Bio 1B Midterm #1 Flashcard (UC Berkeley)

Darwin's Syllogism (5 Parts)

1. Struggle for existence (Malthus)

2. Phenotypic variation exists within populations

3. Survival and reproduction depend partly on phenotype

4. Phenotypic traits are partly heritable

5. Conclusion: Species transform over time through Descent with Modification (Evolution)

Malthusian concept in Darwin's Syllogism

Struggle for existence — the observation that far more individuals are born than can survive, creating continuous competition for resources.

Syllogism

A form of deductive logical argument that arrives at a necessary conclusion from two or more assumed true premises.

Descent with Modification (modern term)

Evolution; the principle that species change across generations as inherited phenotypic modifications accumulate in descendant lineages.

Outcome for an individual with a "profitable" phenotypic variation

Increased likelihood of survival and natural selection, causing the advantageous variation to propagate in future generations through inheritance.

Role of inheritance in natural selection

Connects selective outcomes in one generation to the next; without inheritance, selection cannot alter future population phenotypes.

"Nature red in tooth and claw" vs. "Nature red in fruit and flower"

"Tooth and claw" highlights competition and predation; "fruit and flower" highlights mutualism and evolutionary cooperation.

Evolutionary definition of a "profitable" trait

Any phenotype that enhances an individual's overall reproductive success, whether via direct competition, cooperation, or mutualistic interactions.

Evolutionary justification for worker bee stinging self-sacrifice

Worker bees are sterile; defending the colony promotes the survival of the queen and shared genetic kin, preserving their inherited traits.

Two-step repeating cycle of evolution by natural selection

Step 1: Variation (generated during developmental processes) Step 2: Selection (filtered through ecological interactions)

Relationship between natural selection, adaptation, and fitness

Natural selection is the driver process, adaptation is the dynamic outcome fitting organisms to their environment, and fitness measures reproductive success.

Causal direction between natural selection and adaptation

Natural selection causes adaptation. Over-reproduction creates selection pressures, and the resulting selected traits are called adaptations.

Grant study on Galápagos finches (Geospiza fortis) key finding

Demonstrated rapid natural selection: A 1977 drought favored larger-beaked finches capable of cracking hard seeds, while a subsequent wet El Niño favored smaller-beaked finches.

Reasons evolution cannot produce "perfectly fit" organisms

Trade-offs among conflicting selective demands, along with constraints on available developmental or genetic variation.

Balancing Selection (sickle-cell allele example)

Selection maintaining multiple alleles due to opposing environmental forces: the sickle-cell allele causes disease when homozygous, but grants malaria resistance in heterozygotes.

Evolutionary trade-off in male widow bird tail length

Sexual selection favoring longer tails for mate attraction is balanced by natural selection against longer tails due to increased flight costs and predation risk.

Impact of trade-offs on morphological complexity (Niklas plant models)

Trade-offs are generative: increasing the number of competing selective pressures produces multiple optimal forms and greater structural complexity.

Sense in which phenotypic variation is random vs. non-random

Random because variations do not anticipate future environmental needs; non-random because developmental pathways constrain which traits can actually vary.

Dog vs. cat skull growth allometry

Dog skulls undergo dramatic shape change during growth, coupling adult size selection directly to snout length, whereas cat skulls maintain consistent proportions during growth.

Evolutionary hitchhiking

Direct selection for a target trait causing indirect selection of non-target correlated traits as side effects.

Target of selection challenge in Tyrannosaurus rex

Unclear whether tiny forelimbs were directly selected for or were an evolutionary hitchhiking byproduct of selection for large body size.

Selection without evolution

Occurs when stabilizing selection culls extreme phenotypes (e.g., human birth weights) each generation without shifting the population mean or allele frequencies across generations.

Three primary modes of phenotypic selection

1. Stabilizing selection: Favors intermediate phenotypes and reduces variance.
2. Directional selection: Favors one extreme phenotype and shifts the mean.
3. Disruptive selection: Favors both extreme phenotypes over intermediate forms.

Sexual selection

A specific mode of natural selection operating exclusively on traits that enhance an individual's success in obtaining mates.

Relationship between balancing selection and stabilizing selection

Balancing selection maintains multiple alleles in a population; it is considered a form of stabilizing selection acting on genetic diversity rather than quantitative traits.

Three primary non-adaptive evolutionary mechanisms

1. Genetic drift: Random changes in allele frequencies.

2. Population bottlenecks: Sudden reductions in population size.

3. Founder effects: Colonization by a small group with distinct allele frequencies.

Genetic drift

Random fluctuations in population allele frequencies across generations driven strictly by chance events, independent of natural selection.

Genetic bottleneck

A drastic reduction in population size that randomly alters allele frequencies in the surviving population compared to the original.

Founder Effect

An evolutionary event occurring when a small subset of individuals establishes a new isolated population with allele frequencies that differ by chance from the source population.

Two main categories of evolutionary drivers

1. Adaptive change: Driven by natural selection.

2. Non-adaptive change: Driven by chance events (drift, bottlenecks, founder effects), gene flow, or novel mutations.

Primary source of new genetic mutations

Errors occurring during DNA replication in cell division, rather than environmental damage, because cells possess repair machinery.

Human mutation rate and individual load

Rate is approximately $10^{-8}$ per site per generation, producing around $60$ new mutations per individual from a $3 \times 10^9$ base genome.

Immune evasion mechanism in SARS-CoV-2

A rapid mutation rate (approx $10^{-3}$ per site per year) generates abundant genetic variants, allowing natural selection to favor strains that evade antibodies.

Hardy-Weinberg model purpose

Serves as a null model predicting expected genotype frequencies from allele frequencies under random mating, used to test whether evolution is actively occurring.

Hardy-Weinberg genotype frequency equation

For two alleles with frequencies $p$ and $q$ ($p + q = 1$), expected frequencies are $p^2$ (homozygote 1), $2pq$ (heterozygote), and $q^2$ (homozygote 2).

Hardy-Weinberg evidence of evolution in West African sickle-cell data

Observed genotype counts differed significantly from expected counts ($p^2$, $2pq$, $q^2$) calculated from allele frequencies ($H = 0.909$, $S = 0.091$), demonstrating active selection.

Darwinian properties required for genetic drift

Only phenotypic variation and partial trait heritability; drift does not require a struggle for existence or differential survival based on phenotype.

Parthenogenesis

A form of asexual reproduction where an embryo develops from an unfertilized egg without male genetic contribution.

LUCA

Last Universal Common Ancestor; the hypothesized single-celled common ancestor of Bacteria, Archaea, and Eukaryotes.

Biological Species Concept (BSC)

Defines a species as groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.

Significance of 'potential' interbreeding in the Biological Species Concept

Recognizes geographically separated populations as the same species if they are capable of interbreeding despite never coming into physical contact.

Ring species example (Ensatina eschscholtzii)

A continuous geographic chain of interbreeding adjacent populations encircling California's Central Valley where the terminal populations overlap but cannot interbreed.

Morphological Species Concept (MSC)

Defines species based on structural similarity and distinct morphological gaps separating them from other groups.

Biological basis for agreement between BSC and MSC

Gene flow maintains continuous morphological variation within interbreeding species, whereas reproductive isolation leads to genetic divergence and structural gaps between species.

Chronospecies

Successive stages along an unbranched lineage in the fossil record that exhibit gradual continuous phenotypic shift (anagenesis) without a splitting event.

Cryptic species

Populations that are morphologically indistinguishable but genetically distinct and reproductively isolated.

Cryptic species discovery in Astraptes fulgerator

DNA barcoding revealed that what was considered a single species of Costa Rican skipper butterfly is actually a complex of at least $10$ genetically distinct species.

DNA evidence for two distinct African elephant species

Forest and savanna populations exhibit $7$ to $11$ fixed genetic differences, a divergence comparable to the yardstick difference between African and Asian elephants.

Fixed genetic difference

A nucleotide variation present in $100\%$ of individuals in one population and $0\%$ in another, indicating complete absence of interbreeding gene flow.

Rules of binomial nomenclature

A two-part italicized scientific name consisting of a capitalized Genus name followed by a lowercase species epithet.

Type specimen

A single curated physical specimen preserved in an institution to which the formal scientific name of a species is permanently attached.

Synonymy in taxonomy

A historical record tracking name changes and reclassifications for a taxon over time to connect current literature with historical research.

Challenges of diagnosing species in the fossil record

Inability to observe mating behavior, limited specimen sample sizes, incomplete preservation of soft tissue, and difficulty distinguishing individual variation, sex, or growth stages from species differences.

Speciation

The evolutionary process by which a single ancestral lineage splits into two or more genetically distinct and reproductively isolated descendant lineages.

Anagenesis vs. Cladogenesis

Anagenesis is evolutionary change within an unbranched lineage over time; cladogenesis is the splitting of a lineage into two or more distinct branches.

Prerequisite for speciation under the Biological Species Concept

Disruption of gene flow and establishment of complete reproductive isolation between populations.

Three geographic modes of speciation

1. Allopatric: Speciation in geographic isolation.

2. Parapatric: Speciation in geographically adjacent populations with a narrow contact zone.

3. Sympatric: Speciation occurring within the same geographic area without physical barriers.

Dispersal vs. Vicariance in allopatric speciation

Dispersal occurs when individuals colonize a new geographic area across a pre-existing barrier; vicariance occurs when a new physical barrier splits an existing continuous population.

Rapid evolution in dispersal-driven speciation

Small founder population size leads to strong founder effects, accelerated genetic drift, and intense directional selection in the new environment.

Dodo (Raphus cucullatus) speciation example

Illustrates dispersal-driven allopatric speciation where ancestral flighted pigeons colonized Mauritius and evolved flightlessness and large size in the absence of predators.

Snapping shrimp (Alpheus) speciation example

Illustrates vicariance-driven allopatric speciation caused by the formation of the Isthmus of Panama around $2.5\text{ million}$ years ago, isolating Atlantic and Pacific populations.

Parapatric speciation example (Mimulus guttatus)

Monkey flowers adapted to toxic copper-rich mine soils in California became reproductively isolated from neighboring non-mine populations despite physical proximity.

Sympatric speciation example (Rhagoletis pomonella)

Apple maggot flies shifted host plants from native hawthorn to introduced apples, giving rise to host-specific assortative mating and distinct host races in the same geographic area.

Polyploidy in plant speciation

Cell division errors duplicate chromosome sets, instantly creating postzygotic reproductive isolation from diploid parents, facilitated by self-fertilization in plants.

Prezygotic vs. Postzygotic reproductive barriers

Prezygotic barriers prevent mating or fertilization from occurring; postzygotic barriers prevent hybrid zygotes from developing into viable, fertile adults.

Five prezygotic reproductive barriers

1. Habitat isolation: Mating in different habitats.

2. Temporal isolation: Breeding at different times.

3. Behavioral isolation: Unrecognized courtship signals.

4. Mechanical isolation: Incompatible reproductive structures.

5. Gametic isolation: Sperm and egg failing to fertilize.

Three postzygotic reproductive barriers

1. Reduced hybrid viability: Hybrids fail to develop or survive.

2. Reduced hybrid fertility: Hybrids survive but are sterile.

3. Hybrid breakdown: First-generation hybrids are fertile, but second-generation offspring have reduced fitness.

Reinforcement in speciation

Natural selection strengthening prezygotic reproductive barriers in response to low fitness of hybrid offspring, favoring individuals that mate strictly within their own species.

Fitness benefit of reproductive barriers in local adaptation

Prevents gene flow from eroding or diluting advantageous traits adapted to specific local environments.

Evolutionary trade-off between specialists and generalists

Specialists achieve high local fitness but face smaller ranges and higher extinction risks; generalists have lower peak fitness but lower extinction rates across varying conditions.

Natural selection

The differential survival and reproduction of individuals due to heritable phenotypic differences, leading to adaptation over generations.

Evolution

Descent with modification; changes in inherited traits and allele frequencies of a population across generations.

Fitness

A quantitative measure of an individual's or genotype's reproductive success in contributing offspring to the next generation.

Genotype vs. Phenotype

Genotype is the genetic makeup (allele composition) of an organism; phenotype is the composite of observable characteristics resulting from genotype-environment interactions.

Allele

One of two or more alternative functional sequence variants of a gene located at a specific genomic locus.

Homozygous vs. Heterozygous

Homozygous describes possessing two identical alleles at a given locus; heterozygous describes possessing two distinct alleles at a locus.

Gene flow

The transfer of genetic material between distinct populations through migration and successful interbreeding.

Assortative mating

A non-random mating pattern where individuals preferentially mate with partners exhibiting similar phenotypes or genotypes.