Biology 121: Evolution, Diversity, and Microbiology

Comprehensive vocabulary flashcards covering evolutionary theory, natural selection, speciation, geological timelines, taxonomy, microbiology, virology, and fungi from Biology 121.

Landmark Date & Publication (Darwin)

November 24, 1859, British naturalist Charles Darwin published On the Origin of Species by Means of Natural Selection (subtitled The Preservation of Favoured Races in the Struggle for Life).

Significance of Evolutionary Theory

Natural selection and evolution explain how life changes, but say nothing about purpose or anything beyond the physical.

Two Main Points in The Origin of Species

1) Modern species have descended from common ancestors (evolution), 2) Natural selection is the primary mechanism of evolution.

Aristotle's View

Believed species were immutable (unchanging).

1700s Fossil Discovery

The discovery and study of fossils first suggested that the Earth was very old and that species could change over time (e.g., fossil coelacanth).

Jean-Baptiste Lamarck

One of the first to propose that species evolve over time, incorrectly suggesting the inheritance of acquired characteristics (e.g., giraffe stretching its neck and passing that length to offspring).

Charles Lyell

Scottish geologist who suggested an old Earth had gradually changed through slow, accumulating geological processes (e.g., the Grand Canyon, estimated at 5–6 million years old).

Alfred Russel Wallace

British biologist who independently arrived at the theory of evolution by natural selection around the same time as Darwin.

Darwin's Voyage on the H.M.S. Beagle

Sailed from 1831 to 1836, collecting extensive specimens (such as his famous beetle collection) and comparing species across global regions.

Observation 1: Overproduction

Populations produce more individuals than can possibly be supported by the environment (e.g., Christmas Island red crabs producing massive swarms).

Observation 2: Limited Resources

The amount of environmental resources (food, water, shelter, sunlight) stays relatively constant (e.g., vultures fighting over carcasses and wolves snapping at each other).

Inference 1: Competition

Because more offspring are born than limited resources can support, not all individuals survive and reproduce.

Observation 3: Variation

No two individuals in a population are exactly alike (e.g., lion prides and variable clam shell patterns).

Inference 2: Natural Selection

Individuals with inherited variations that make them best suited to their environment will, on average, be more likely to survive and reproduce.

Inference 3: Heritability & Evolution

Traits are passed from one generation to the next; over generations, differential survival and reproduction lead to a population changing over time (adaptation).

Rule 1 of Evolution

Individuals do not evolve; natural selection acts on individuals, but only populations evolve.

Rule 2 of Evolution

Natural selection works only with heritable traits; only genetically coded traits are subject to natural selection.

Rule 3 of Evolution

Evolution does not have a goal; it occurs in response to local environmental conditions of the present, not future ones.

Artificial Selection Definition

Humans substituting their desires for natural selection by enforcing unequal reproductive success over millennia.

Dog Domestication Example

The gray wolf (Canis lupus) is the ancestor of all modern dogs, domesticated over tens of thousands of years into diverse breeds (Great Danes, Chihuahuas, Beagles).

Wild Mustard (Brassica oleracea) Artificial Selection

Produced different agricultural strains: Stem $\rightarrow$ Kohlrabi; Leaves $\rightarrow$ Kale; Flower buds and stem $\rightarrow$ Broccoli; Lateral leaf buds $\rightarrow$ Brussels sprouts; Terminal leaf bud $\rightarrow$ Cabbage; Flower buds $\rightarrow$ Cauliflower.

Antibiotic Resistance Case Study

MRSA (Methicillin-resistant Staphylococcus aureus). Adding an antibiotic eliminates non-resistant bacteria, leaving resistant strains to survive, reproduce, and shift the population's genetic makeup.

Other Real-World Selection Examples

Insecticide-resistant malaria mosquitoes, herbicide-resistant weeds, and peppered moths in England (light vs. dark morphs shifting based on bird predators hunting against light lichen trees or soot-darkened industrial trees).

The Australian Rabbit Epidemic

European rabbits introduced in 1788 with few natural predators multiplied to 10 billion by the 1920s, prompting construction of the No. 1 Rabbit Proof Fence ($1{,}837\,\text{km}$ / $1{,}139\,\text{miles}$, begun 1901).

Myxoma Virus (Australia)

Introduced in 1950, dropping rabbit numbers from 600 million to 100 million. Viral resistance increased since the 1970s, prompting release of a second strain (Korean RHDV1/K5) in 2017.

Unity and Diversity of Life Evidence

All cells utilize DNA made from the exact same chemical building blocks, demonstrating common ancestry alongside diverse cellular forms.

Fossil Record Formation

Organisms die, fall into sediment, and are compressed into rock over millions of years (e.g., fossilized fish Lepidotes, trilobites like Huntonia linguifer, insects in amber).

Relative Dating

Older fossils are generally buried further down in sequential rock strata layers.

Radiometric Dating (Carbon-14)

Living organisms incorporate carbon isotopes ($^{12}\text{C}$ and radioactive $^{14}\text{C}$) in known ratios. Upon death, stable $^{12}\text{C}$ remains constant while $^{14}\text{C}$ decays.

Half-life of Carbon-14

$5{,}700\,\text{years}$. Measuring the remaining $^{12}\text{C}\text{-to-}^{14}\text{C}$ ratio determines fossil age up to roughly $51{,}300\,\text{years}$.

Whale Evolution Transitional Lineage

Transition from land-dwelling artiodactyls to fully aquatic cetaceans: Indohyus $\rightarrow$ Pakicetus $\rightarrow$ Ambulocetus $\rightarrow$ Kutchicetus $\rightarrow$ Rodhocetus $\rightarrow$ Dorudon $\rightarrow$ modern Odontocetes and Mysticetes (including Basilosaurus possessing vestigial rear legs).

Other Classic Transitional Forms

Archaeopteryx (reptile-bird link), Tiktaalik (fish-tetrapod link bridging aquatic-to-terrestrial between 395–315 mya), and 'Lucy' (Australopithecus hominid skull).

Biogeography Definition

The study of the geographic distribution of past and present species.

Australian Marsupial Biogeography

Continental drift separated landmasses. Geographic isolation allowed marsupials (red kangaroo Macropus rufus, koala Phascolarctos cinereus) to dominate Australia, whereas they were largely outcompeted by placental mammals elsewhere.

Homologous Structures

Animal forelimbs (bat wings, porpoise flippers, human arms) are constructed from the exact same fundamental bone architecture, reflecting shared ancestry.

Embryology Evidence

Comparative analysis of vertebrate embryos (chicken and human) reveals shared developmental features like pharyngeal pouches and tails.

Bioinformatics

Employs computational tools to process biological and genetic data.

Molecular Homology

Closely related species share greater percentages of identical DNA and protein sequences.

Primate DNA Comparisons

Chimpanzee: $100\%$; Human: $\sim 98\text{--}99\%$ (approx. $98\%$ in slides); Gorilla: $\sim 97\%$; Old World Monkey: $\sim 92\%$.

Population Definition

A group of individuals of the same species living in the same place at the same time capable of meeting and mating (e.g., a pack of wolves).

The Gene Pool

Consists of all versions of all the genes carried by all individuals in a population.

Microevolution

A generation-to-generation change in a population's gene pool, leading over many generations to gradual adaptation to the local environment.

Sources of Genetic Variation

1) Mutations (random DNA changes creating new genes/alleles), 2) Sexual Recombination (crossing over and independent assortment).

Darwinian Fitness

The contribution an individual makes to the gene pool of the next generation compared to others; the best suited to survive and reproduce.

Genetic Drift

A change in a gene pool due to chance events rather than natural selection; strongest impact in small or isolated populations.

The Bottleneck Effect

A drastic reduction in population size due to a catastrophe or event (e.g., cheetah numbers crashing in the 1800s), leaving a small, random survivors' gene pool.

The Founder Effect

When a few individuals migrate to a new, isolated habitat, establishing a new population with limited genetic diversity.

Gene Flow

The genetic exchange among populations due to migration, dispersal, or interbreeding (e.g., drifting pine pollen); tends to reduce differences between gene pools over time.

Sexual Selection

A form of natural selection depending on an individual's ability to obtain a mate.

Intersexual Selection

Females choosing mates based on specific displays or traits (e.g., peacocks with long tails).

Intrasexual Selection

Direct competition among same-sex individuals (usually males, such as red deer locking antlers) for access to mates.

Macroevolution

Encompasses major evolutionary changes on a large scale in the history of life, including speciation.

Nonbranching Evolution

An ancestral population changes gradually over time into a single modified species.

Branching Evolution

An ancestral population splits into two or more distinct populations, increasing biodiversity.

Novel Features & Exaptation

Structures serving one role gradually shift to serve another (e.g., dinosaur feathers originally for sensory/insulation exapting for flight).

Adaptive Radiation

Entering an empty ecological niche triggers an explosion of diversity (e.g., evolution of flight allowed bats to colonize nighttime aerial niche, resulting in 1,400+ species).

Precambrian Era (4.6 billion to 541 mya)

4.6 bya Earth forms; 3.5 bya oldest prokaryotes; 2.1 bya oldest eukaryotes; Oxygen Revolution released free $\text{O}_2$.

Paleozoic Era (541 to 251 mya)

541 mya ocean animal diversity explosion (trilobites); 420 mya plants colonize land; 370 mya animals migrate to land (Tiktaalik); 251 mya end-Permian extinction event.

Mesozoic Era (251 to 65 mya)

230 mya first dinosaurs appear; 100 mya flowering plants dominate; 65 mya massive meteorite impact wipes out non-avian dinosaurs, clearing niches for mammals.

Cenozoic Era (65 mya to Present)

Rapid mammal diversification; ~200,000 years ago appearance of anatomically modern humans.

Plate Tectonics

Earth's crust composed of large plates floating on hot mantle, continuous movement rearranging continents (Pangea breakup ~200 mya, Atlantic opening ~100 mya).

Catastrophic Volcanism

Major geological upheavals (Siberian Traps, Toba supervolcano ~74,000 years ago) spewed ash/gas, triggering global volcanic winters and near-extinction bottlenecks.

Biological Species Concept Definition

A population of individuals capable of interbreeding to produce healthy, fertile offspring.

Meadowlark Species Example

Eastern meadowlark (Sturnella magna) and Western meadowlark (Sturnella neglecta) look alike but occupy different habitats and do not naturally interbreed.

Domestic Dog Species Name

All dogs belong to the single species Canis lupus familiaris.

Exceptions to Species Definition

Bacteria reproduce asexually, extinct organisms cannot be tested for mating capability.

Behavioral Isolation

Members identify each other through specific courtship rituals or displays (e.g., peacocks).

Temporal Isolation (Mating Time Differences)

Species reproduce only at specific times, seasons, or years.

Habitat Isolation

Species living in slightly different habitats may never meet.

Mechanical Incompatibility

Anatomical differences prevent physical mating (e.g., specialized wasp pollination of orchids).

Gametic Incompatibility

Gametes (sperm and egg) from different species usually cannot fertilize each other (e.g., sea urchin spawning).

Hybrid Weakness

Offspring of two different species may be unfit or sterile (e.g., a mule produced by a horse and a donkey).

Graduated Model of Speciation

Species acquires small adaptations gradually over millions of years (e.g., horse evolution: Eohippus $\rightarrow$ Mesohippus $\rightarrow$ Miohippus $\rightarrow$ Pliohippus $\rightarrow$ Equus ferus caballus).

Punctuated Equilibrium Model

Long periods of stasis interrupted by occasional rapid bursts of speciation (e.g., Cambrian explosion 530 mya).

Allopatric Speciation

Occurs when a physical barrier isolates populations (e.g., Grand Canyon separating white-tailed antelope squirrel Ammospermophilus leucurus and Harris's antelope squirrel Ammospermophilus harrisii).

Sympatric Speciation

Occurs suddenly due to large-scale genetic changes without a physical barrier (e.g., Emmer wheat and wild wheat interbred to form sterile hybrid, self-fertilizing into modern bread wheat Triticum aestivum).

Taxonomy Definition

The identification, naming, and classification of species.

Three Domains of Life

Domain Bacteria, Domain Archaea, and Domain Eukarya.

Taxonomic Hierarchy (Largest to Smallest)

Domain $\rightarrow$ Kingdom $\rightarrow$ Phylum $\rightarrow$ Class $\rightarrow$ Order $\rightarrow$ Family $\rightarrow$ Genus $\rightarrow$ Species (Mnemonic: "King Philip came over for great soup!").

Binomial Nomenclature Rules

Scientific names use Genus species. Genus is uppercase and italicized, species is lowercase and italicized (e.g., Panthera tigris).

Tiger Classification Breakdown

Domain Eukarya $\rightarrow$ Kingdom Animalia $\rightarrow$ Phylum Chordata $\rightarrow$ Class Mammalia $\rightarrow$ Order Carnivora $\rightarrow$ Family Felidae $\rightarrow$ Genus Panthera $\rightarrow$ Species Panthera tigris.

Phylogenetic Trees

Hypotheses about evolutionary history of related species; tips represent recently evolved species, relatedness determined by most recent common ancestor.

Clade & Cladistics

A clade is any group consisting of an ancestral species and all its descendants; analysis of clades is cladistics.

Tetrapods Definition

Animals with four limbs = Amphibians + Amniotes.

Amniotes Definition

Reptiles + Mammals.

Reptilian Tree Structure

Lepidosaurs (tuataras, lizards, snakes) are sister group to Archosauria (crocs, dinosaurs, birds). United by Diapsid skull.

Derived Characters on Trees (Sequential Milestones)

1. Jaws $\rightarrow$ 2. Calcium-hardened skeleton $\rightarrow$ 3. Four limbs (Tetrapods) $\rightarrow$ 4. Amniotic egg (Amniotes) $\rightarrow$ 5. Hair and mammary glands (Mammals).

Microscopic Organisms Size Spectrum

Atoms (~$0.1\,\text{nm}$), small molecules (~$1\,\text{nm}$), lipids (~$10\,\text{nm}$), proteins (~$10\,\text{nm}$), ribosomes (~$100\,\text{nm}$), viruses (~$100\,\text{nm}$), smallest bacteria (~$1\,\mu\text{m}$), most bacteria (~$10\,\mu\text{m}$), most plant/animal cells (~$100\,\mu\text{m}$), fish eggs (~$1\,\text{mm}$), bird eggs (~$1\,\text{cm}$ to $0.1\,\text{m}$).

Instrument Viewing Ranges

Electron microscopes (atoms to bacteria); Light microscopes (bacteria to plant/animal cells); Unaided human eye (fish eggs to bird eggs).

Origin of Earth & Life Dates

Earth formed ~4.6 billion years ago; life likely appeared ~3.9 billion years ago.

Biogenesis Hypothesis

The formation of new living organisms through a series of stages under unique primordial Earth conditions.

Urey-Miller Experiment (1953)

Simulated early Earth atmosphere ($\text{CH}_4$, $\text{NH}_3$, $\text{H}_2$), water vapor, and lightning electrodes, yielding nucleotides, amino acids, and glucose.

First Duplicating Molecule

RNA may have been the first duplicating molecule possessing sugar-phosphate backbone, bases, and hydrogen bonds.

Prokaryotes Overview

First life on Earth; small, simple cells; sole life forms for the first billion years.

Domain Bacteria

Unicellular, found everywhere. Some pathogenic (Helicobacter pylori causes stomach ulcers), vast majority beneficial.

Domain Archaea

Unicellular, often found in extreme conditions (anoxic, extreme heat, extreme salinity).

Prokaryotic Cellular Structures

Cell wall (protection), capsule (sticky outer layer for surfaces/protection), flagella (mobility), endospore (thick-shelled container for harsh conditions).

Binary Fission

Asexual reproduction where prokaryotes split in half (DNA replication $\rightarrow$ Cytokinesis $\rightarrow$ Two identical daughter cells).

Asexual Bacterial DNA Transfer

Transformation, Transduction, Conjugation, Plasmid transfer.

Conjugation Detail

Donor uses sex pilus (pili) to form mating bridge and transfer chromosome/plasmid (e.g., Neisseria gonorrhoeae).