BIOL 243 - Theme 5: Phylogeny, Macroevolution, History of Life

Be able to explain in own words homology (characters) and the principle of parsimony

• homology refers to traits that are similar due to shared ancestry. These traits are used to infer evolutionary relationships

  • homologous characters = traits shared due to common ancestry. These are traits used to build phylogenies

• the principle of parsimony states that the best phylogenetic tree is the one that requires the fewest evolutionary changes

  • this minimizes assumptions about how many times traits evolved

  • parsimony helps identify the most likely evolutionary pattern

takeaway: parsimony = fewest trait changes, not necessarily fewer branches

Compare and contrast homology and homoplasy

• homology: traits are similar due to shared ancestry

• homoplasy: traits are similar due to independent evolution, not shared ancestry

takeaway: homologous = inherited from a common ancestor, homoplasy = look alike, but evolved separately

Describe the steps and techniques used in inferring phylogenies based on a set of data

1. select species to include in the phylogenetic tree

2. identify heritable characters (morphological, molecular, etc.) for comparison

3. score characters across species (e.g., presence/absence of that character, DNA sequence)

4. identify homologous traits, especially synapomorphies (shared, derived traits from a common ancestor)

5. use the principle of parsimony to select the tree that requires the fewest evolutionary changes

takeaway: focus on homologous traits and shared ancestry to build the most likely evolutionary history

Understand relationships between groups of species inferred by a given phylogeny

• species that share a more recent common ancestor (i.e., connected by a recent node) are more closely related

• you can rotate branches around a node—the relationships stay the same

• the order of tips doesn’t matter—its about the branching pattern, not the left-right position

• look for shared nodes to understand who’s related to whom

takeaway: the more recently two species diverged, the more closely related they are

Be able to recognize a monophyletic group, paraphyletic group, polyphyletic group

• monophyletic group (clade): includes a common ancestor and all of its descendants

  • a complete branch of tree, best for showing evolutionary relationships

• paraphyletic group: includes the common ancestor and only some of its descendants

  • leaves out part of the clade. ex. grouping reptiles but leaving out birds

• polyphyletic group: includes organisms from different ancestors, but not the most recent common ancestor of the group

  • grouped based on superficial similarity, not ancestry (e.g., grouping bats and birds just because they both fly)—usually grouped together due to convergent evolution

takeaway: mono = all descendants, para = some, poly = not even the same ancestor

Distinguish between microevolution and macroevolution

• microevolution—small-scale changes in allele frequencies within a population (happens over short timescales and within species)

• macroevolution—large-scale evolutionary changes that occur above the species level (includes speciation, extinction, and major transitions)

takeaway: micro=within species, macro=between species or bigger patterns over time

Distinguish between anagenesis and cladogenesis and relate these processes to the patterns of phyletic gradualism and punctuated equilibrium

• anagenesis:

  • one species gradually transforms into another without branching

  • the ancestral species is completely replaced

  • no increase in species number—just one lineage changing over time

  • depicted as one straight line, not branching

  • associated with gradual equilibrium

• cladogenesis:

  • one species splits into two or more species

  • results in branching (original species may or may not continue)

  • associated with punctuated equilibrium

takeaway: anagenesis=change without splitting, cladogenesis=speciation by splitting lineages

Define an adaptive radiation

rapid diversification of a single ancestral species into multiple new species that are adapted to different ecological niches

• often triggered by:

  • new environments,

  • competition for one resource, leading to phenotypic variations to be able to access other resources

  • evolution of a new trait (e.g., wings, jaws)

takeaway: one species turns into many specialized species, fast

Discuss hypotheses for the origin of biological molecules and describe the Urey-Miller experiment

• Hypothesis: Biological molecules (like amino acids) could have formed abiotically in Earth's early reducing atmosphere, given the right energy inputs (e.g., lightning, UV).

• Urey-Miller experiment (1953): Simulated early atmosphere in a lab with gases (CH₄, NH₃, H₂, H₂O) and electric sparks.

  • Result: Formed organic molecules, including amino acids.

• Showed that the building blocks of life can form without cells, under prebiotic conditions.

Explain the ecological importance of the shift to an oxygen atmosphere, and the reasons for the slow rise of oxygen

• Cyanobacteria were able tot do photosynthesis and began releasing O₂ ~2.7–2.5 bya.

• At first, O₂ reacted with iron in oceans → formed banded iron formations → delayed its buildup in air.

• Eventually, O₂ accumulated in atmosphere → the Great Oxygenation Event:

  • Caused extinction of many anaerobic microbes

  • Enabled aerobic respiration (more energy-efficient)

  • Allowed evolution of larger, more complex cells (eukaryotes)

Describe the first eukaryotes and timing of major events of the history of life

• Eukaryotes evolved ~1.5 bya via endosymbiosis:

  • An archaeal host engulfed aerobic bacteria → became mitochondria

  • Later, some engulfed cyanobacteria → became chloroplasts (in plants/algae)

• Major timeline:

  • 3.5 bya – First prokaryotes

  • 2.5 bya – Oxygenation

  • 1.5 bya – Eukaryotes

  • 650 mya – Multicellular animals

  • 530 mya – Cambrian Explosion

  • 475 mya – Plants invade land

  • 360 mya – Origin of seeds (seed plants—gymnosperms—evolved)

  • 252 mya – Great Dying (mass extinction)

Describe the Cambrian Explosion

• ~530 mya, animal life rapidly diversified in the fossil record.

• Nearly all major animal phyla (body plans) appeared.

• Traits evolved: mouths, eyes, limbs, skeletons, segmentation

• Hypotheses for cause:

  • Increased oxygen

  • Evolution of predation/grazing

  • Calcium-rich oceans → allowed shell formation

Explain the criteria used to define mass extinctions and explain the evolutionary importance of mass extinctions

• A mass extinction is when ≥75% of species die out over a geologically short time.

• Causes: asteroid impacts, climate shifts, volcanism

• Evolutionary impacts:

  • Remove dominant species

  • Open niches → trigger adaptive radiation

  • Some surviving groups recover poorly → "dead clades walking"