BIS2C Lab Practical Study Guide V3

Now with Additional Practice Problems! Terms repeat, so Enable Override in Learn. Terms Bolded, Italicized, and Underlined are Lab 8 Group Presentation Summaries. Send any errors or changes needed. Please don't use just this to study, also use the other study resources. Good Luck!

Rooted Tree

A phylogenetic tree with a designated root, showing a common ancestor from which all taxa in the tree descend.

Unrooted Tree

A phylogenetic tree without a specified root, depicting relationships among taxa but not the direction of evolutionary lineage.

Monophyletic

A group that includes a common ancestor and all of its descendants.

Sister Group

Two taxa or groups that are each other's closest relatives, arising from the same node in a phylogenetic tree.

Clade

A group of organisms that includes an ancestor and all its descendants; equivalent to a monophyletic group.

Homology

Similarity in traits or features among organisms due to shared ancestry.

Homoplasy

A similarity in traits or features not due to shared ancestry, often caused by convergent evolution or evolutionary reversals.

Convergent Evolution

The independent evolution of similar traits in unrelated lineages, often due to similar environmental pressures.

Outgroup

A taxon or group outside the taxa being studied, used as a reference point to root a phylogenetic tree and infer ancestral traits.

Congruence

Agreement among different data sets or traits in supporting the same phylogenetic relationships.

Conflict

Disagreement among data sets or traits regarding the phylogenetic relationships of taxa.

Polytomy

A node in a phylogenetic tree with more than two branches, indicating uncertainty or unresolved relationships.

Lab 1 Key Concepts
Basic Anatomy of a Phylogeny and Data Matrix

Roots (Phylogeny)

The base of a tree, representing the most recent common ancestor of all taxa in the tree.

Taxa

The organisms or groups (e.g., species, genera) shown at the tips of the phylogeny.

Sister Taxa

Two taxa that share an immediate common ancestor. They form a "sister group."

Characters

Traits or features used to infer relationships (e.g., presence of a backbone).

Character States

The condition of a character in a taxon (e.g., backbone present or absent).

Polytomies

Nodes with three or more branches, indicating uncertainty in relationships or simultaneous divergence.

In a data matrix, rows represent taxa, and columns represent characters. The states of the characters (e.g., 0 for absent, 1 for present) are coded to analyze relationships.

Evaluating Phylogenies: Monophyly vs. Non-Monophyly
Monophyly

A group that includes a common ancestor and all its descendants (e.g., mammals).

Non-Monophyly

Paraphyly

Polyphyly

Groups taxa based on similarities but excludes their most recent common ancestor (e.g., flying animals like bats, birds, and insects).

Homology vs. Homoplasy
Homology

Homoplasy

Similar traits not due to shared ancestry, resulting from:
Convergent Evolution

Evolutionary Reversals

Reverting back to an ancestral state (e.g., loss of limbs in snakes).

Phylogeny as a Hypothesis

Comparing different trees to evaluate how well they explain the data.

Constructing a Data Matrix, Generating Trees, and Parsimony
Data Matrix

Start by coding characters (e.g., 0 for absent, 1 for present).

Tree Generation

Use software or manual methods to draw possible trees showing evolutionary relationships.

Parsimony

Select the simplest tree that minimizes the number of evolutionary changes (e.g., gain or loss of traits).

Parsimony Informative Characters

A trait or site in a sequence alignment that exhibits variability among multiple taxa (species) and has at least two different character states, each occurring in at least two taxa

Rooting (Building a Phylogeny)

Add an outgroup (a distantly related taxon) to provide a reference point and infer the direction of evolutionary changes.

Interpretation

Understand the relationships and infer common ancestors from the tree structure.

Using Parsimony to Map Character Changes

Character Conflict

Different characters suggest conflicting trees. Conflict is common when traits evolve independently or are influenced by homoplasy.

Causes of Homoplasy with Examples
Convergent Evolution

Evolutionary Reversals

Traits revert to an ancestral state (e.g., re-evolution of flightlessness in some birds).

Parallel Evolution

Similar traits evolve in closely related taxa independently.

Cladograms, Phylograms, and Chronograms
Cladograms

Phylograms

Show relationships, with branch lengths proportional to the amount of evolutionary change.

Chronograms

Represent evolutionary relationships, with branch lengths scaled to time

Coccus

Spherical or round Bacterium shape

Bacillus

Rod-Shaped Bacterium shape

Rod

Cylindrical, rod-like Bacterium shape

Spiral

Twisted or spiral Bacterium shape

Helical

Spiral-shaped bacterium with a helical or corkscrew-like structure

Lateral Gene Transfer

The transfer of genetic material between unrelated organisms in a manner other than traditional reproduction

Horizontal Gene Transfer

The transfer of genetic material between unrelated organisms in a manner other than traditional reproduction

Conjugation

Method of LGT

Direct transfer of DNA through physical contact between two cells, often via a structure called a pilus

Sex Pilus

Transferring structure formed between two cells in LGT conjugation

Transformation

Method of LGT

The uptake of foreign DNA from the environment

Transduction

Method of LGT

The transfer of genetic material via a virus

Amoeboid

Movement in protists using pseudopodia, temporary cytoplasmic projections.

Flagellate

Movement in protists via flagella, whip-like structures.

Ciliate

Movement in protists using numerous short cilia, hair-like projections.

Phase Contrast

Microscopy technique enhancing contrast of transparent specimens.

Primary Endosymbiosis

Engulfment of a prokaryote by a eukaryote, origin of mitochondria and chloroplasts.

Secondary Endosymbiosis

Engulfment of a eukaryote that already underwent primary endosymbiosis, forming complex eukaryotic cells.

Tertiary Endosymbiosis

Engulfment of a eukaryote that already underwent secondary endosymbiosis.

Plasmodial Slime Mold

Slime mold existing as a multinucleate single cell.

Cellular Slime Mold

Slime mold consisting of individual cells that aggregate to form multicellular structures.

Distance Matrix

Table showing pairwise evolutionary distances among taxa based on genetic or morphological data.

Nucleus

Organelle in eukaryotic cells housing genetic material (DNA).

Mitochondria

Organelles in eukaryotic cells responsible for energy production via cellular respiration.

Chloroplast

Organelles in plant and algal cells responsible for photosynthesis.

Basics of Compound Microscopy

Compound microscopes use multiple lenses to magnify specimens, enabling detailed observation.

Slide Preparation

Clean slide and cover slip, mount sample in water or stain, cover with slip to protect.

Endosymbiotic Theory

Explains organelle origins in eukaryotes from engulfed prokaryotes, leading to mitochondria and chloroplasts.

Movement in Microbial Eukaryotes

Euglena, Blepharisma, Paramecium, Naegleria, Chlamydomonas, Stentor use flagella or cilia for movement.

Phylogenies and Disease Origins

Phylogenies help trace pathogen origins and spread, such as HIV from primates.

Naegleria Experiment

Studied phenotypic plasticity in Naegleria, showing its ability to switch between movement forms based on environmental conditions.

Distance Matrix for Phylogeny

Table of evolutionary distances between taxa, used to construct phylogenetic trees.

Phototrophy

Obtaining Energy from Light

Chemotrophy

Obtaining Energy from Inorganic Oxidation

Organotrophy

Obtaining Hydrogen or Electron donors from Organic substrates

Lithotrophy

Obtaining Hydrogen or Electron donors from Inorganic substrates

Heterotrophy

Obtaining Carbon from Organic Substances

Autotrophy

Obtaining Carbon from Carbon Dioxide/Inorganic Substances

Photoorganoheterotroph

Energy Source: Light

Electron Source: Organic

Carbon Source: Organic

Photolithoautotroph

Energy Source: Light

Electron Source: Inorganic

Carbon Source: Carbon Dioxide

Chemoorganoheterotroph

Energy Source: Chemical Compounds

Electron Source: Organic

Carbon Source: Organic

Chemolithoheterotroph

Energy Source: Chemical Compounds

Electron Source: Inorganic

Carbon Source: Organic

Chemolithoautotroph

Energy Source: Chemical Compounds

Electron Source: Inorganic

Carbon Source: Carbon Dioxide

Haplontic

A life cycle where the haploid stage is dominant, and the diploid stage is limited to a zygote.

Diplontic

A life cycle where the diploid stage is dominant, and the haploid stage is limited to gametes.

Alternation of Generations

A life cycle alternating between haploid (gametophyte) and diploid (sporophyte) stages.

Gametophyte

The haploid stage in a plant’s life cycle that produces gametes.

Sporophyte

The diploid stage in a plant’s life cycle that produces spores.

Archegonia

Female reproductive structures in plants that produce eggs.

Antheridia

Male reproductive structures in plants that produce sperm.

Gametangia

Organs in plants and algae that produce gametes.

Sporangium

Structure where spores are produced.

Spore

A reproductive cell capable of developing into a new organism.

Sori

Clusters of sporangia found on fern leaves.

Vascular Tissue

Plant tissue that transports water, nutrients, and food, including xylem and phloem.

Xylem

Vascular tissue transporting water and minerals from roots to other plant parts.

Phloem

Vascular tissue transporting sugars and nutrients throughout the plant.

Tracheid

Thin Tube-like cells in the xylem for water conduction.

Vessel Element

Thick, Segmented Tube-like cells in the xylem for water conduction.

Sieve Tube Element

A phloem cell that conducts sugars and nutrients

Companion cell

A specialized cell in the phloem that supports the function of sieve tube elements

Waxy Cuticle

A waterproof layer covering plant surfaces to prevent water loss.

Dominance

The stage (gametophyte or sporophyte) predominating in a plant's life cycle.

Independence

The ability of a plant stage to survive without the other.

Stem

Main structural axis of a plant supporting leaves and flowers, conducting water and nutrients.

Leaf

Photosynthetic organ of a plant.

Root

Organ of a plant that anchors and absorbs water and nutrients.