Evolution Exam 1 Study Guide

What is science?

There is no proof or truth; there is theories that can be falsifies or supported

How is science different from religion?

Science does not and cannot invoke the supernatural it’s all about testing; bound by laws of the universe unlike religion where there is absolute truth, rights and wrongs

Is there necessarily a conflict between science and religion?

Science is not in conflict with religion, like a weather report. They are different domains, as religion is supernatural, faith, belief and truth

What is the utility of evolution?

helps in making predictions about how viruses and other pathogens might evolve, crucial in developing effective therapeutics and vaccines

Ex. H5N1 bird flu virus would evolve to transmit between humans, evolution of viruses like HIV and SARS-CoV-2

How can evolution illuminate the study of human disease?

Understanding disease emergence: different strains of bird flu would evolve to eventually transmit to humans, or Zika and mosquitos that feed on humans

Predicting disease outbreaks (Ebola), tracking viral evolution (HIV from monkey to human or Covid), understanding drug resistance (HIV vs AZT), multi-level selection for strains of disease and transmission

Why do drugs like AZT eventually fail in treatment of HIV?

Variation in the rts of different strains of HIV, amino acids of the rt site coded by nucleic acids and is inherited. Some inherited variants of HIV recognize and remove AZT.

HIV virus shows a high rate of variation (mutation rate) because its copying is error-prone, this variation can be inherited, variation is selected, and selected for.

Evolution is why AZT fails and HIV will always be here, resistance

What are the three principles of Darwinian evolution?

1. Organisms vary

2. Variation is inherited - passed from parent to offspring, mechanism of inheritance can be completely unspecified

3. Variation is selected - subject to natural selection: some variants survive and reproduce more than others

How does understanding Darwin and his world help us to understand his theory?

Middle classes of Victorian England = progressive era, time of change and scientific improvements to world; capitalistic society after the fall of royals = natural order = civilizing influence on world → England’s expansion

Uniformitarianism = present is key to past → geological time scale = idea of history to life on Earth

Led to Darwin questioning while on his sea journey, why climatically similar places (SA and England) had distinct creatures, why are the fossils of SA/ England like their modern creatures? He had a progressive mindset when it came to evolution.

What are vestiges?

a part or organ of an organism that has become reduced or functionless in the course of evolution, useful for very ancient events in evolution

Ex. wisdom teeth, snake hooks

What is a uniformitarian view?

The present is the key to the past, same natural laws and processes that operate in the universe now have always operated in the universe

Does the Earth’s history always conform to this view?

evolution is not always gradual or progressive, so no

geological timescale conforms, but vestigials break this view

If something occurs in nature, is it necessarily morally “right”?

Morally isn’t involved in all aspects of nature. Genes have no morally, they typically operate on an individual level of selection, just wanting to replicate and grow.

Eugenics would suggest that improving human population by eliminating bad genes is right and natural, but it is not morally right.

Did Darwin understand the basis for heredity?

Darwin did not understand the basis for heredity (Mendel’s work did), as he did not know about genes, and could not answer how variation occurred or how it was inherited.

How did Mendel “solve” Darwin’s difficulties?

Mendel’s work explained how variation was inherited though his work with pea plants. He found that traits were inherited through genes (units) that had alleles (different forms).

Mechanism of inheritance

Is evolution always gradual and progressive?

No evolution is not always gradual or progressive, it can be regressive and sometimes there are vestiges left in organisms that are no longer needed.

No direction to evolution

What is the darkest chapter in the history of evolutionary biology?

Eugenics - letting the unfit perish or actively preventing such individuals from reproducing (individual level of selection)

Was Darwin a eugenicist?

No, he was not: eugenics is selected for at the level of the individual but selected against at the level of the group, human morals oppose eugenics.

Multi-level theory

How did Darwin see evolution acting in human society?

Levels-of-selection → sometimes group level thinking is better as it helps everyone, this is morality’s evolution. Moral individuals have more offspring than immoral (individual selection) one’s. Leads to group (tribe) evolution.

Sympathy, individual (“noblest nature” natural empathy) vs group (US vs China Covid protocols), group loyalty (japanese workers)

What was the basis for the evolution of morality?

Group level selection → helping the group → morality and altruistic behaviors = help to make individuals stronger through bonds

“bonds allowed the group to present a united front to less-fortunate neighbors, thereby providing backup for dispatching rivals in combat with little risk to self”

Conflict Mediation

Human societies can be seen as levels of selection, especially when it comes to infectious diseases

How does “survival of the fittest” embody the concepts of fitness and adaptation?

"survival of the fittest" embodies both fitness ("survival") and adaptation ("fittest" in the sense of "fittedness" between the organism and environment)

How does the response of Darwin’s Finches to the ENSO event in 1977 illustrate basic evolutionary principles?

Climate → food → selection → "survival of fittest," i.e., the individuals best adapted to eating large seeds survive and reproduce, so the population of finches as a whole now has larger beaks

Population evolved for the trait of bill size and continues to evolve

How can the ancestral state for finches of HIV be reconstructed?

Need to know the systematics (history) of the group to infer what the primitive condition was. Could use nucleotide sequence data to construct a phylogram “tree thinking”

How can “tree-thinking” be used to illuminate evolutionary questions?

tree thinking - reconstructing the history of life in a cladogram. The cladogram was created with data other than those that we are reconstructing the history of

Ex. elongated shell trait → explain the evolutionary history of group like the evolution of feathers and flight in birds

Why is the origin of life such a difficult evolutionary question? no sister group to all of life

What are sister-group relationships?

Sister groups are each other’s closest relatives helps with comparative method

How can the geological time scall and fossils complement “tree-thinking”?

Fossils can also be useful in figuring out what the starting point was (fossils aren’t “ancestors")

Geological time scale embodies the “uniformitarian” principles. Rocks give an indication of which species came first in terms of relative time (biostratigraphy)

How are geological time and radiometric time similar and different?

Geological gives a relative time while radiometric dating (ratio of carbon 14 to carbon 12 in atmosphere) gives a chronological time based on atomic clock. Both deal with time, but use different methods (rocks vs atoms)

What is “fractionation”?

Remnants of early life will be slightly poorer in 13C than inorganic carbon, sulfur same

Ratio of different isotopes

How are statistical and mathematical approaches similar and different?

Differences:
Mathematics is about proving things, while science, including statistics, is not, Mathematical models are used to generate hypotheses
Statistics deals with probabilities and is based on the idea that there is always some uncertainty associated with observations
Mathematical models use equations, and in those equations, variables have defined relationships (e.g., y = x), while statistical models have variables with an error term (y = x +/- error)

Similarities:
Both are essential for developing and testing evolutionary hypotheses.
Both are important for understanding evolutionary processes at multiple levels
Both use models, although the kinds of models and how they are used differ

How much insight are evolutionary experiments done with bacteria likely to provide for, say, finches?

molecular mechanisms, demonstrate key evolutionary principles, such as how selection acts on heritable variation, all contribute to developing and testing evolutionary hypotheses, which can then be further tested by more experiments: e.g., for Darwin’s finches

What is the “modern synthesis” definition of evolution and how does it differ from Darwin’s definition?

MS: change in allele frequencies within populations; change in the genetic makeup of populations over time (gene/ allele focused)

Difference: MS deals with genes directly, Darwin did not know about genes and focused on “heritable variation being subject to natural selection”

How is multi-level view of evolution different from and similar to Darwin’s view?

Similarities:
Heritable variation is subject to selection - differential reproduction is driver of evolutionary change
Natural history is used
Survival of the fittest

Differences:
D - organism is unit of selection / MLV - selection acts on multiple, nested levels (genes, cells, chromosomes, groups of organisms) and the conflict between levels
D - does not know selection mechanisms / MLV - mechanism of selection

MLV expands Darwin’s original thoughts on selection to genes, human societies and explains the factors/ reasons behind it.

At what levels in the biological hierarchy can selection occur?

All levels: genes, MGE, chromosomes, cells, organisms, groups of organisms

At what levels in the biological hierarchy can “evolution = a change in allele frequency” occur?

Genes: gene dup, MGE increase their fq

Chromosomes: chromosomal inversions so group of alleles inherited together

Multicellular organisms: more food and then multiply

Societies/ groups: human response to pathogens

What does selection on individual usually favor?

Selfishness or defection (cancerous cells) as they enhance organisms (individual’s) own survival and reproduction

Ex. Cannibals can thrive in a group because they choose themselves
Virus quick replication and spread regardless of killing the host

What does selection on groups usually favor?

Cooperation as this benefits the group overall, altruism (programmed cell death = no cancer), selfish tendencies are constrained. Vertical transmission puts members in the same boat

Ex. strong public health measures (safe sex practices)

Why do conflicts between levels of selection occur?

Group vs individual - Coop. vs selfish

Nested hierarchies: higher level units are made up of lower level units (cells replicate too much causes cancer in organism) = conflicting interests

Ex. Virus replication is favored by individual virus, but it may kill the host before spreading, so there must be balance between viral replication and host survival, same for cannibals - if too many whole population collapse

What are the two most relevant levels of selection when HIV infects a human host?

Individual virus and group of viruses in single human host

What does selection on the individual HIV within a host usually favor?

Faster replication

What happens to the group of HIV if the human host dies before transmission can occur?

The entire group of HIV viruses within that host will also die out

How can levels-of-selection view generally illuminate infectious disease?

Individual virus selection favors rapid replication, while group of viruses level favors a balance between replication and transmission (Goldilock virus).

Selection pressures like transmission, virulence, and evolution of pathogens

How is SARS-CoV-2 expected to evolve?

Forever, always in human society, like the common cold or HIV.

SARS-CoV-2 exhibits a high rate of variation due to its error-prone copying mechanisms → selection pressure on SARS-CoV-2 favors strains that are more readily transmitted → more rapidly transmitted strains can become more deadly

How does human society mirror these conflicts?

Human societies mirror the conflicts seen in multi-level selection through the tension between individual interests and the needs of the group, which can be observed in various aspects of social organization and behavior

Individual Liberties vs. Centralized Authority

How is human society similar to and dissimilar to other levels of the biological hierarchy?

Similarities:
Group-level selection
Conflicts between levels of selection
Cooperation and altruism
Synergism and antagonism

Differences:
Heritability is hard to explain in human society
Intentionality, humans plan
Mobility and migration, humans move a lot

How does the cannibal example illustrate basic levels-of-selection themes?

Individual-level selection, cannibals benefit from consuming others - advantageous for individual organism

Group-level selection, cannibals are detrimental overall to the group

Conflicts between levels - conflict between selection at the level of the individual and selection at the level of the population

Migration makes individual-level selection more favorable because cannibals can find more groups to colonize

Was Darwin’s theory widely accepted in the 19th century?

Not really

What major difficulty with Darwin’s theory was perceived?

Lack of a solid explanation for the source of variation and how that variation was inherited

Darwin could not answer the fundamental questions, "Where does variation come from?" and "How is variation inherited?"

How did Mendel’s data resolve the major difficulties of Darwin’s theory?

Mendel’s data showed how variation is maintained, how traits are passed from one generation to the next, and ultimately provided a crucial mechanism of evolution that was lacking from Darwin’s original theory

How do Mendel’s data emphasize the need for statistical analysis in biology and genetics?

Due to discrepancies between his reported results and what would be expected based on probability, with proper statistics

• small population

• misclassification ¾ chance that selfed hets have red flowers, chance for 10 offspring of selfed het is 1/20

• Expected vs Observed: 0.37 vs 0.33 red and 0.63 vs 0.67 white, Mendel’s 2:1 (0.666:0.333)

• Preconceived notions

What was the modern synthesis?

Integration of Darwin's theory of evolution by natural selection with Mendelian genetics, paleontology, and a lot of good natural history that occurred in the 1930s and 1940s

"evolution = change in allele frequencies within populations"

What is a gene?

A stretch of DNA that codes for a distinctive type of RNA or protein product

What are alleles?

Versions of the same gene that differ in their base sequence

Why are genetic mutations particularly significant in evolutionary biology?

Ultimate source of most heritable variation, which is essential for evolution to occur.

Without mutations, there would be no new alleles, and therefore, no new traits for natural selection to act upon

What are point mutations?

Changes in the base sequence of DNA that produce new alleles, occurs at a single location in the DNA sequence.

What are transitions and transversions?

Transitions: These involve the substitution of one purine base (A or G) for another purine, or one pyrimidine base (C or T) for another pyrimidine

Transversions: These involve the substitution of a purine base for a pyrimidine base or vice versa

Why do conserved areas of the genome indicate selection?

Exhibit very little variation across different species or within a species over time. The preservation of these regions suggests that they are functionally important and under strong selective pressure to remain unchanged

Essential genes, regulatory elements, don’t change because they’re needed exactly how they are, and if they change it can kill the organism

Where do new genes come from?

Gene dup = unequal crossing over

Retro transposition = processed mRNA, lacking introns, is copied into DNA by the reverse transcriptase enzyme (rt) and inserts into a new location in the genome

Non-coding DNA = For example, a mutation in a stop codon after a speciation event can convert non-coding DNA into coding sequence

What is the result of chromosome inversions?

Prevent crossing → do not produce viable gametes when they recombine → group of alleles being inherited together as a single unit

Communist Manifesto (Lamarck’s theory aligns)

inheritance of acquired characteristics; organism must strive for the acquisition of novel characteristics (giraffe’s neck getting longer)

How does polyploidy contribute to genetic variation?

Increasing genetic material → undergo mutations without being constrained (1 copy maintains function, 1 mutates) → synergy between selection at the level of gene and organism → gene families → new adaptations → reproductive isolation and speciation or phenotypic variation

What are the factors that must be considered when measuring and comparing mutation rates?

Type of mutation: loss-of-function (LOF) mutations, point (transition or transversions), insertions/deletions, inversions

• Replacement (nonsynonymous) or silent (synonymous)

• Lethal, deleterious, neutral, or beneficial

Germline or somatic mutations: germ cells are passed on

Replication rate: Per base pair, per gene, per genome

Selection & Trade offs: speed vs accuracy more investment and energy = quick rep and accurate. Selection acts on phenotypes, for better fitness, against loss of fitness.

What are the sources that contribute to variation in mutation rates?

Energy allocation, trade offs, number of cell divisions, germline, environmental adaptation, mutation rates, exposure to water, proofreading enzymes, rep slippage

What is a trade-off?

Refers to a negative genetic correlation between two traits or functions, where an increase in one trait or function is associated with a decrease in another

How can the trade-off between speed and accuracy be broken?

Energy Allocation, more energy in rep = faster and more accurate

What are the typical effects of mutation?

Lethal, deleterious, neutral, and beneficial