?

It may indicate a deviation from Hardy-Weinberg equilibrium due to factors like non-random mating or natural selection.

What is the Wahlund effect?

It occurs when genetic data from two or more populations with different allele frequencies are combined, leading to an overestimate of expected heterozygosity.

What are null alleles?

Alleles that are present but not detected, which can lead to underestimating observed heterozygosity.

What is nucleotide diversity (π)?

A measure of polymorphism representing the average number of nucleotide differences per site between any two DNA sequences in a population.

What influences genetic diversity in populations?

A multitude of factors, including environmental conditions, population size, and reproductive strategies.

What is the significance of the scarlet tiger moth in genetic studies?

It serves as an example for calculating allele and genotype frequencies in the context of Hardy-Weinberg equilibrium.

What is the expected frequency of heterozygotes under Hardy-Weinberg equilibrium?

It is represented by 2pq, where p and q are the frequencies of the two alleles.

What is the expected outcome when allele frequencies are equal (p=q=0.5)?

The frequency of heterozygotes is at its maximum.

What is the role of random mating in maintaining Hardy-Weinberg equilibrium?

It ensures that all male-female combinations are equally likely, which is crucial for predicting genotype frequencies.

What is the impact of natural selection on Hardy-Weinberg equilibrium?

Natural selection can disrupt HWE by favoring certain genotypes over others.

How can migration affect allele frequencies in a population?

Migration can introduce new alleles or change the frequencies of existing alleles, potentially leading to a deviation from HWE.

What is the significance of calculating expected numbers of individuals under HWE?

It allows researchers to test if observed and expected genotype frequencies are statistically different.