BIO120: Speciation, Phylogenetics, Macroevolution, and Ecology

Comprehensive vocabulary flashcards covering BIO120 lecture topics: speciation mechanisms, phylogenetics, macroevolutionary dynamics, multilevel selection, and physiological ecology.

Natural Selection

The evolutionary process where organisms with helpful traits are better able to survive and reproduce ("survival of the fittest").

Genetic Drift

The change in the frequency of an allele within a population over time due to random chance.

Mutation

A permanent change in the DNA sequence of an organism.

Gene Flow

The movement of genetic material or alleles from one population to another.

The Species Problem

The scientific debate and challenge of how to best define a species, giving rise to numerous competing species concepts.

Taxonomic (Morphological) Species Concept

A species concept based primarily on distinct, measurable phenotypic and morphological differences.

Biological Species Concept (BSC)

A species concept formulated by Ernst Mayr defining a species as a group of interbreeding natural populations that are reproductively isolated from other groups.

Allopatric Speciation

Speciation that occurs when a population is split into physically isolated groups by an extrinsic physical geographic barrier (e.g., river or canyon), blocking initial gene flow.

Sympatric Speciation

Speciation that occurs within the same geographic area or habitat without physical or spatial separation, driven by polyploidy, sexual selection, or habitat choice.

Pre-zygotic Reproductive Isolating Barriers

Isolating mechanisms that prevent mating or fertilization between different populations, thereby preventing the formation of a zygote.

Lysin/VERL Interaction

A coevolving molecular "lock and key" fertilization system in abalone, in which the sperm lysin protein binds to the egg vitelline envelope receptor (VERL) to ensure species-specific fertilization.

Post-zygotic Reproductive Isolating Barriers

Isolating mechanisms that prevent the normal development, survival, or fertility of hybrid zygotes after fertilization occurs.

Intrinsic Post-zygotic Barriers

Developmental inviability, sterility, or abnormal development inherent to hybrid genotypes (e.g., sterile mules produced from a male donkey with $62$ chromosomes and a female horse with $64$ chromosomes).

Extrinsic Post-zygotic Barriers

Post-zygotic isolation resulting from an ecological mismatch between the hybrid phenotype and the environment, such as poorly adapted aberrant patterns in aposematic Heliconius hybrids.

Genetic Distance ($D$)

A quantitative measure of the degree of genetic differentiation between biological samples, frequently serving as a proxy for divergence time.

Ecological Speciation

The process by which new species form because populations of the same species adapt to divergent ecological environments or resources (e.g., benthic vs. limnetic sticklebacks).

Hybridization

The exchange of genetic material or alleles across a species boundary as a result of occasional inter-species mating.

Polyploidy

The state of an organism, tissue, or cell having more than two complete homologous sets of chromosomes.

Allopolyploidy

A form of polyploidy resulting from the duplication of chromosome sets following hybridization between two distinct species ($AA \times A^*A^* \rightarrow AA A^*A^*$).

Autopolyploidy

A form of polyploidy resulting from chromosome duplication within a single species (e.g., $AA \rightarrow AAAA$) through meiotic non-disjunction without hybridization.

Taxonomy

The theory and practice of classifying and naming organisms.

Systematics

The scientific study of biological diversity and the evolutionary relationships among organisms.

Taxon

A single named taxonomic unit at any hierarchical level of biological classification.

Metapopulation

A network of geographically separated populations that remain linked by gene flow across landscapes.

Node

A branching point on a phylogenetic tree that denotes a historical lineage splitting event, where an ancestral lineage divides into two descendant lineages.

Branch

A line on a phylogenetic tree representing a single ancestor-descendant lineage connecting an ancestor to its direct descendant.

Tip (OTU)

The terminal endpoint of a phylogenetic tree representing the youngest descendants under consideration, without represented descendants in the tree.

Sister Groups

Two descendant taxa or clades that are the immediate descendants of the same common ancestor on a phylogenetic tree.

Monophyletic Group (Clade)

A natural evolutionary grouping consisting of a common ancestor and all of its descendants, where the number of clades equals the number of nodes ($n - 1$ for $n$ species).

Ancestral Trait

A character state that was present in the ancestor of the taxonomic group under consideration.

Derived Trait

A character state that evolved later within a lineage through modification of the ancestral state.

Synapomorphy

A shared, derived character state that evolved in the immediate common ancestor of a clade and is inherited by members of that clade.

Homology

Trait similarity observed in different taxa that is attributable to inheritance from a shared common ancestor.

Homoplasy

Trait similarity observed in different taxa resulting from independent evolutionary origins, such as convergent evolution or character reversals, rather than common ancestry.

Principle of Parsimony

The optimality criterion in phylogenetic reconstruction that prefers the hypothesized tree requiring the minimum total number of evolutionary character state transitions.

Molecular Clock

The hypothesis that DNA sequences evolve at a relatively constant rate over time, allowing sequence divergence ($D$) to estimate divergence time ($t$) via $D = 2rt$.

Macroevolution

The study of evolutionary processes, diversity dynamics, and phenotypic patterns across species over geological timescales.

Cambrian Explosion

The rapid evolutionary proliferation of complex animal body plans, sensory organs, and mineralized skeletons starting approximately $540\text{--}520\text{ Ma}$ over an interval of $20\text{--}30\text{ MY}$.

Net Diversification Rate ($r$)

The net rate of biodiversity change calculated as the speciation rate ($\lambda$) minus the extinction rate ($\mu$): $r = \lambda - \mu$.

Mass Extinction

An episode of catastrophic biodiversity loss in which more than $75\%$ of Earth's species are eliminated within a geologically short time period.

Adaptive Radiation

The rapid evolution of phenotypic and ecological diversity within a multiplying lineage originating from a single common ancestor.

Ecological Opportunity

The availability of underutilized ecological resources or habitats, created by colonization of new regions, extinction of competitors, or key innovations.

Key Innovation

The evolution of a novel phenotypic trait (such as nectar spurs in Aquilegia) that provides access to previously inaccessible resources and triggers rapid lineage diversification.

Species Selection

Selection operating at the species level, occurring when species vary heritably in their speciation rates ($\lambda$) or extinction rates ($\mu$).

Transposable Elements (TEs)

Self-replicating DNA sequences (transposons) whose replication occurs independently of host cellular replication, enabling over-representation in gametes ($>50\%$).

DDM1 Gene

A regulatory gene involved in DNA methylation; mutations in DDM1 decrease genome methylation, leading to rampant reactivation of silenced transposable elements.

Transposition-Selection Balance

The equilibrium abundance of transposable elements maintained by the opposing forces of self-replication and natural selection purging deleterious insertional mutations.

Evolutionary Rescue

The rapid genetic adaptation of a declining population facing severe environmental change that restores positive population growth and prevents extinction.

Ecology

The scientific study of how organisms interact with one another and with their physical and biological environment, derived from the Greek "oikos" (home).

Systems Thinking

An ecological framework analyzing living biological systems as complex, dynamic networks with emergent properties that cannot be understood merely by dissecting individual parts.

Endosymbiotic Theory

The theory championed by Lynn Margulis stating that complex eukaryotic cells and organelles (like mitochondria) arose from cellular mergers and symbiosis rather than direct competition.

Population

All the individual organisms belonging to the same species living in a designated geographic area at the same time.

Community

All the populations of different species co-occurring and interacting in a specified geographic area at the same time.

Ecosystem

The complete ecological unit formed by a biological community interacting together with its non-living abiotic physical and chemical environment.

The Sixth Extinction

The ongoing anthropogenic mass extinction event, marked by population and range declines in $32\%$ of known vertebrate species ($8,851\text{ of }27,600$).

Ecological Niche

The full suite of physiological tolerances and environmental resource requirements that define where an organism can survive, grow, and reproduce.

Hutchinsonian Niche

An conceptualization of the ecological niche as an $n$-dimensional hypervolume where each axis corresponds to a distinct ecological factor or environmental gradient.

Range of Tolerance

The spectrum of conditions along an environmental gradient delimited by lethal zones, survival zones, growth zones, and narrow reproduction zones.

Adiabatic Lapse Rate

The rate at which heated rising air cools as elevation increases, occurring at a rate of approximately $5\text{--}10\,^\circ\text{C/km}$.

Physical Ecology (Ecophysiology)

The study of an organism's physiological adaptations, energy/nutrient acquisition, and physical tolerance limits in the context of its ecological environment.

Homeostasis

The energy-requiring physiological maintenance of internal stability (such as optimum temperature and osmotic balance) in response to fluctuating external environmental conditions.