Phylogeny, Speciation, History of Life, and Biodiversity: Study Notes

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Phylogenetic Trees and Evolutionary Relationships

Introduction to Phylogenetic Trees

Phylogenetic trees are diagrammatic hypotheses that represent the evolutionary relationships among various biological species based on similarities and differences in their physical or genetic characteristics. These trees are fundamental tools in evolutionary biology for visualizing patterns of descent and inferring the history of life.

Phylogenetic Tree: A branching diagram showing the inferred evolutionary relationships among species or groups.
Hypothesis: Phylogenetic trees are considered hypotheses because they are based on available data and may change with new evidence.
Parts of a Tree: Includes branches, nodes (branch points), root, taxa (tips), and sister taxa.
Orientation: The root represents the most recent common ancestor; time typically flows from root to tips.

Example: A tree showing the evolutionary relationships among mammals, birds, and reptiles, with the root representing their common ancestor.

Key Terms in Phylogenetics

Taxon (plural: Taxa): Any named group of organisms (e.g., species, genus, family).
Lineage: A sequence of species that form a line of descent.
Character/trait: Any heritable attribute (e.g., presence of hair, number of limbs).
Character Transition: The evolutionary change from one character state to another.
Monophyletic Group (Clade): Includes an ancestor and all its descendants.
Paraphyletic Group: Includes an ancestor and some, but not all, descendants.
Polyphyletic Group: Does not include the most recent common ancestor of all members.
Root: The base of the tree, representing the most recent common ancestor.
Sister Taxa: Two taxa that are each other's closest relatives.
Parsimony: The principle that the simplest explanation (fewest evolutionary changes) is preferred.

Interpreting Phylogenetic Trees

Branch points (nodes) represent common ancestors.
Rotating branches around a node does not change relationships.
Relative relatedness is determined by the most recent common ancestor.
DNA data often provides more accurate trees than phenotypic data due to convergent evolution and phenotypic plasticity.

Example: If species A and B share a more recent common ancestor with each other than with C, A and B are more closely related.

Building and Using Phylogenetic Trees

Characters are used to infer relationships; shared derived characters (synapomorphies) are especially informative.
Most parsimonious tree is the one with the fewest character transitions.
Trees can be used to infer evolutionary relationships, divergence times, and patterns of evolutionary change.

Species Concepts and Speciation

Defining Species

Biological Species Concept: Species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.
Gene Flow: Unites populations within a species; reproductive isolation divides species.
Morphological Species Concept: Species are defined by morphological (structural) features; useful when reproductive data is unavailable.
Ecological Species Concept: Species are defined by their ecological niche; useful for asexual organisms and those with distinct ecological roles.

Example: The Eastern and Western Meadowlarks are morphologically similar but are reproductively isolated by differences in song (behavioral isolation).

Reproductive Barriers

Prezygotic Barriers: Prevent mating or fertilization between species.
- Habitat Isolation: Species occupy different habitats.
- Temporal Isolation: Species breed at different times.
- Behavioral Isolation: Differences in mating behaviors prevent interbreeding.
- Mechanical Isolation: Morphological differences prevent mating.
- Gametic Isolation: Gametes cannot fuse to form a zygote.
Postzygotic Barriers: Prevent hybrid offspring from developing into viable, fertile adults (e.g., mule hybrids between horses and donkeys are sterile).

Modes of Speciation

Allopatric Speciation: Occurs when populations are geographically separated, leading to divergence (e.g., Darwin's finches on the Galápagos Islands).
Sympatric Speciation: Occurs without geographic separation, often via polyploidy (especially in plants), habitat differentiation, or sexual selection.
Vicariance: Physical splitting of a population by a barrier (e.g., mountain formation).
Dispersal: A few individuals colonize a new area, leading to divergence.

Hybrid Zones and Speciation Outcomes

Hybrid zones occur where two species meet and interbreed.
Outcomes depend on hybrid fitness and migration rates: reinforcement, fusion, or stability.

Conceptual Issues in Speciation

Essentialist thinking (species as fixed entities) can lead to misconceptions; speciation is a gradual process.
Ring species illustrate speciation over space rather than time (e.g., gulls around the Arctic Circle).
Extinction can accentuate differences between surviving species.

The History of Life on Earth

Radiometric Dating and the Geologic Record

Half-life: The time required for half of the parent isotope to decay into the daughter isotope.
After n half-lives, the fraction of parent isotope remaining is .
Carbon-14 dating is used for recent fossils (up to ~50,000 years); uranium dating is used for older rocks.
The "clock" starts when the organism dies (C-14) or when rock solidifies (Uranium).

Major Eras and Events

Precambrian (4.6 bya – 541 mya): Origin of life, atmospheric oxygen from cyanobacteria, first eukaryotes, and multicellularity.
Paleozoic Era (541–252 mya): Cambrian explosion, colonization of land by plants, arthropods, vertebrates; evolution of amniotic egg; Permian extinction.
Mesozoic Era (252–66 mya): Radiation of dinosaurs, emergence of mammals, rise of angiosperms, K-Pg extinction (asteroid impact, 66 mya).
Cenozoic Era (66 mya–present): Adaptive radiation of mammals, evolution of humans, extinction of Pleistocene megafauna.

Mass Extinctions and Biodiversity

Background extinction: Normal, ongoing extinction rate.
Mass extinction: Large, rapid loss of species (e.g., Permian, K-Pg events).
Evidence suggests a 6th mass extinction is underway, driven by human activity.

Key Terms in Geologic Time

Radioisotope: Unstable isotope that decays over time (parent and daughter forms).
Fossil: Preserved remains or traces of ancient organisms.
Eon, Era, Period: Hierarchical divisions of geologic time.
Cambrian Explosion: Rapid diversification of animal life ~541 mya.

Biodiversity: Domains and Major Groups of Life

Overview of Biodiversity

Arthropods dominate described species (~75%), but most species are microbial.
Three domains of life: Bacteria, Archaea, Eukarya.

Domain	Example Organisms	Key Features
Bacteria	Escherichia coli	Prokaryotic, peptidoglycan cell wall
Archaea	Halophiles, Thermophiles	Prokaryotic, unique membrane lipids, extremophiles
Eukarya	Animals, Plants, Fungi, Protists	Eukaryotic cells, membrane-bound organelles

Metabolic Diversity

Photoautotroph: Uses light energy and CO2 (e.g., plants).
Chemoheterotroph: Uses organic molecules for energy and carbon (e.g., animals).

Prokaryotes: Bacteria and Archaea

Bacteria play key ecological roles (e.g., nitrogen fixation, decomposition).
Some are beneficial (e.g., Lactobacillus), others harmful (e.g., Streptococcus).
Extremophiles: Archaea that live in extreme environments (e.g., thermophiles in hot springs, halophiles in salty lakes).

Eukaryotes: Protists, Plants, Fungi, Animals

All eukaryotes have membrane-bound organelles and a nucleus.
Protists: Diverse group, mostly unicellular, some photosynthetic, others heterotrophic.
Plants: Adapted to land with vascular tissue, seeds, and flowers; alternation of generations life cycle.
Fungi: Heterotrophic, cell walls of chitin, body composed of hyphae and fruiting bodies.
Animals: Multicellular, heterotrophic, lack cell walls, unique tissues (e.g., muscle, nerve).

Major Plant Groups

Group	Key Traits	Example
Nonvascular	No vascular tissue, dominant gametophyte	Mosses
Seedless Vascular	Vascular tissue, no seeds	Ferns
Gymnosperms	Seeds, no flowers	Pine trees
Angiosperms	Seeds, flowers, fruit	Oak trees

Major Animal Phyla

Phylum	Key Traits	Symmetry	Example
Porifera	No true tissues, filter feeders	Asymmetrical	Sponges
Cnidaria	Stinging cells, two tissue layers	Radial	Jellyfish
Mollusca	Muscular foot, shell (often)	Bilateral	Snails
Annelida	Segmented body	Bilateral	Earthworms
Nematoda	Unsegmented, cuticle	Bilateral	Roundworms
Arthropoda	Exoskeleton, jointed appendages	Bilateral	Insects
Echinodermata	Water vascular system, 5-part radial symmetry (adults)	Radial (adults)	Sea stars
Chordata	Notochord, dorsal hollow nerve cord	Bilateral	Humans

Chordate Features

Notochord
Dorsal hollow nerve cord
Pharyngeal slits
Post-anal tail

These features are present at some stage in all chordates; in humans, the notochord becomes part of the intervertebral discs, and the dorsal hollow nerve cord forms the central nervous system.

Key Evolutionary Innovations

Amniotic egg enabled reproduction away from water (amniotes include reptiles, birds, mammals).
Jaws, legs, hair/fur, and endothermy are important vertebrate innovations.

Additional info:

Alternation of generations in plants involves a multicellular diploid sporophyte and a multicellular haploid gametophyte.
Polyploidy is a major mechanism of sympatric speciation in plants due to their ability to tolerate genome duplications.
Phenotypic plasticity can complicate species identification based on morphology alone.