BIOL 3030 Bernal Exams

T/F - When building phylogenetic trees, Maximum Likelihood approaches tend to be more accurate than Maximum Parsimony and Distance methods.  

True

T/F - The book Origin of Species provides concise and detailed explanations of the origin of vestigial traits, as well as a detailed explanation of why variation continues to exist despite strong natural selection. 

False

T/F - Co-evolution takes place when the changes in one species can lead to changes in fitness in another species. 

True

T/F - The trees 1 and 2 in the example below are showing the same relationships among the different taxa.

True

T/F - One of the characteristics of natural selection as described by Darwin is that it can prepare species for environmental conditions that will exist thousands of years into the future (i.e. predictive properties). 

False

T/F - Following Lamarck’s ideas, vertebrates would have to develop spines independently multiple times in order to explain the diversity of tetrapods we see today.

True

T/F - Phylogenies represent hypotheses, and as such they can be revised and changed when presented with new evidence. 

True

T/F - Empedocles' ideas of how animals become well adjusted to their environments is tightly associated with spontaneous generation. 

True

T/F - Evolution refers to the phenotypic and molecular changes that occur during the lifetime of an organism, from the early developmental stages into adulthood. 

False

T/F - Homologous traits can have different functions, but they share common ancestry. 

True

T/F - The forelimbs of horses, bats and dolphins have very different functions, but based on the phylogeny of mammals we can identify that the structures have the same origin. This is an example of an analogous trait. 

False

T/F - The phenotype of an individual can change depending on the genotype, as well as the environmental conditions the organism is developing in.

True

T/F - A species of bird lives at very high altitude, and it thrives at very cold temperatures and low humidity. Due to the effects of climate change, their habitat is getting warmer and more humid. These new conditions are leading to a decline in the number of offspring. This is an example of antagonistic pleiotropy. 

True

T/F - Hypothesis and theory are very similar terms in the sciences, and can be used interchangeably when describing new ideas and observations.

False

The dorsal fins of dolphins and fish allow them to maintain their position while swimming. This represent a good example of:

Analogous traits

The vomeronasal organ is considered an important organ for the detection of smells in many species of reptiles and mammals. Humans show evidence of a reduced vomeronasal organ that according to most scientists is not functional. 

This is an adaptation for many species of tetrapods but a vestigial trait in humans

The ocean sunfish (Mola mola) produces up to a billion small eggs every time it reproduces. Scientists predict that this is an adaptive strategy as a result of high predation during juvenile stages. Most other species in the same family produce fewer offspring that are larger in size. This is an example of:

Variation in life history traits

Models such as Jukes-Cantor and General Times Reversible are associated with the estimating _______ trees.

Maximum Likelihood and Bayesian

_________ considered the raw material for natural selection to operate. 

Phenotypic variation

T/F - The following statement about the evolution of complex organs is TRUE: They are possible because intermediate states can be beneficial

True

In the phylogeny below, there is a group of primates known as the "Georgian", which is composed by species A, B, C and D. The species E and F form the "Alabamian" group. This relationship would be a considered:

Monophyletic

T/F - The following statement is in line with the ideas of Uniformitarianism: The coast line was eroded over thousands of years by tropical storms and tidal waves

True

One of the first scientists to propose ideas about slow gradual change, especially in terms of geological features:

Charles Lyell

In the phylogeny below, the traits observed in the species A, B and C represent an example of:

Homoplasy

The following scenario closely aligns with the ideas presented by both Darwin and Wallace:

Species of birds in islands and mainland have similar features because of common descent

In the phylogeny below, the species B, D and F form the "Alabamian group". Based on their relationship, the Alabamian group would be considered:

Polyphyletic

__________ phylogenies are very well known to be susceptible to "long-branch attraction". 

Maximum Parsimony

_______ is the branch of biological sciences associated with the classification of organisms based on their evolutionary history and genetic similarities. 

Systematics

In the following phylogeny of insects, the wings observed in species A and B are an example of:

Homoplasy

Capsaicin is an alkaloid that makes certain peppers spicy, so most species of mammals avoid their fruits. Scientists have recently discovered that a species of Asian tree shrew (mammal) that is immune to the effects of Capsaicin and related alkaloids. This represents an example of: 

Evolutionary arms race (maintenance of diversity)

T/F - The following statement best describes natural selection: Heritable phenotypic variation leads to differential reproductive success

True

In the phylogeny below, the trait in orange (B, C & E) represents an example of:

Homoplasy

_____ methods make use of evolutionary models to provide more accurate estimates of the relationships between groups.

Maximum likelihood and Bayesian

T/F - The following ideas is NOT in line with the principles of Inheritance of Acquired Characteristics: Changes take place during the life-time of an organism, and traits would have to evolve multiple times for multiple species to have them

 

True

Mention two of the main differences between the ideas presented by Charles Darwin vs. the ideas presented by Lamarck:

Lamarck - traits gained during organisms life time Darwin - traits inherited along generations

Larmarck - Traits changes when the needed to Darwin - Idea of Natural Selection

Mention two of the limits of natural selection:

Physical constraints

Nature of variation

What were two of the problems that remained after the "The Origin of Species" was first published: 

Vestigial traits

Complex organs

T/F - The loci G, M, C & R are responsible for the production of a protein that is important for immune function in beta fish. The haplotypes GMCR and GMcr produce the necessary proteins, while the haplotype gmCR does not produce the final protein product that is needed for immunity. This would lead to a negative linkage disequilibrium coefficient for alleles gm in beta fish.

True

T/F - Genetic drift is considered the main mechanism for changes in allele frequencies among populations with >100 million individuals.

False

T/F - The c-value paradox indicates that genomes of vertebrates are much larger than the genomes of plants and invertebrates. 

False

T/F - Coalescent theory suggests: a population that recently experienced a selective sweep has more recent time to coalescence than a population under stabilizing selection.

True

T/F - Genetic hitchhiking occurs when there is strong association between a two highly deleterious loci. 

False

T/F - Due to the infrequent combinations of certain alleles, latent genetic variation can lead to the production of extreme phenotypes in a population.

True

T/F - In a finite population, the selection coefficient is the sole determinant of whether or not a mutation will be fixed. 

False

T/F - Strong assortative mating can lead to an increase in the accumulation of recessive deleterious genotypes in a population.

True

T/F - Polygenic traits are synonymous to Mendelian traits, as they are associated with a single locus and few alleles, and they are controlled by dominance/recessive relationships. 

False

T/F - Recombination via chromosomal crossing-over is one of the main mechanisms for breaking down physical linkage and linkage disequilibrium. 

True

The spike protein in the Covid-19 strain is estimated to be under strong positive selection, when compared to other coronaviruses. Mathematically, this means that the spike protein has a ratio of non-synonymous to synonymous mutations:

Ka/Ks = 3

This type of event can result in large populations with low genetic diversity:

Population bottleneck

T/F - Assortative mating (strong sexual selection) is an assumption of the Hardy-Weinberg model.

False

T/F - The following statement about epigenetic changes via histone modification is TRUE: Tight bundles of condensed chromatin inhibit gene expression

True

Mutations that take place in the whole body of an organism (including the production of gametes), and can be passed from one generation to the next:

Germ-line mutations

Geographic features and fossil data can provide information on the rate of change of DNA sequences, and this rate is known as: __________

Molecular clocks

One of the main principles resulting from the inheritance work of Mendel:

 

Individuals have two gene copies at each locus, which segregate during gamete production

Which of the following types of mutation has a higher likelihood of altering a protein product?

Insertion/deletions

What is the frequency of the genotype A₁A₁, if the allele frequency of the allele frequency A₂=0.65? 

0.12

Seeing the two diagrams below, we can infer the following processes are going on:

Strong positive selection / Balancing selection

The weight of chickens is a continuous trait that is controlled by a large number of genes. This is an example of: 

A quantitative and polygenic trait

Based on Haldane’s rule a positive mutation will have a higher probability of fixation in a population with:

s=0.1; Ne=1,000

s=0.2; Ne=100

s=0.7; Ne=1,000,000

s=0; Ne=1,000

s=0.7; Ne=1,000,000

Narrow sense heritability can be best described by: 

The phenotypic variation that can be explained by the additive genetic variance

T/F - The following statement about effective population size is ACCURATE: Effective population size might be smaller than the size of the whole population

True

When heterozygotes produce phenotypes that have higher fitness than homozygotes: 

Overdominance

T/F - The following statement about Darwin and the Origin of Species is FALSE: Darwin was aware of the work of Gregor Mendel, and was able to incorporate it to the last version of the Origin of species

True

The following statement is in line with the Neutral Theory of Molecular Evolution:

Most of the molecular genetic variation is selectively neutral

Two identical twins are separated at birth, and live with families in different countries. These families have very different diets, income, and levels of stress. Years later one of the twins develops multiple health issues while the other is healthy. This is most likely related to:

Epigenetic mechanisms modify gene expression in different environments

Broad sense heritability aim to understand

The proportion of the phenotypic variance explained by the genotype

A species of lizard in the Florida Everglades has two genotypes associated with different behaviors: Genotype aB has the ability to feed on crickets, while Genotype AB has the ability to feed on wasps. If the Genotype aB increase dramatically, the number of crickets will decrease. This can lead to an increase on the Genotype frequency for individuals that feed on wasps. This represent an example of:

Underdominance

When alleles in different genes interact, and they influence the phenotype in non-additive ways:___ Meanwhile, when one gene can modify multiple phenotypes, this is called:___

Epistasis, pleiotropy

Scientists from Florabama university studied a group of frogs that were sensitive to insecticides. After many years, the frog population collapsed, and the species was declared endangered. Conservation efforts were successful and now the population is estimated at 20,000 individuals. However, there are still concerns remain due to the low genetic divergence. This is an example of ___.

A decade later, the construction of a large highway separated one of the populations of frogs, isolating it from all other groups. The reduced Ne and limited mating partners led to the accumulation of deleterious recessive alleles and reduced heterozygosity. This is called ___. 

Bottleneck effect, Inbreeding depression

What are the two types of epigenetic mechanisms discussed in class? Please define each one.

DNA Methylation - Methyl group attaches to DNA histone to stop DNA expression

Histone Modification - Histones are wound tightly to stop transcription from occuring

___ occurs when an advantageous mutation arises in a particular gene, and the alleles associated with it quickly become fixed all individuals of a population. They can be accompanied by ___, where neutral or slightly deleterious alleles are linked to the beneficial mutation.

Selective sweep, Genetic hitchhiking

T/F - For parapatric speciation to occur, it is necessary for individuals of a given species to colonize a very isolated location (an island for example) that is geographically distant from the main population. 

False

T/F - Sexual conflict is part of intersexual selection, and it is seen when a trait or behavior increases the fitness of both sexes.

False

T/F - The Punctuated Equilibrium Model suggests that the rate of evolutionary change occurs gradually and very slowly over time, through intermediate steps in the fossil record. 

False

T/F - "Minimal gene set", or genes associated with basic functions that are shared across a broad range of organisms, are key to understand the earliest living organisms. 

True

T/F - In protocells, phospholipids could stabilize simple lipid membranes, providing a selective advantage for cells that were able to synthesize or incorporate them. 

True

T/F - The C-value paradox suggests that genome size increases as the phenotypic complexity of the individual increases. 

False

T/F - Cis-regulatory elements can modify the expression of multiple genes, and one the expression of one gene can be modified by multiple cis-regulatory elements.

True

T/F - Today, it is broadly accepted that the different developmental stages of an organism directly reflect the phylogenetic relationships (i.e. ontogeny recapitulates phylogeny). 

False

T/F - The evolutionary species concept suggests that a species is a group of individuals with similar ecological niche and intense competition, which make them distinct from other such groups. 

False

T/F - Eukaryotic genomes are mostly composed of transposable elements and introns, while protein-coding genes represent a much smaller proportion. 

True

________ species have a higher probability of extinction. 

Endemic species with narrow ranges of distribution

Why is the estimated age of eukaryotes different when estimated with fossils than when it is compared with phylogenetic methods? 

The phylogeny estimates the age of the most recent common ancestor of living organisms, but fossils may represent earlier eukaryotes that went extinct

During the last glacial maximum, large areas of land became covered in ice sheets. Fish populations inhabited remote lakes that were geographically isolated from each other. As the ice sheets retreated, the Great Lakes formed and many of the isolated fish groups went through a range expansion, and now many of these species have overlapping ranges. However, species that were isolated during the glacial period have complete reproductive isolation and hybridization has never been reported. What mode of speciation is this, and what is the mechanism of reproductive isolation?

Allopatric speciation followed by range expansion

One of the main challenges of the fossil evidence: 

Fossil record is biased towards species that were very abundant at a specific time

They are "selfish" genetic elements that can replicate and proliferate. They usually represent a large portion of eukaryotic genomes: 

Transposable elements

______ refers to the condition when the somatic traits develop slower than the reproductive traits, compared to a common ancestor. 

Neoteny

Hox genes are _______ in their order and sequence, but ________ in more complex animals

highly conserved, clusters have duplicated

Hox genes are considered to be very important for development, because: 

They control the anterior-posterior axis and the positioning of structures in animals

T/F - All of the following is considered to be one of the benefits of DNA: 

DNA has more efficient replication than RNA, and with less errors

Having DNA allows RNA to mainly be used for protein production

DNA is a more stable molecule than RNA

True

The biological species concept has the following limitations: 

It is challenging to assign species for fossils and bacteria

The Earth formed from the accretion of gasses and dust approximately

4.5 billion years ago

What is the leading hypothesis for the origin of the eukaryotic organelles (e.g.: mitochondrion, and chloroplast)?

These were originally free-living cells that started living inside of other cells

T/F - The following statement about the "early RNA world" hypothesis is ACCURATE: Initially RNA served both for information storage as well as molecular functions

True

T/F - The following statement about genomes is TRUE: Genome size could be related with size of the cell/nucleus and the number of "self-replicating" elements

True

T/F - Gene regulatory elements are associated with: 

They can influence the activity of multiple genes

Phenotypic changes between closely related species

They can regulate gene expression during development

True

One of the main COSTS of asexual reproduction

Difficult to overcome the accumulation of deleterious alleles

The Last Universal Common Ancestor: 

Represents the ancestor of all living organisms alive today, but not the first living organism

T/F - The following statement about gene duplications is TRUE: It is one of the mechanisms that allows increasing phenotypic complexity

True

One of the first steps in the origin of multicellular individuals is:

Division of cell types in somatic cells and cells associated with reproduction