Evolution Exam 2 V2

2. What is polyploidy? Why is it important in evolution?

Heritable condition of having more than two complete sets of chromosomes. It can lead to instant sympatric speciation and novel gene functions.

3. Define mutation. Why is it necessary for evolution?

A permanent alteration in the DNA sequence. It is the ultimate source of all novel genetic variation upon which selection and drift act.

4. The genetic code is redundant. What does this mean? Why is this beneficial?

Multiple codons code for the same amino acid (synonymous codons). It protects organisms against harmful effects of point mutations (silent mutations).

5. What is a gene? How has our definition changed over 100+ years?

Originally defined as a discrete unit of inherited physical trait; now understood as a complex region of genomic DNA encoding functional RNA or protein products, including regulatory regions.

6. How is DNA packaged into chromatin and chromosomes?

DNA wraps around histone proteins to form nucleosomes, which coil into chromatin fibers and condense into visible chromosomes during division.

7. What is the effect of histone acetylation on gene expression?

It relaxes chromatin structure (euchromatin), increasing accessibility for transcription factors and promoting gene expression.

8. What is the effect of DNA methylation on gene expression?

It typically condenses chromatin and represses/silences gene transcription.

9. Describe epigenetic inheritance. Is it important to evolutionary change?

Transgenerational transmission of phenotypic variations (e.g., DNA methylation) without altering base sequences. Its evolutionary role is debated, as many marks are erased across generations.

10. What is maternal effect? Is it an example of epigenetics?

Phenotype determined by parent's genotype/environment (e.g., mRNA/proteins stored in egg). Not strictly epigenetics, as it isn't a direct modification of offspring DNA/chromatin.

11. Is there a relationship between genome size and organismal complexity? Why or why not?

No (C-value paradox). Genome size varies widely due to non-coding DNA, transposable elements, and repetitive sequences, not structural complexity.

12. Point mutation (synonymous vs. nonsynonymous)

Synonymous: Base change that does not alter the amino acid sequence. Nonsynonymous: Base change that alters the resulting amino acid sequence.

12. Frame shift mutation

Insertion or deletion of nucleotides not in multiples of three, altering the entire reading frame downstream.

12. Chromosomal inversions

A segment of a chromosome breaks off, flips 180 degrees, and reattaches, suppressing recombination in heterozygotes.

12. Chromosomal deletions

Loss of a chromosome segment containing genetic material.

12. Chromosomal duplications

Generation of an extra copy of a chromosome segment, providing raw material for gene duplication and divergence.

12. Chromosomal fission

Splitting of a single chromosome into two distinct chromosomes.

12. Chromosomal fusion

Joining of two separate chromosomes into a single larger chromosome (e.g., human chromosome 2).

12. Chromosomal translocations

Rearrangement of a chromosomal segment to a non-homologous chromosome.

13. Which mutations/chromosomal changes are most common vs. most impactful?

Point mutations are the most common; large structural changes (duplications, fusions, translocations) are the most impactful.

14. What is the purpose of sexual reproduction from an evolutionary standpoint?

To generate novel genetic combinations and speed up adaptation through recombination while purging deleterious mutations.

15. List four stages where genetic information is reshuffled in sexual reproduction/meiosis.

1. Crossing over (prophase I). 2. Independent assortment (metaphase I). 3. Random fertilization. 4. Sister chromatid segregation (anaphase II).

16. What environmental factors can cause mutation?

Ionizing radiation (UV, X-rays), chemical mutagens (alkylating agents, reactive oxygen species), and thermal stress.

17. Genetic polymorphism

The simultaneous occurrence in a population of two or more discrete, genetically determined phenotypes (e.g., ABO blood groups).

17. Polyphenism

A single genotype producing discrete alternative phenotypes in response to different environmental conditions (e.g., seasonal butterfly coloration).

17. Quantitative traits

Phenotypes that exhibit continuous variation and are controlled by multiple genes interacting with the environment (e.g., human height).

18. What is QTL analysis? What is its purpose?

Quantitative Trait Loci analysis; statistical method linking phenotypic variation with specific genomic markers to identify genes underlying polygenic traits.

19. Short-lived vs. long-lived environmentally induced phenotypic variation

Short-lived: Reversible acclimation (e.g., suntanning, muscle hypertrophy). Long-lived: Permanent developmental plastic responses (e.g., water flea neck teeth induction).

20. Are trait variations due to environment or genetics?

Both; variation is an interaction between genetic predisposition and environmental influence ($V_P = V_G + V_E + V_{G \times E}$).

21. What is the purpose and premise of a common garden experiment?

Grows different populations in a uniform environment to test whether phenotypic differences are genetically based ($V_G$) or environmentally induced ($V_E$).

22. What effects can mutations have on protein production?

Can alter protein structure, reduce or eliminate function (loss-of-function), create novel function (gain-of-function), or change expression levels.

23. Define fitness in an evolutionary context.

The relative reproductive success of an individual or genotype (contribution of offspring to the next generation's gene pool).

24. Overall, the net effect of mutations in a gene affecting phenotype is:

d. disadvantageous

25. If a mutation happens to be advantageous, it is most likely to be:

c. slightly advantageous

26. Does a mutation arise in response to environmental stimuli?

No. Mutations arise randomly with respect to fitness needs; the environment selects for advantageous variants after they occur.

27. Why is the cumulative effect of low mutation rates significant?

Populations consist of many individuals over many generations, generating millions of new mutations across the genome overall.

1. What is microevolution?

Small-scale changes in allele frequencies within a population or species over short timeframes.

2. What is macroevolution?

Large-scale evolutionary changes over long periods at or above the species level (e.g., origin of new taxa, mass extinctions).

3. How can microevolution lead to macroevolution?

Macroevolution is the long-term accumulation of microevolutionary changes (mutations, selection, drift) coupled with reproductive isolation over millions of years.

4. Do we know how many species there are on earth? Explain your answer.

No. Only ~1.5–2 million are named, but estimates range from 8–100 million because many microscopic, deep-sea, and tropical canopy species remain undescribed.

5. Why are there more species in the tropics than in temperate or polar regions?

Due to greater long-term climate stability, higher solar energy/primary productivity, and higher speciation rates relative to extinction rates.

6. What is Wallace’s Line? Why does it exist?

A boundary separating Asian and Australian fauna in the East Indies, created by a deep ocean trench that land species could not cross even during low ice-age sea levels.

7. What is biogeography? When was the field created and by whom?

The study of the geographic distribution of organisms across space and time; created in the mid-19th century by Alfred Russel Wallace.

8. Biogeography shows us what three things?

1. How continental drift matches current species distributions. 2. That closely related species tend to live in geographical proximity. 3. How physical and climate barriers restrict or aid dispersal.

9. Major patterns of distribution depend upon what three things?

Speciation, Extinction, and Dispersal/Vicariance.

10. What is the significance of Wallace’s biogeographical regions?

They demonstrated that Earth is divided into distinct biological realms (e.g., Neotropical, Australasian) based on shared evolutionary history rather than current climate alone.

11. Define endemic.

Naturally found only in one restricted geographic area.

11. Define native.

Naturally occurring in a region without human intervention.

11. Define nonnative (exotic).

Introduced to a region outside its natural range by human activity.

11. Define invasive.

A nonnative species that spreads rapidly and causes ecological or economic harm.

12. Why are multiple lines of evidence often necessary to understand complex patterns of biodiversity (for example, the marsupial lineage)?

Because modern geographic locations alone cannot explain historical shifts; combining fossils, continental drift (Gondwana split), and molecular data is required.

13. How are speciation and extinction drivers of macroevolution?

Their relative rates determine net gains or losses in global biodiversity over geological time.

13. How are changing environments drivers of macroevolution?

Climate shifts, volcanism, or continental drift alter habitats, opening new niches or driving extinctions.

14. Define turnover.

The total number of speciation events plus extinctions in a clade over a given timeframe (Turnover = Originations + Extinctions).

15. Define standing diversity.

The net count of living species or taxa present in a clade at a given point in time.

16. Does evolution occur quickly or slowly or somewhere in between? Explain your answer.

Both. It occurs slowly during stable periods (gradualism) and rapidly in bursts during major environmental shifts or following mass extinctions (punctuated equilibrium).

17. Define anagenesis.

Evolutionary change within a single unbranched lineage where one species transitions into another.

17. Define gradualism.

The theory that species evolve steadily via small, continuous changes over long periods.

17. Define punctuated equilibrium.

The theory that long periods of evolutionary stasis are interrupted by brief, rapid bursts of speciation.

18. What is adaptive radiation? Describe two examples.

The rapid evolution of a single ancestral species into many ecologically diverse species. Examples: 1. Galápagos Finches (beak diversification). 2. Hawaiian Silverswords or African Cichlids (filling open niches).

19. What can lead to the opening of new niches?

Mass extinction of competitors, key evolutionary innovations (e.g., wings, flowers), or colonization of new geographical regions.

20. What is special about the Cambrian Explosion? Why has this time period received so much focus from evolutionary biologists?

Occurred ~541 Mya; almost all major modern animal phyla and complex body plans appeared in a short geological timeframe.

21. How many mass extinctions have been documented in the fossil record? Which was the largest?

Five. The Permian-Triassic extinction (~252 Mya) was the largest (~96% of marine species died).

22. Why are mass extinctions evolutionarily important?

They clear dominant groups, freeing up ecological niches and driving adaptive radiations for surviving lineages.

23. What can cause mass extinctions?

Asteroid impacts, massive volcanism (flood basalts), sudden climate shifts, ocean anoxia, or sea-level changes.

24. What is the 6th mass extinction? Are we currently experiencing this?

The ongoing, human-driven loss of biodiversity via habitat destruction, climate change, and pollution; yes, current extinction rates confirm we are entering it.

1. Who drew the first phylogenic tree? How did this mark a departure from traditional classification?

Charles Darwin (1837/1859); it replaced static, hierarchical ladder systems (Scala Naturae) with dynamic, branching evolutionary descent from common ancestors.

2. What is a clade?

A monophyletic group consisting of a single common ancestor and all of its descendants.

3. How do you read and interpret simple phylogenetic trees?

Nodes = common ancestors / speciation events; Branches = lineages evolving over time; Sister Taxa = closest relatives sharing an immediate common ancestor.

4. What is the difference between a rooted and unrooted phylogenetic tree?

Rooted: Includes a common ancestor at the base, showing the direction of evolutionary time. Unrooted: Shows relationships among taxa without indicating temporal direction or the common ancestor.

5. How do you determine if different representations of a phylogenetic tree are equivalent?

Trees are equivalent if rotating branches around nodes maintains identical ancestor-descendant relationships.

6. Describe Linnaeus’ classification system (1735). How many kingdoms did he recognize?

Binomial nomenclature system; recognized 2 kingdoms (Animals and Plants).

7. Describe Robert Whittaker’s classification system (1969). How many kingdoms did he recognize?

Expanded classification to 5 kingdoms (Monera, Protista, Fungi, Plantae, Animalia).

8. How have we 'cheated' on the classic taxonomy system to make things fit?

By adding intermediate ranks (e.g., superorders, subclasses) and using rankless phylogenetic clade systems (like PhyloCode).

9. Why is the tree of life often drawn as an interconnected web at the base?

It depicts Horizontal Gene Transfer (HGT), endosymbiosis, and gene swapping, showing the base of life as an interconnected web rather than a single trunk.

10. What is a derived character? How does it differ from an ancestral character? Are these terms relative?

Derived (Apomorphy): Novel trait evolved after splitting from common ancestors. Ancestral (Plesiomorphy): Trait inherited from a distant common ancestor. Relative? Yes (e.g., hair is derived for mammals relative to vertebrates, but ancestral for primates relative to humans).

11. Define monophyletic, paraphyletic, and polyphyletic.

Monophyletic: Ancestor and all descendants. Paraphyletic: Ancestor and some (not all) descendants. Polyphyletic: Taxa grouped without including their most recent common ancestor.

12. What is a synapomorphy?

A shared, derived trait unique to a monophyletic clade.

13. What is a homoplasy?

A shared trait resulting from convergent evolution or evolutionary reversal, not common ancestry (e.g., wings in birds and bats).

14. Why do evolutionary biologists tend to accept ‘the most parsimonious tree’?

Because parsimony assumes the tree requiring the fewest evolutionary changes/mutations is the most plausible.

15. What is a polytomy?

An unresolved node splitting into three or more lineages simultaneously, indicating uncertain relationships or rapid speciation.

16. What is the importance of fossil evidence to the construction of phylogenetic trees?

Fossils provide absolute geological dates, reveal extinct lineages, show transitional intermediate forms, and calibrate molecular clocks.

17. How were Ted Daeschler and Neil Shubin able to determine where to search for fossils of Tiktaalik?

They targeted rocks of the right age (~375 million years old), right environment (sedimentary/freshwater), and exposed at the surface (Ellesmere Island, Canada).

18. How do intricate structures (such as the octopus eye) evolve?

Complex structures evolve incrementally through small, functional modifications over time, with each intermediate stage providing a selective advantage.

19. Describe the evolution of the mammalian middle ear anatomy from early synapsids.

Two bones forming the lower jaw joint in ancestral synapsid reptiles (quadrate and articular) shrank and migrated to the inner ear to form the mammalian malleus and incus.

20. What is an exaptation?

A trait originally evolved for one function that is later co-opted for an entirely new function.

21. What are some possible early uses of feathers in the bird lineage?

Thermal insulation, courtship display, or egg brooding prior to being adapted for flight.

22. Birds are most closely related to what extant lineage?

Crocodilians (forming the living archosaurs).

Mendelian genetics

Dominant alleles mask recessive ones. Law of Segregation: Alleles separate during gamete formation. Law of Independent Assortment: Genes on different chromosomes segregate independently.

polygenic inheritance

Multiple genes influence a single continuous trait (e.g., human height).

pleiotropic inheritance

A single gene influences multiple unrelated phenotypic traits.

codominance

Both alleles are fully expressed in heterozygotes (e.g., AB blood type).

incomplete dominance

Heterozygotes express an intermediate, blended phenotype (e.g., pink flowers from red x white).

epistasis

One gene masks or alters the phenotypic expression of another gene.

protein structure

Primary (sequence) -> Secondary (alpha-helices/beta-sheets) -> Tertiary (3D folding) -> Quaternary (multi-subunit arrangement).

nucleic acid structure

Nucleotide polymers (sugar, phosphate, base). DNA is double-stranded (A-T, C-G); RNA is single-stranded (A-U, C-G).

replication

Semi-conservative synthesis of DNA prior to cell division using DNA polymerase.

transcription

DNA template is transcribed by RNA polymerase to make mRNA.

translation

Ribosomes decode mRNA codons using tRNAs to build amino acid chains.

gene expression/regulation

Mechanisms controlling when, where, and how much protein is produced from a gene.