1
Q
What is the primary goal of ecologists?
A
To understand the factors that affect the distribution and abundance of organisms in their environment.
2
Q
What do evolutionary biologists aim to study?
A
They study how the characteristics of organisms change over time, using tools like the fossil record or experiments (e.g. bacteria studies).
3
Q
How are ecology and evolution connected?
A
Ecological factors (e.g. predation, environment) can drive evolution, and evolutionary changes in species can affect ecological dynamics.
4
Q
How do the approaches of ecologists and evolutionary biologists differ in scale?
A
Ecologists focus on spatial scales, while evolutionary biologists focus more on temporal scales (time).
5
Q
What are algal blooms, and why are ecologists interested in them?
A
Sudden increases in algal populations; ecologists want to know what causes them.
6
Q
What human activity contributes to algal blooms?
A
Nitrogen run-off from agriculture and other sources.
7
Q
What are two harmful types of algae mentioned?
A
Dinoflagellates (e.g. toxic blooms off Florida’s coast; impact tourism and fisheries).
Microcystis (produces microcystin which can kill pets).
8
Q
Are algal blooms always unnatural?
A
No, they have historically occurred seasonally, but are now increasing in frequency and severity due to human impact.
9
Q
What is industrial melanism?
A
The evolutionary change in pigmentation of organisms in response to industrial pollution.
10
Q
Describe how the peppered moth is an example of ecology affecting evolution.
A
Light-colored moths were camouflaged against lichen-covered trees in the 1800s. When pollution killed the lichens and darkened the trees, dark-colored moths were better camouflaged, increasing their survival and frequency.
11
Q
What environmental change triggered natural selection in the peppered moth?
A
Pollution from coal-burning killed lichens and darkened tree trunks.
12
Q
What was the central question Bassar wanted to answer?
A
Whether evolutionary adaptations of guppies affected their ecological impacts.
13
Q
In which environments do guppies experience high and low predation?
A
Low predation: Coexist with killifish (omnivores).
High predation: Coexist with cichlids (carnivores).
14
Q
How do high predation (HP) and low predation (LP) environments affect the pond ecosystems differently?
A
HP guppies: More algae, more leaf litter, higher pond productivity.
LP guppies: Fewer invertebrates, less leaf litter.
15
Q
What type of evolutionary process is suggested in the guppy experiment?
A
Local adaptation and geographic isolation leading to ecological divergence.
16
Q
When did the Big Bang occur and what elements were formed initially?
A
About 10–15 billion years ago; it produced hydrogen and helium from quarks, which formed protons and neutrons.
17
Q
How were elements heavier than hydrogen and helium formed?
A
Through nuclear fusion in protostars (up to iron), and supernovae for all heavier elements.
18
Q
What is a solar nebula and how did it affect Earth’s conditions?
A
A cloud of gas and dust formed from supernova debris; it led to Earth’s unique life-supporting conditions like liquid water, iron core, and stable climate.
19
Q
What four elements made up early molten Earth?
A
Iron (Fe), Magnesium (Mg), Silicon (Si), and Oxygen (O).
20
Q
When did Earth and its crust form?
A
Earth: 4.6 billion years ago; Crust: 4.2–4.1 bya as Earth cooled.
21
Q
How do we date rocks using zircon?
A
Zircon traps Uranium-238, which decays into Lead-206 with a half-life of 4.47 billion years. The decay ratio helps date the rock.
22
Q
How are sedimentary rocks and fossils dated?
A
Using the rock layers (strata) and crystals in volcanic ash found nearby.
23
Q
What were the three stages of Earth’s atmosphere?
A
Primary: H₂ and He — lost to solar wind.
Secondary: From volcanic outgassing and impacts — rich in CO₂, N₂, H₂O; no O₂.
Tertiary: Mainly N₂ and O₂ — formed as CO₂ dissolved in oceans and reacted with silicates.
24
Q
Why was early Earth’s atmosphere reducing, and why is that important?
A
It had no free oxygen and donated electrons, allowing organic molecules to accumulate, which is essential for the origin of life.
25
When did Earth's oceans form, and how?
Around 3.8 billion years ago, when Earth cooled below 100°C, allowing water vapor to condense into liquid.
26
Why is the ocean salty?
Acidic gases dissolved rocks, and rivers carried ions and minerals into the oceans.
27
What is the earliest evidence of life?
Biomarkers like enriched ¹²C in rocks (~3.85–4.1 bya).
## Footnote
Fossils such as stromatolites and microbial structures dated to ~3.5 bya.
28
Why is ¹²C/¹³C ratio used to detect life?
Biological processes favor lighter ¹²C, leading to enrichment in biological materials.
29
What did the Miller-Urey experiment demonstrate?
Simulating Earth’s early atmosphere produced amino acids, nucleic acid bases, and organic compounds — all abiotically.
30
What is panspermia and what supports it?
The idea that life or organic molecules came from space.
## Footnote
Evidence includes: Murchison meteorite (amino acids, purines). ALH84001 (Mars) (magnetite & possible microbes). Organic molecules detected in interstellar space (methane, formaldehyde, etc.).
31
What does panspermia suggest about organic molecule formation?
That organic matter can form abiotically throughout the universe.
32
Why is RNA considered key in the origin of life?
RNA can store genetic information and catalyze chemical reactions — acting like both DNA and enzymes.
33
What are ribozymes?
RNA molecules that act as enzymes, capable of catalyzing reactions and processing RNA.
34
What experiment supports RNA evolution?
Joyce (1992) evolved a ribozyme in the lab to work better with Ca²⁺ instead of Mg²⁺ through multiple selection rounds.
35
How might RNA have formed on early Earth?
On charged clay surfaces (e.g. iron pyrite), which aligned nucleotides and catalyzed polymerization. Thermal cycles may have split strands, allowing replication.
36
What paradox does the RNA world solve?
Proteins need nucleic acids to form, but nucleic acids need proteins. RNA could do both, solving this chicken-and-egg problem.
37
What did Joyce (1992) demonstrate with evolving ribozymes?
He isolated a ribozyme from Tetrahymena that could cut and attach RNA. After 12 selection rounds, variants that worked better with Ca²⁺ dominated, showing RNA evolution by selection.
38
What is RNA-catalyzed RNA polymerization?
Lab-made ribozymes can synthesize short RNA strands (~14 nucleotides) with enzyme-like activity, suggesting RNA once self-replicated.
39
How might RNA have led to DNA and proteins?
RNA may have encoded proteins, including reverse transcriptase, which copied RNA into DNA. DNA is more stable, allowing for larger genomes and better information storage.
40
How did protocells likely form?
Lipid bilayers formed micelles or vesicles, isolating RNA inside. These vesicles could grow, divide, and evolve, mimicking basic cellular life.
41
How can RNA cause protocell growth and division?
RNA synthesis builds charge → ions and water enter → osmotic pressure causes vesicle to swell and divide when membranes interact.
42
What are the basic requirements for life?
Liquid water – solvent for biochemical reactions.
## Footnote
Energy – for assembling molecules, replication, movement, etc.
43
How do organisms obtain energy?
Phototrophs – use light (400–700 nm).
## Footnote
Chemoorganotrophs – use organic chemicals.
Chemolithotrophs – use inorganic compounds (e.g., H₂, Fe²⁺, S compounds).
44
What are chemolithotrophs and where are they found?
Found in deep-sea hydrothermal vents; use inorganic chemicals to make organic matter, often in symbiosis with animals like tubeworms.
45
Why is energy so important in biology?
It limits growth, survival, reproduction, and must be allocated efficiently due to internal and external constraints.
46
What are essential elements for life?
28 elements, mainly CHOPNS (Carbon, Hydrogen, Oxygen, Phosphorus, Nitrogen, Sulfur). Organisms extract and concentrate them from the environment.
47
What determines elemental availability?
Environment type, geological history, and evolutionary adaptation (e.g., red algae need less iron than green algae due to changing Fe availability).
48
What are the trophic classifications of organisms based on carbon?
Autotrophs: Use inorganic C (CO₂).
## Footnote
Heterotrophs: Use organic C (carbs, proteins, fats).
49
What limits algal growth in aquatic environments?
Low nitrogen and phosphorus; algal blooms often occur with increased nutrient input (e.g., runoff).
50
What’s the difference between acclimation and adaptation to nutrient availability?
Acclimation: Short-term response (e.g., changing root:shoot ratio).
## Footnote
Adaptation: Long-term evolutionary change in metabolism or nutrient use.
51
What were Earth’s early environmental conditions?
Anaerobic, hot, rich in gases like H₂, CO₂, N₂, SO₂. No oxygen present.
52
What were two hypotheses for the first organism’s metabolism?
Chemolithoautotroph: Used H₂ for energy and CO₂ for carbon (favored).
## Footnote
Heterotroph: Used abiotically formed organic matter (less likely due to dilution).
53
What traits did early organisms likely have?
Anaerobic
## Footnote
Prokaryotic (bacteria/archaea)
Hyperthermophilic & halophilic
Possibly similar to methanogens.
54
What evidence supports early chemolithoautotrophs?
Modern hyperthermophiles are near root of phylogenetic tree.
## Footnote
Use H₂ for energy and Fe/S as electron acceptors. Magnetite deposits (Fe₃O₄) from Archaean show iron metabolism.
55
How did early microbial communities evolve?
Biofilms formed, with layered organisms using each other's metabolic byproducts as energy sources.
56
What type of photosynthesis evolved first?
Anoxygenic (no O₂ release), using sulfur compounds and bacteriochlorophyll.
57
When did oxygenic photosynthesis evolve?
~3.5–2.7 bya via cyanobacteria using water as an electron donor, releasing O₂.
58
Why did O₂ not accumulate in the atmosphere at first?
It reacted with Fe in oceans and volcanic gases. Accumulation began ~2.45 bya.
59
What were the major effects of oxygenation?
Enabled aerobic respiration (more efficient than fermentation).
## Footnote
Changed ocean chemistry (e.g., sulfur and nitrogen cycling). Formed ozone layer (O₃), protecting life from UV. Toxic to anaerobes, forcing them into isolated habitats. Life evolved enzymes to detoxify reactive oxygen species (e.g., superoxide dismutase).
60
What are the main characteristics of prokaryotic cells?
No nucleus or membrane-bound organelles
## Footnote
DNA in a single circular chromosome
70S ribosomes
Peptidoglycan cell wall
Divide by binary fission
Generally small.
61
What distinguishes eukaryotic (animal) cells from prokaryotes?
Larger size
## Footnote
Has nucleus, mitochondria, cytoskeleton
80S ribosomes
Divide via mitosis
Capable of endocytosis.
62
What is the endosymbiotic theory?
Proposed by Lynn Margulis; mitochondria and chloroplasts were once free-living bacteria engulfed by an archaeal host → evolved into obligate symbionts.
63
What bacteria are mitochondria and chloroplasts derived from?
Mitochondria → Proteobacterium
## Footnote
Chloroplast → Cyanobacterium.
64
What supports the endosymbiotic origin of mitochondria and chloroplasts?
Own circular DNA (bacterial-like)
## Footnote
Double membranes
Similar electron transport chains
Sensitive to antibiotics
Have 70S ribosomes.
65
What is secondary endosymbiosis?
A eukaryote engulfs another eukaryote that already contains a chloroplast (from cyanobacteria).
## Footnote
Example: Cryptomonads have a nucleomorph (remnant nucleus of engulfed algae).
66
What is the significance of Lokiarchaeota?
Discovered near deep-sea vents
## Footnote
Shares genes with eukaryotes
Has actin, does endocytosis
Prometheoarchaeum syntrophicum (2020) supports the archaeal host model of eukaryotic origin.
67
What are the 3 domains of life identified by Carl Woese?
Bacteria
## Footnote
Archaea
Eukarya.
68
What is molecular phylogeny based on?
rRNA gene sequences – used to determine evolutionary relationships.
69
What is horizontal gene transfer (HGT)?
Gene transfer between species (not parent to offspring) via viruses, plasmids, or during endosymbiosis.
## Footnote
Example: 20% of E. coli genome from HGT.
70
When did Eukarya originate and what are the 4 traditional kingdoms?
Origin: ~2.7–1.7 BYA
## Footnote
Kingdoms: Plants, Animals, Fungi, Protists.
71
What defines protists?
Mostly unicellular eukaryotes, diverse in lifestyle (e.g., parasitic, autotrophic, heterotrophic).
72
What are key features of Excavates?
Unicellular, many are parasitic.
## Footnote
Anaerobic.
Often lack mitochondria.
Include: Trichonympha (symbiont in termites), Entamoeba histolytica (dysentery), Trypanosoma (sleeping sickness; has kinetoplast).
73
What defines protists?
Mostly unicellular eukaryotes, diverse in lifestyle (e.g., parasitic, autotrophic, heterotrophic)
74
What are key features of Excavates?
Unicellular, many are parasitic
## Footnote
Anaerobic, often lack mitochondria, include: Trichonympha (symbiont in termites), Entamoeba histolytica (dysentery), Trypanosoma (sleeping sickness; has kinetoplast)
75
What are Chromalveolates?
Diverse group from secondary/tertiary endosymbiosis; includes: Alveolates (e.g., Dinoflagellates, Apicomplexa), Stramenopiles (e.g., Diatoms, Oomycetes, Brown algae)
76
What are dinoflagellates known for?
Red tides, bioluminescence, paralytic shellfish poisoning, coral symbionts
77
What is Apicomplexa?
Obligate parasites with complex life cycles (e.g., Plasmodium → malaria)
78
What are diatoms?
Photosynthetic, silica cell walls
## Footnote
Major primary producers (~25% of global photosynthesis)
79
What are oomycetes?
Fungal-like water molds
## Footnote
Cause plant diseases: grape mildew, potato blight
80
What is Phaeophyta?
Brown algae (e.g., seaweed); multicellular, no unicellular forms
81
What are key traits of Rhizaria?
Heterotrophic, produce calcium carbonate skeletons, use pseudopodia to feed
## Footnote
Contribute ~1/3 of zooplankton
82
Who belongs to Archaeplastida?
Red algae, Green algae, Land plants
## Footnote
Originated via primary endosymbiosis of cyanobacteria
83
What is Chlamydomonas?
A model unicellular green alga
## Footnote
Volvox = colonial form, Chara = green algae with structures like land plants → possible ancestor
84
What are Unikonts?
Include amoebae, slime molds, fungi, animals
## Footnote
Choanoflagellates are closest relatives to animals → similar to sponge cells
85
What is evolution?
Evolution is descent with modification—the change in inherited traits of a population over generations
86
What is a lineage?
A chain of ancestor–descendant connections over time.
87
What is natural selection?
A process where lineages with higher fitness (faster replication) become more common over time.
88
What causes variation in fitness?
Genetic differences affect replication success; this leads to selection.
89
Q: What is adaptation?
A heritable trait that increases fitness in a given environment and arises through natural selection.
90
Can evolution happen without natural selection?
Yes. Other mechanisms:
- Mutation
- Migration
- Genetic drift
BUT Only natural selection creates adaptations.
91
Q: What is fitness?
The genetic contribution of a lineage to the next generation.
92
What’s the difference between absolute and relative fitness?
Absolute fitness (wᵢ): growth rate or # of offspring
Relative fitness: absolute fitness compared to others (e.g., wᵢ / wₐᵥg)
93
How do mutations drive evolution?
Mutations create genetic variation. Rare beneficial mutations can spread through populations if they increase fitness.
Example: Mega-plate experiment → bacteria evolved antibiotic resistance in 11 days through beneficial mutations.
94
Q: What are the 6 key lines of evidence for evolution?
Common descent
Homologous traits
Fossils
Extinction and succession
Developmental biology
Convergent evolution
95
What is common descent?
All organisms share a common ancestor. Universal traits (like DNA) are inherited from LUCA (Last Universal Common Ancestor).
96
What are homologous traits?
Traits shared due to inheritance from a common ancestor (e.g., vertebrate limb bones).
97
What does the fossil record show?
A chain from ancestors to descendants; Extinct species with shared features; Evolutionary transitions (e.g., horse evolution over 55 MY).
98
What does extinction imply about evolution?
Most species go extinct (~5 MY lifespan); New species arise through speciation; Major groups replace each other over time.
99
What is convergent evolution?
Independent evolution of similar traits in unrelated lineages due to similar selective pressures (e.g., sharks, whales, fish).
100
Why is adaptation often imperfect?
Evolution is contingent on available materials; Works like a tinkerer, not a designer; Example: human eye has a blind spot.
101
How does development reveal evolutionary history?
Early developmental stages are conserved; Changes early in development have large effects.
102
How does the environment drive selection?
Environments impose pressures → organisms adapt; Example: Galápagos finches underwent adaptive radiation based on available resources.
103
Is evolution “just” a theory?
No. A theory is a well-supported framework of explanations; Evolution is supported by extensive evidence and comprises many testable hypotheses.
104
What defines evolution?
Change in the genetic composition of a population over time; Driven by mutation, selection, drift, migration; Leads to diversity, adaptation, and new species.
105
What is phylogeny?
The evolutionary history of a lineage or lineages (populations, genes, or species).
106
What is a phylogenetic tree?
A visual representation of a phylogeny.
107
What is the difference between pedigree and phylogeny?
Pedigree: individuals; nodes represent recombined genomes from two parents; any number of offspring. Phylogeny: populations; nodes represent populations; usually branching with two descendant branches.
108
What do nodes represent in a phylogenetic tree?
Common ancestors for all descendant lineages.
109
What is a clade?
A common ancestor and all its descendants (a monophyletic group).
110
Are tips of a phylogenetic tree more advanced or evolved?
No, tips are not necessarily more advanced; no existing species is ancestral to any other.
111
What defines monophyletic, paraphyletic, and polyphyletic groups?
Monophyletic: all species from a common ancestor. Paraphyletic: leaves out some taxa sharing a common ancestor. Polyphyletic: includes taxa from multiple common ancestors.
112
How are characters and character states defined?
Characters are heritable traits; character states are conditions of the character (e.g., wings present or absent).
113
How do biologists distinguish ancestral vs derived characters?
Using fossils and outgroups to identify ancestral (shared with outgroup) vs derived (not shared) states.
114
What is a synapomorphy?
A shared derived character state inherited from a common ancestor.
115
What is homoplasy?
Similarity in traits not due to common descent caused by convergent evolution or evolutionary reversals.
116
What is the principle of maximum parsimony?
The preferred evolutionary hypothesis requires the fewest evolutionary steps.
117
How can fossils aid phylogenetic analysis?
Fossils constrain divergence times by dating related clades and provide evidence for evolutionary transitions.
118
What is the significance of coelacanths in evolution?
Coelacanth fins are homologous to tetrapod limbs, sharing a common ancestor ~500 MYA.
119
What is Tiktaalik?
A transitional fossil between fish and tetrapods showing limb homologies more similar to tetrapods.
120
Can homologous traits be obvious or not?
They can be obvious (e.g., orangutan vs human feet) or subtle (e.g., mammalian ear bones homologous to reptilian jaw bones).
121
What is the evolutionary significance of birds being dinosaurs?
Birds descended from dinosaurs; feathers evolved before flight, initially for species recognition and later co-opted for flight (exaptation).
122
What are the two classes of mutations in sequence data?
Synonymous substitutions (do not change protein, evolve neutrally) and nonsynonymous substitutions (change protein, subject to selection).
123
What does a dN/dS ratio indicate?
dN/dS = 1 means neutral evolution; <1 purifying selection; >1 positive selection.
124
How is dN and dS calculated?
dN = # nonsynonymous mutations / # nonsynonymous sites; dS = # synonymous mutations / # synonymous sites.
125
What type of selection acts on the BRCA1 gene in primates and humans?
Purifying selection in primates; positive selection in humans.
126
How does Pseudomonas aeruginosa adapt in cystic fibrosis (CF) lungs?
Strong positive selection drives adaptation to the lung environment.
127
What key ideas relate to mutation rates in genes and genomes?
Different sites and regions evolve at different rates; neutral sites evolve clock-like and help time events.
128
What is macroevolution vs microevolution?
Macroevolution: evolution above species level; Microevolution: allele and gene frequency changes within populations.
129
What is speciation?
Genetic changes within populations leading to new evolutionary lineages.
130
What are three key patterns in life's diversity?
Increasing diversity over time, uneven diversification among lineages, and some environments have more species.
131
What is biogeography?
Study of species distribution across space and time.
132
How do dispersal and vicariance explain biogeographical patterns?
Dispersal: population movement with limited return; Vicariance: geographic barriers dividing populations.
133
How did marsupials evolve according to phylogeny and fossil records?
Originated from South America, fossils in China and North America, Australian marsupials derived from S. American lineages.
134
What is anagenesis and cladogenesis in macroevolution?
Anagenesis: gradual change without splitting; Cladogenesis: speciation with splitting, often faster.
135
What is punctuated equilibrium?
Long periods of stasis interrupted by brief rapid changes, possibly due to fossil record gaps.
136
How is diversity (D) balanced in macroevolution?
Diversity = originations - extinctions.
137
What defines adaptive radiation?
Rapid diversification (originations >> extinctions) into ecological niches, driven by ecological opportunity.
138
What creates ecological opportunity?
Vacant niches, absence of competitors or predators, and key innovations.
139
What is an evolutionary novelty?
A new genetically based trait introduced into a lineage.
140
What is the paradox of novelty?
Changing a functional trait often reduces fitness despite natural selection working with available material.
141
What is the EAD model?
Exaptation (new role for existing genes), Amplification (increase gene copies), Divergence (gene copies evolve new functions).
142
How did E. coli evolve citrate metabolism aerobically?
Gene duplication and mutation allowed citT expression in oxygen presence, leading to citrate specialization.
143
How did snake venom evolve?
Venom genes derived from defensin genes, duplicated and expressed in venom glands, changing protein function.
144
What was the Cambrian explosion?
Sudden appearance of diverse animal body forms ~541 MYA, preceded by genetic groundwork and ecological opportunities.
145
What role do developmental genes play in evolution?
Control early body plan development; mutations can cause major morphological changes.
146
What causes extinction?
Small population size, deleterious mutations, hunting, habitat loss.
147
What is background vs mass extinction?
Background extinction: normal rate; Mass extinction: large increase often linked to events like volcanism or asteroid impacts.
148
What is significant about the K-T boundary?
Layer with high iridium suggesting asteroid impact 66 MYA causing mass extinction including mollusks.
149
What is the basic logic of evolution through selection?
Some genetic variants replicate faster than others, faster replicating lineages contribute more offspring to the next generation, causing faster replicating lineages to replace slower ones.
150
What creates genetic variation?
Mutations occurring occasionally during DNA replication create genetic variation.
151
What is a mutation?
Any change in the genetic sequence that can be inherited by offspring.
152
How is DNA organized in eukaryotes vs prokaryotes?
Eukaryotes have multiple chromosomes; prokaryotes usually have circular DNA.
153
How is genetic information converted to protein?
DNA is transcribed to RNA, then translated into proteins; this process is fundamentally the same in eukaryotes and prokaryotes.
154
What type of genetic material do viruses like SARS-CoV-2 use?
Some viruses use RNA instead of DNA.
155
What are proteins made of?
Chains of amino acids.
156
What is the genetic code redundancy?
There are 64 codons but only 20 amino acids, so mutations that change the codon but not the amino acid are called synonymous or silent.
157
What are pseudogenes?
Genetic sequences that are not used or expressed.
158
How do prokaryotes differ in gene organization?
Prokaryotes often organize genes into operons producing common proteins.
159
Are all genes always expressed?
No, some genes are turned on or off; microRNAs can block translation and affect gene expression.
160
What is alternative splicing?
A process in eukaryotes where one gene can produce multiple proteins by splicing RNA differently.
161
What is ploidy?
The number of copies of unique chromosomes in a cell.
162
How do gene duplications affect evolution?
Gene duplications can explain rapid diversification and the rise of new clades.
163
What is the C-value paradox?
Genome size does not correspond to organismal complexity, often due to pseudogenes and mobile genetic elements.
164
What are the main types of mutations?
Point mutations, insertions, deletions, gene duplications, inversions, chromosome fusions, and whole genome duplications.
165
What is the difference between germline and somatic mutations?
Germline mutations are heritable and affect gametes; somatic mutations affect body cells and are not heritable.
166
What controls complex adaptations?
Hierarchical regulatory networks, such as Hox genes, control complex adaptations during development.
167
What is the effect of mutations on fitness?
Most mutations are deleterious, some neutral, and very few beneficial; beneficial mutations usually cause small improvements.
168
How does recombination affect evolution?
Recombination generates new genetic combinations by unlinking mutations and assembling independently arising mutations into the same genome.
169
Why has sexual reproduction been selected over asexual reproduction?
Sexual reproduction allows evolution to happen faster by creating more genetic combinations.
170
What is the difference between genotype and phenotype?
Genotype is the genetic makeup; phenotype is the observable characteristic resulting from genotype and environment.
171
What is phenotypic plasticity?
A single genotype produces multiple phenotypes depending on environmental conditions.
172
What does quantitative genetics study?
Traits showing continuous phenotypic variation influenced by multiple genes and environmental factors.
173
How do genes and environment influence traits like human height?
Genes and environment interact; phenotype (P) is the sum of genetic (G) and environmental (E) effects: P = G + E.
174
What is quantitative trait locus (QTL) analysis?
It examines known genetic markers across the genome to identify those linked to high or low values of a trait.
175
What does a high LOD score indicate in QTL analysis?
A strong association between a genetic marker and a trait that is unlikely due to chance.
176
What important note is there about markers used in genetic studies?
Markers are usually not the gene of interest themselves but linked regions used to infer associations.
177
What is a population in evolutionary biology?
A group of interacting and potentially interbreeding individuals of the same species.
178
What is a genetic locus?
The specific location of a gene or DNA sequence on a chromosome; can refer to an allele, segment, or even a single nucleotide.
179
What is genotype?
The combination of alleles carried by an individual at one or more loci.
180
What does population genetics study?
The distribution and frequency of alleles in populations over space and time.
181
How is evolution defined in population genetics?
Change in allele frequencies from one generation to the next.
182
How can we tell if a population is evolving?
By tracking changes in allele or genotype frequencies over generations and comparing observed frequencies to a null model (Hardy-Weinberg equilibrium).
183
What are the assumptions of the Hardy-Weinberg null model?
Diploid individuals, infinite population size, no fitness differences among genotypes, no mutation, random mating, no migration.
184
What does Hardy-Weinberg equilibrium predict?
Allele frequencies remain constant across generations if assumptions hold, and genotype frequencies follow p², 2pq, q² proportions.
185
What causes deviations from Hardy-Weinberg equilibrium?
Genetic drift, natural selection, mutation, migration, non-random mating.
186
What is genetic drift?
Random fluctuations in allele frequencies due to sampling effects in finite populations.
187
How does genetic drift affect populations?
Can cause alleles to become fixed or lost, reducing genetic variation; effects are stronger in small populations.
188
What are bottlenecks and founder effects?
Bottleneck: temporary reduction in population size; founder effect: a small group establishes a new population, both cause drift and reduce variation.
189
What is inbreeding?
Mating between related individuals, increasing the chance that alleles are identical by descent.
190
What is the inbreeding coefficient (F)?
The probability that two alleles at a locus in an individual are identical by descent.
191
What is inbreeding depression?
Reduced fitness caused by increased homozygosity of deleterious recessive alleles due to inbreeding.
192
What is fitness in evolutionary terms?
The ability to survive to reproductive age, mate successfully, and produce viable offspring.
193
What is relative fitness (w)?
The fitness of a genotype standardized relative to others, often compared to mean population fitness.
194
How do mutations affect evolution?
Mutations introduce new alleles; their fate depends on fitness effects and genetic drift.
195
What is mutation-selection balance?
Equilibrium where deleterious mutations are introduced by mutation but removed by selection, maintaining a low allele frequency (p ≈ sqrt(μ/s) in haploids).
196
How does natural selection act in populations of different sizes?
More effective in large populations; drift dominates in small populations.
197
What is balancing selection?
Selection that maintains genetic diversity, e.g., heterozygote advantage or negative frequency-dependent selection.
198
Give an example of heterozygote advantage.
Sickle cell anemia heterozygotes have increased malaria resistance.
199
What is negative frequency-dependent selection?
Common phenotypes are selected against while rare phenotypes are favored, maintaining diversity.
200
What is migration in population genetics?
Movement of individuals between populations, which can homogenize allele frequencies.
201
What is Fst?
A measure of genetic divergence among subpopulations; values near 0 indicate little divergence, near 1 indicate high divergence.
202
How does subdivision affect heterozygosity?
Subdivision increases inbreeding within subpopulations, causing fewer heterozygotes than expected under random mating.
203
Why is migration called the “glue” holding subpopulations together?
Because it counters divergence by mixing alleles among subpopulations, reducing genetic differentiation.
204
What is the fundamental cause of natural selection?
Genetic variation arises from imperfect replication of DNA/RNA, and variants that replicate faster leave more offspring.
205
In the Qβ RNA virus experiment
what adaptations were observed?
206
How is the selection coefficient (s) estimated experimentally?
By competing genetically marked evolved and ancestral strains and tracking their frequency changes over time.
207
What is the purpose of 'evolve and resequence' experiments?
To archive populations, reconstruct evolutionary history, and examine the effects of mutations.
208
What are polygenic traits?
Traits influenced by many genes, resulting in continuous variation in phenotypes.
209
What components make up phenotypic variance (Vp)?
Genetic variance (Vg) + Environmental variance (Ve).
210
Define broad-sense heritability (H²).
The proportion of phenotypic variance attributable to genetic differences.
211
What is the selection differential (S)?
The difference in the mean phenotype of selected parents versus the population mean.
212
How do traits respond to selection?
The response (R) depends on heritability (h²) and the selection differential (S): R = h² × S.
213
How did beak size in Galapagos finches change in response to drought?
Strong selection favored larger beaks to crack harder seeds, increasing beak size.
214
What evolutionary pattern is seen repeatedly in stickleback fish?
Parallel evolution of reduced armor in freshwater populations.
215
Why is the low-eda allele favored in freshwater sticklebacks?
Armor production is costly, so the low-eda allele reduces armor where predators differ.
216
How have humans caused evolutionary change in domesticated species?
Artificial selection for desirable traits and bottlenecks reduced genetic diversity.
217
What is a common outcome of widespread pesticide or antibiotic use?
Evolution of resistance due to strong selection and large populations.
218
How does hunting and fishing affect wild populations?
They select for earlier reproduction and smaller body size, affecting population sustainability.
219
What is a neutral allele?
An allele that takes a long time to fix in a population because it’s not under selection.
220
Define selective sweep.
Rapid fixation of a beneficial allele due to positive selection.
221
What is genetic hitchhiking?
When nearby mutations increase in frequency because they are linked to a selected allele.
222
How does recombination affect genetic hitchhiking?
It slowly breaks linkage between alleles over time.
223
What signature does strong selection leave on genetic diversity?
Reduced diversity around the selected site due to elimination of low fitness variants.
224
Describe the pattern of diversity around a selected site.
A V-shaped reduction in genetic diversity along the genome.
225
Why does diversity remain low near selected sites for a time?
Because recombination can’t quickly break linkage.
226
Example of genetic hitchhiking in humans?
Lactose tolerance alleles linked with cattle domestication show broader linked DNA regions.
227
What percentage of humans maintain lactase production as adults?
About 30%.
228
What are synonymous substitutions?
Mutations that do not change the protein sequence.
229
What are nonsynonymous substitutions?
Mutations that change the protein sequence.
230
What does a dN/dS ratio of 1 mean?
Neutral evolution—nonsynonymous mutations evolve at the same rate as synonymous ones.
231
What does dN/dS > 1 indicate?
Positive selection.
232
What does dN/dS < 1 indicate?
Purifying (negative) selection.
233
What evolutionary pattern was observed in the BRCA1 gene?
Positive selection in humans
234
Why might BRCA1 mutations be positively selected despite cancer risk?
They may confer other evolutionary advantages balancing the risk.
235
What pathogen shows stronger selection in chronic infections?
Pseudomonas aeruginosa.
236
What does higher dN/dS in chronic Pseudomonas isolates suggest?
Strong selection in chronic infection environments.
237
How do neutral sites help evolutionary studies?
They evolve at a constant rate
238
How can sequence data reveal selection?
By analyzing linkage patterns and comparing nonsynonymous vs synonymous substitution rates.
239
What is BRCA1?
A gene that suppresses breast cancer by repairing DNA damage.
240
What fuels evolutionary change?
Genetic variation.
241
What is the source of genetic variation?
Mutation.
242
What is a mutation?
Any heritable change to the DNA sequence.
243
What are the two main types of mutations?
Somatic (non-heritable) and germ-line (heritable).
244
Which type of mutation is evolutionarily relevant?
Germ-line mutations.
245
What is DNA?
A molecule that stores genetic information for building proteins.
246
How is DNA copied?
By base-pairing: A with T
247
What is a gene?
A sequence of DNA that codes for a protein.
248
How is DNA organized in eukaryotes?
Into multiple linear chromosomes.
249
How is DNA organized in prokaryotes?
Usually a single circular chromosome
250
What is the process from DNA to protein?
DNA → mRNA (transcription) → protein (translation).
251
What reads mRNA to make proteins?
Ribosomes using tRNA.
252
What is a codon?
A 3-nucleotide sequence in mRNA that codes for an amino acid.
253
How many codons are there?
64
254
Why is the genetic code redundant?
Multiple codons code for the same amino acid.
255
What is a synonymous (silent) mutation?
A mutation that does not change the amino acid.
256
What is a nonsynonymous mutation?
A mutation that changes the amino acid.
257
What are proteins made of?
Chains of amino acids.
258
What do proteins do?
They form cell structures and carry out cellular functions.
259
What is the genome?
The entire genetic material of an organism.
260
What is the C-value paradox?
Genome size doesn’t always match organismal complexity.
261
What are pseudogenes?
Non-functional sequences in the genome.
262
What is recombination?
Exchange of genetic material between chromosomes.
263
What does recombination do?
It creates new genetic combinations but not new mutations.
264
What is a polygenic trait?
A trait influenced by many genes and the environment.
265
What is a polyphenism?
A single genotype producing different phenotypes based on environment.
266
What does P = G + E mean?
Phenotype equals genetics plus environment.
267
What is a QTL (Quantitative Trait Locus)?
A genomic region linked to variation in a quantitative trait.
268
What is the Fisher-Muller hypothesis?
Sexual reproduction increases adaptation by combining beneficial mutations.
269
What does Fisher’s geometric model predict?
Most mutations are deleterious; few are beneficial.
270
Why is linking genotype to phenotype hard?
Because traits are often influenced by many genes and environmental factors.
Biol 112
flashcards
Decks in class (6)
# Cards
