Exam 3 Study Guide

Ancient DNA Problems & Solutions
Q: What are the main problems with ancient DNA?
A: Contamination (from bacteria/fungi or modern humans) and highly degraded DNA (short 100-200bp fragments). Solutions include targeting mitochondrial DNA (more abundant), using Alu-repeat regions to avoid contamination, and working with cold/dry preserved specimens.

PCR Revolution
Q: Why did PCR revolutionize ancient DNA research?
A: Before PCR (pre-1985), cloning DNA was slow and labor-intensive. PCR allowed amplification of tiny, degraded fragments from specimens like the Denisovan finger bone (2010).

DNA Preservation Conditions
Q: What conditions favor DNA preservation?
A: Cold, dry, anoxic environments (permafrost, amber) best preserve DNA. Warm/wet conditions accelerate degradation. Example: 700,000-year-old horse DNA preserved in Canadian permafrost.

Group Selection
Q: What is group selection?
A: The idea that natural selection can act on whole groups, not just individuals.

Kin Selection Advantage
Q: Why is kin selection better than group selection?
A: Group selection is mathimatically flawed, has no clear mechanism, and is rare in nature. Kin selection works better due to Hamilton's Rule (rB > C), genetic evidence and predictive power.

Green Beard Effect
Q: What is the green beard effect?
A: A rare case where a single gene causes: A visible trait ("green beard"), Ability to recognize others with the same trait, Altruistic behavior toward those individuals. Example is Red fire ant workers kill queens without a specific gene.

Biological Species Concept
Q: Define the Biological Species Concept.
A: Species are groups of actually or potentially interbreeding organisms reproductively isolated from other such groups (Mayr 1940). Example: Quagga vs. plains zebra hybrid viability.

Phylogenetic Species Concept
Q: Define the Phylogenetic Species Concept.
A: The smallest diagnosable cluster with a parental pattern of ancestry/descent (Cracraft 1983). Example: Mammoth-Asian elephant-African elephant phylogeny.

Reproductive Isolation Examples
Q: Give examples of pre- and post-mating isolation.
A: Pre-mating: Gryllus crickets (spring vs fall mating seasons). Post-mating: Horse × donkey produces sterile mules.

DNA Testing for Isolation
Q: Why use DNA to test reproductive isolation?
A: Genetic markers reveal if populations share alleles (gene flow) or are diverged (isolated). Example: SE U.S. fish showed distinct clades despite geographic overlap.

Species Concept Limitations
Q: Why are species concepts limited?
A: BSC fails for fossils/asexual species; PSC can split populations arbitrarily (e.g., Greya moths with gene flow between clades).

Greya Moths PSC Problem
Q: When does PSC fail for Greya moths?
A: Greya mitellae nests within G. piperella phylogeny, making clean species divisions impossible despite reproductive isolation. Issue: Incomplete lineage sorting → Recent divergence causes conflicting gene trees (e.g., Locus 1 groups B+C; Locus 2 groups A+C).

Locus 1 Tree: (A, (B, C))

Locus 2 Tree: (B, (A, C))

Allopatric Speciation Model
Q: Describe allopatric speciation.
A: Physical barrier divides population, stopping gene flow. Subpopulations evolve independently (e.g., snapping shrimp divided by Panama Isthmus).

Allopatric Evidence
Q: Evidence for allopatric speciation?
A: Vicariance (SE U.S. fish/plants split by ancient sea levels) and founder effects (Greya mitellae from G. piperella subset).

Vicariance
Q: Define vicariance.
A: Geographic separation of populations by barriers (e.g., mountain rise), leading to independent evolution. Evidence: Mirror phylogenies in Amazonian species.

Founder Effect Speciation
Q: Define founder effect speciation.
A: Small, isolated population diverges rapidly (e.g., island kingfishers). Evidence: Derived species nest within ancestral clades (Greya moths).

Vicariance vs Founder Phylogenies
Q: Compare their phylogenetic patterns.
A: Vicariance shows symmetric splits; founder effects show derived species nested within ancestral diversity.

Mayr's Founder Mechanism
Q: Why is Mayr's founder mechanism rejected?
A: He proposed severe bottlenecks drive speciation, but most isolates (e.g., Greya mitellae) retain genetic diversity. Modern view emphasizes selection + mild drift.

Disruptive Selection
Q: Describe disruptive (diversifying) selection.
A: A form of natural selection that favors extreme phenotypes over intermediate forms, potentially leading to speciation.

Sympatric Speciation Process
Q: How does sympatric speciation overcome recombination?
A: Requires:

Strong disruptive selection (e.g., host specialization in apple maggot flies)
Assortative mating (preference for same-host mates)
Genetic linkage of adaptive and mating traits
(Find specific mechanisms in powerpoints)

Sympatric Speciation Examples
Q: What are examples of sympatric speciation?
A:

Apple maggot flies (Rhagoletis) - ongoing divergence on apple vs hawthorn hosts
Arctic charr in Icelandic lakes - multiple ecotypes in single lakes
Lake Apoyo cichlids - new species evolved within the lake
Kentia and curly palms

Proving Sympatric Speciation
Q: How demonstrate sympatric rather than allopatric speciation?
A: Must show:

Current sympatry of sister species
No historical geographic barriers
Ecological divergence without isolation
Genetic signatures of disruptive selection
(Find evidence requirements in powerpoints)

Parapatric Speciation
Q: Describe parapatric speciation.
A: Find information from powerpoints (sweet vernal grass example).

Polyploid Definition
Q: Define polyploid.
A: An organism with >2 complete chromosome sets (e.g., tetraploid 4n, hexaploid 6n). Common in plants like wheat (6n) and potato (4n).

Autopolyploid Speciation
Q: Describe autopolyploid speciation.
A: Speciation via genome duplication within a species. Example: Cultivated potato (Solanum tuberosum) originated from diploid ancestors through chromosome doubling.

Allopolyploid Speciation
Q: Describe allopolyploid speciation.
A: Speciation via hybridization + genome doubling between species. Example: Bread wheat (Triticum aestivum, 6n) formed from three ancestral species through sequential polyploidization events.

Plant Polyploid Advantages
Q: Why more polyploid plants than animals?
A: Plants can:

Self-fertilize (establish populations from single individuals)
Reproduce vegetatively (maintain sterile hybrids)
Tolerate genome duplications better developmentally
Animal exceptions: Parthenogenic stick insects and snails.

Recombinational Speciation
Q: Describe recombinational speciation with example.
A: Fertile hybrid species form without ploidy change via chromosome recombination. Example: Helianthus anomalus sunflowers originated from H. annuus × H. petiolaris hybrids with reshuffled genomes.

Coevolution Definition
Q: Define coevolution.
A: Reciprocal evolutionary change between interacting species (e.g., hosts-parasites, plants-pollinators).

Medical Coevolution
Q: How does evolution affect medicine and drug resistance?
A: Germs (like TB/cholera) evolve to survive medicines (antibiotic resistance). The more we use antibiotics, the faster resistance spreads. TB → Some strains now survive multiple drugs (MDR-TB). Cholera → Overused antibiotics make it harder to treat.

Genetic Drift
Q: What is genetic drift?
A: Random allele frequency changes, stronger in small populations. More impactful in small populations due to sampling error and founder effect / bottleneck

Genetic Bottleneck
Q: What is a genetic bottleneck?
A: Severe population reduction lowers diversity (e.g., Quagga extinction).

Founder Effect
Q: What is the founder effect?
A: Small colonizing population has non-representative allele frequencies (e.g., Greya mitellae from G. piperella subset).

Hardy-Weinberg Equilibrium
Q: Conditions for H-W equilibrium?
A: No mutations, No natural selection, Random mating, Extremely large population size, No gene flow (migration)