Evolutionary Biology: Phylogenetics, Origin of Life, Speciation, Mechanisms, and Descent with Modification

Flashcards testing core concepts, historical figures, mathematical equations, mechanisms, and examples across all five sources covering evolutionary biology.

What is binomial nomenclature, and who established it?

A two-part Latin naming system for species consisting of the genus name (capitalized) and the specific epithet or species name (lowercase), both italicized; established by Carolus Linnaeus in 1753.

What are the seven main hierarchical taxonomic categories in order from broadest to most specific?

Kingdom, Phylum, Class, Order, Family, Genus, Species.

In phylogenetic tree anatomy, what do internal nodes, sister taxa, and outgroups represent?

An internal node (branch point) represents a speciation event where lineages diverge; sister taxa share an immediate common ancestor; an outgroup (basal taxon) diverges early in the history of a group near the common ancestor.

What defines a species according to the Phylogenetic Species Concept?

A species is defined as the smallest set of organisms that share a common ancestor (a tip on a phylogeny) and can be distinguished from other sets by a unique set of genetic or morphological traits.

How do monophyletic, paraphyletic, and polyphyletic groups differ in phylogenetic classification?

A monophyletic group (clade) consists of an ancestral species and all of its descendants; a paraphyletic group consists of an ancestral species and some, but not all, descendants; a polyphyletic group includes distantly related taxa but omits their most recent common ancestor.

Which genetically conserved regions are typically used in molecular systematics for prokaryotes, animals, and plants?

Ribosomal RNA (rRNA) for prokaryotes and fungi, mitochondrial DNA (mtDNA) for animals, and chloroplast DNA (cDNA) for plants.

What is the principle of maximum parsimony in phylogenetic reconstruction?

It assumes that the tree requiring the fewest evolutionary events (the fewest appearances or changes of shared derived characters) is the most likely tree.

What is the difference between orthologous genes and paralogous genes?

Orthologous genes result from a speciation event, are found in different species, and retain equivalent functions; paralogous genes result from gene duplication within a single species and can diverge to acquire new functions.

How is a molecular clock calibrated, and what assumption does it make?

It assumes that certain genes evolve at a constant rate so that nucleotide substitutions are proportional to time since divergence; it is calibrated by graphing genetic differences against branch point dates known from the fossil record.

How did major classification systems evolve from Linnaeus (1735) to Whittaker (1969) and Woese (1990)?

Linnaeus proposed a 2-Kingdom system (Plantae and Animalia); Whittaker proposed a 5-Kingdom system (Monera, Protista, Fungi, Plantae, Animalia); Carl Woese proposed a 3-Domain system (Bacteria, Archaea, Eukarya) based on rRNA and genomic data.

What is the current scientific consensus on the age of Earth, and how was it determined?

Approximately $4.54 \times 10^9 \text{ years}$ ($4.54 \text{ billion years}$), determined through radiometric dating of meteorites, lunar rocks, and Earth's oldest minerals.

What environmental conditions characterized early Earth during the Hadean Eon?

Liquid water formed early ($\text{time} \neq \text{unknown}$, stable hydrosphere at $\text{age} \text{ of Earth} \rightarrow 4.3 \text{ Gya}$), and a dynamic atmosphere of $\text{CO}_2$, $\text{CH}_4$, $\text{NH}_3$, $\text{H}_2$, and $\text{H}_2\text{S}$ reacted under energy inputs like lightning and UV radiation.

What was the key finding of the Miller-Urey experiment regarding the origin of life?

It demonstrated that organic molecules such as amino acids can form abiotically from simple inorganic precursors ($\text{CH}_4$, $\text{NH}_3$, $\text{H}_2\text{O}$, $\text{H}_2$) when supplied with an electrical energy source.

What effect do clay minerals such as montmorillonite have on protocell assembly?

Montmorillonite clay acts as a catalyst that greatly increases the rate of lipid vesicle self-assembly from precursor molecules.

What is the RNA World Hypothesis, and what catalytic molecules support it?

It proposes that self-replicating RNA served as the primary genetic and catalytic material in early life; it is supported by ribozymes, which are RNA molecules capable of catalyzing chemical reactions and copying short RNA sequences.

What is LUCA, when is it estimated to have lived, and how many protein-coding genes did it likely possess?

LUCA is the Last Universal Common Ancestor of all living cellular organisms; a 2024 analysis estimated it lived around $4.2 \text{ billion years ago}$ and possessed approximately $2,600$ protein-coding genes.

How do original horizontality and superposition determine relative rock layer ages?

Original horizontality states that sedimentary rock layers are deposited horizontally; superposition states that in undeformed strata, older layers lie below younger layers.

What is a radioisotope half-life, and how much Carbon-14 remains after 5,730 years?

A half-life is the time required for $50\text{\%}$ of a parent radioisotope to decay into a daughter isotope; after $5,730\text{ years}$ (one half-life), exactly $50\text{\%}$ of the original Carbon-14 remains.

How do anagenesis and punctuated equilibria differ in their explanations of evolutionary tempo?

Anagenesis is the gradual transformation of an entire unbranched lineage over time; punctuated equilibria consists of long periods of stasis interrupted by brief episodes of rapid morphological change and speciation.

What defines a species under the Biological Species Concept?

A group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, and do not produce viable, fertile offspring with other such groups.

What are the five prezygotic reproductive barriers that block fertilization?

Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, and gametic isolation.

What are the three postzygotic reproductive barriers that prevent hybrid zygotes from developing into viable, fertile adults?

Reduced hybrid viability, reduced hybrid fertility, and hybrid breakdown.

What are the three possible evolutionary outcomes for a hybrid zone over time?

Reinforcement (strengthening of reproductive barriers when hybrids are less fit), Fusion (weakening of reproductive barriers leading to merging of species), and Stability (continued production of hybrids due to persistent parent migration).

What is the difference between allopatric speciation and sympatric speciation?

Allopatric speciation occurs when populations are geographically isolated; sympatric speciation occurs without geographic isolation in populations living in the same area.

How did the formation of the Isthmus of Panama demonstrate allopatric speciation?

The formation of the isthmus $2.8 \text{ million years ago}$ separated marine populations between the Atlantic and Pacific Oceans, causing sister species like the Panamic porkfish (Anisotremus taeniatus) and porkfish (Anisotremus virginicus) to evolve in geographic isolation.

What is the difference between autopolyploidy and allopolyploidy?

An autopolyploid is an individual with more than two chromosome sets derived from a single species ($> 2\text{ sets}$); an allopolyploid is a fertile polyploid derived from hybridization between two different species followed by chromosome duplication.

What three mechanisms of sexual reproduction generate genetic variation in populations?

Crossing over during meiosis, independent assortment of chromosomes during meiosis, and random fertilization.

What are the Hardy-Weinberg equations for allele frequencies and genotype frequencies at a locus with two alleles?

For allele frequencies: $p + q = 1$; for genotype frequencies: $p^2 + 2pq + q^2 = 1$, where $p^2$ is the homozygous dominant frequency, $2pq$ is the heterozygous frequency, and $q^2$ is the homozygous recessive frequency.

What are the five essential conditions for a population to remain in Hardy-Weinberg equilibrium?

1. No selection, 2. No mutation, 3. No migration (gene flow), 4. Extremely large population size (no genetic drift), 5. Random mating.

What is genetic drift, and how did the bottleneck effect affect Illinois Greater prairie chickens?

Genetic drift is random fluctuation in allele frequencies due to chance events in small populations. Habitat loss severely reduced Illinois Greater prairie chickens to fewer than $50$ birds in 1993, reducing alleles per locus to $3.7$ and egg hatching rates to below $50\text{\%}$.

How do directional, disruptive, and stabilizing selection alter phenotypic distributions?

Directional selection favors individuals at one extreme of a phenotypic range; disruptive selection favors individuals at both phenotypic extremes over intermediate variants; stabilizing selection favors intermediate variants and acts against extreme phenotypes.

What are two forms of balancing selection that maintain stable phenotype frequencies?

Frequency-dependent selection (where fitness depends on how common the phenotype is, e.g., Perissodus microlepis) and heterozygote advantage (where heterozygotes have higher fitness than both homozygotes).

How does the sickle-cell allele (\beta^S) demonstrate heterozygote advantage in malaria-endemic areas?

Homozygotes (\beta^S\beta^S) suffer lethal anemia, and normal homozygotes (\beta^A\beta^A) have higher mortality from malaria; heterozygotes (\beta^A\beta^S) have the highest fitness because they are partially protected against both anemia and malaria.

How did Jean-Baptiste Lamarck's proposed mechanism of evolution differ from Charles Darwin's?

Lamarck proposed that species originate by spontaneous generation and evolve via the inheritance of acquired characteristics; Darwin proposed that species descend with modification from common ancestors via natural selection acting on heritable variation.

How did Thomas Malthus's work influence Darwin's concept of natural selection?

Malthus argued that human population growth outpaces food supply, leading to famine; Darwin applied this idea to nature to formulate the concept of the 'struggle for existence.'

What is uniformitarianism, and which geologist popularized it in Principles of Geology?

Popularized by Charles Lyell (1830), uniformitarianism is the principle that geological processes operating today operated in the past at the same rate, establishing the concept of deep time.

What three broad observations about living organisms are explained by descent with modification?

The unity of life (shared characteristics from a common ancestor), the diversity of life (accumulated modifications), and the match between organisms and their environments.

Why was the 1861 discovery of Archaeopteryx significant for evolutionary theory?

It provided striking fossil evidence of a transitional form exhibiting characteristics of both non-avian dinosaurs and modern birds.

Why are the forelimb bones of humans, cats, whales, and bats considered homologous structures?

They share a structural arrangement (humerus, radius, ulna, carpals, metacarpals, phalanges) inherited from a common ancestor, adapted for different functions.

How does biogeography explain the presence of Galaxiidae freshwater fish in both South America and Australia?

Galaxiidae species share a common ancestor that lived prior to the breakup of the supercontinent Pangaea, resulting in their distribution following continental drift.