Ecology and Evolution Exam III
Phylogenetic trees
● Phylogeny - evolutionary history and relationships between a group of organisms
○ Represented in a phylogenetic tree, which is made up of nested hierarchies of
clades / monophyletic groups
● Root - single ancestral lineage on a tree to which all organisms in the tree relate
● Branch point / node - place where a single lineage splits into distinct new lineages
(represents an extinct ancestor)
○ Can rotate while still representing the same tree
○ These can be scaled for time, DNA similarity, etc.
● Sister taxa - two lineage points that diverged from the same branch point
● Polytomy - a branch with more than two groups / taxa
● Basal taxon - a branch that has not diverged significantly from the root ancestor
● Most recent common ancestor (MRCA) - the youngest common ancestor for a group/taxa
● Systematics - field of classifying organisms based on evolutionary relationships
● Taxonomy - the science of classifying organisms
● Binomial nomenclature - the naming system of using an organism’s genus and species
● Domain → kingdom → phylum → class → order → family → genus → species
● Taxon - a single level in the taxonomic classification system
○ Has a set of characters / attributes that potentially allow its differentiation from
others (morphological, physiological, molecular, etc.)
● Character states - different conditions of a character / trait
● Taxa can have similar character states due to:
○ Homology - similarity due to inheritance from a common ancestor
○ Analogy - similarity due to convergent evolution, not same ancestor
● Since characters can be similar due to homology or analogy, data from many characters is
required to classify and organize relationships of organisms
● For each character you need:
○ Ancestral - the version of the character found in older ancestors
○ Derived - the character found in recent ancestors / descendants
● Systematists often aim to build a phylogeny in which taxa are hierarchically grouped by
shared derived traits
● Maximum parsimony - applying the simplest, most obvious way with the least number of
steps
● Molecular systematics - technique using the molecular evidence to identify phylogenetic
relationships (ie. DNA sequencing)
○ It is easy to get data for thousands of DNA bases with modern technology
● Horizontal gene transfer - transfer of genes between unrelated species
● Web of life - a phylogeny that incorporates both vertical and horizontal gene transfer
,Introduction to prokaryotes
● Three main domains of life: bacteria, archaea, and eukarya
● Archaea and eukarya are grouped together, even though the bacteria and archaea make up
the prokaryotes
○ Prokaryotes are not a monophyletic group
● Prokaryotes - single celled organisms that lack organelles and do not have a nuclear
membrane
● Prokaryotic geologic history
○ They were the first life on Earth, the oldest fossils being from 3.5 billion years
ago
○ The atmosphere of the early Earth was anoxic (had no oxygen)
○ Early prokaryotes converted solar energy to chemical energy but did not produce
O2 as a byproduct
○ Cyanobacteria were the first organisms to make O2 as a byproduct of their energy
production about 2.6 billion years ago
■ They do oxygenic photosynthesis metabolism
■ They increased the levels of O2 in the atmosphere, allowing for the
evolution of aerobic metabolism
○ It is difficult to draw boundaries between prokaryotic species due to horizontal
gene transfer (most likely 1 million to 1 trillion species, but we have very limited
knowledge of them)
● Prokaryotic diversity
○ Traditionally studied and classified using cultures (collecting sample that grow in
different medias and temperatures)
○ Metagenomics - the process of collecting a sample and sequencing its DNA
■ This has revealed a lot about uncharacterized diversity
● Prokaryotic abundance
○ In terms of total volume, archaea and bacteria are the dominant organisms on
Earth
● Prokaryotic forms and reproduction
○ They are unicellular and lack membrane-bound organelles
○ They have circular chromosomes
○ They have a protective cell wall and some have a capsule around the cell wall
○ Some have flagella for locomotion (rotates like a propellor)
○ They can be spherical, rod shaped, and spiral shaped cells
■ Archaea can be spheres, rods, spirals, triangles, or squares
● Protective cell walls
○ Contains peptidoglycan, a polysaccharide that gives the cell wall its strength
○ Gram stain binds to peptidoglycan but can’t penetrate the cell wall
■ Gram positive = peptidoglycan is on the exterior/outside of the cell wall
, ■ Gram negative = peptidoglycan is on the interior of the cell wall
● Prokaryotic asexual reproduction via binary fission
○ DNA uncoils and duplicates → cell grows in size → DNA moves to the poles of
the cell → cell pinches in and divides → two identical daughter cells created
○ There is no opportunity for recombination in binary fission (genetic diversity
doesn’t result from fission)
● Horizontal gene transfer:
○ Transformation - uptake of DNA from the environment
○ Transduction - bacteriophage (virus) transfers DNA between cells
○ Conjugation - direct DNA transfer via cell-to-cell contact
○ This is different from sexual reproduction because it only goes one way and only
transfers small amounts of genes
● Prokaryotic evolutionary rates:
○ Reproduction is fast, so there is more opportunity for mutation and evolution
○ High genetic diversity
○ Can respond to selective pressures very quickly (ex: “superbugs”)
Prokaryotic metabolism & role in the ecosystem
● Bacteria and archaea are able to live in a wide variety of environments
○ Extreme environments (ie. no light, high/low pH, high/low temperatures)
○ They have a variety of ways to produce energy
● Metabolism requires an energy source (either chemical bonds or sunlight) and a carbon
source
○ Phototrophs - use sunlight
○ Chemotrophs - break chemical bonds
○ Autotrophs - get inorganic carbon via CO2
○ Heterotrophs - get organic carbon via C–H bonds
● Photoautotroph (plants, algae, cyanobacteria)
● Photoheterotroph (only bacteria and archaea)
● Chemoheterotrophs (animals, fungi, bacteria, and archaea)
● Chemoautotrophs (only bacteria and archaea)
● Carbon cycle:
○ Photo- and chemo- autotrophs convert CO2 to organic carbon
○ Prokaryotes and fungi are the main decomposers that break down organic matter
to be reused, making organic compounds available to other organisms
● Nitrogen cycle:
○ Nitrogen is a very important element to life
○ Plants can’t directly take in N2 gas from the atmosphere
○ Nitrogen fixation: when gaseous nitrogen is transformed/fixed into more readily
available forms such as ammonia
Phylogenetic trees
● Phylogeny - evolutionary history and relationships between a group of organisms
○ Represented in a phylogenetic tree, which is made up of nested hierarchies of
clades / monophyletic groups
● Root - single ancestral lineage on a tree to which all organisms in the tree relate
● Branch point / node - place where a single lineage splits into distinct new lineages
(represents an extinct ancestor)
○ Can rotate while still representing the same tree
○ These can be scaled for time, DNA similarity, etc.
● Sister taxa - two lineage points that diverged from the same branch point
● Polytomy - a branch with more than two groups / taxa
● Basal taxon - a branch that has not diverged significantly from the root ancestor
● Most recent common ancestor (MRCA) - the youngest common ancestor for a group/taxa
● Systematics - field of classifying organisms based on evolutionary relationships
● Taxonomy - the science of classifying organisms
● Binomial nomenclature - the naming system of using an organism’s genus and species
● Domain → kingdom → phylum → class → order → family → genus → species
● Taxon - a single level in the taxonomic classification system
○ Has a set of characters / attributes that potentially allow its differentiation from
others (morphological, physiological, molecular, etc.)
● Character states - different conditions of a character / trait
● Taxa can have similar character states due to:
○ Homology - similarity due to inheritance from a common ancestor
○ Analogy - similarity due to convergent evolution, not same ancestor
● Since characters can be similar due to homology or analogy, data from many characters is
required to classify and organize relationships of organisms
● For each character you need:
○ Ancestral - the version of the character found in older ancestors
○ Derived - the character found in recent ancestors / descendants
● Systematists often aim to build a phylogeny in which taxa are hierarchically grouped by
shared derived traits
● Maximum parsimony - applying the simplest, most obvious way with the least number of
steps
● Molecular systematics - technique using the molecular evidence to identify phylogenetic
relationships (ie. DNA sequencing)
○ It is easy to get data for thousands of DNA bases with modern technology
● Horizontal gene transfer - transfer of genes between unrelated species
● Web of life - a phylogeny that incorporates both vertical and horizontal gene transfer
,Introduction to prokaryotes
● Three main domains of life: bacteria, archaea, and eukarya
● Archaea and eukarya are grouped together, even though the bacteria and archaea make up
the prokaryotes
○ Prokaryotes are not a monophyletic group
● Prokaryotes - single celled organisms that lack organelles and do not have a nuclear
membrane
● Prokaryotic geologic history
○ They were the first life on Earth, the oldest fossils being from 3.5 billion years
ago
○ The atmosphere of the early Earth was anoxic (had no oxygen)
○ Early prokaryotes converted solar energy to chemical energy but did not produce
O2 as a byproduct
○ Cyanobacteria were the first organisms to make O2 as a byproduct of their energy
production about 2.6 billion years ago
■ They do oxygenic photosynthesis metabolism
■ They increased the levels of O2 in the atmosphere, allowing for the
evolution of aerobic metabolism
○ It is difficult to draw boundaries between prokaryotic species due to horizontal
gene transfer (most likely 1 million to 1 trillion species, but we have very limited
knowledge of them)
● Prokaryotic diversity
○ Traditionally studied and classified using cultures (collecting sample that grow in
different medias and temperatures)
○ Metagenomics - the process of collecting a sample and sequencing its DNA
■ This has revealed a lot about uncharacterized diversity
● Prokaryotic abundance
○ In terms of total volume, archaea and bacteria are the dominant organisms on
Earth
● Prokaryotic forms and reproduction
○ They are unicellular and lack membrane-bound organelles
○ They have circular chromosomes
○ They have a protective cell wall and some have a capsule around the cell wall
○ Some have flagella for locomotion (rotates like a propellor)
○ They can be spherical, rod shaped, and spiral shaped cells
■ Archaea can be spheres, rods, spirals, triangles, or squares
● Protective cell walls
○ Contains peptidoglycan, a polysaccharide that gives the cell wall its strength
○ Gram stain binds to peptidoglycan but can’t penetrate the cell wall
■ Gram positive = peptidoglycan is on the exterior/outside of the cell wall
, ■ Gram negative = peptidoglycan is on the interior of the cell wall
● Prokaryotic asexual reproduction via binary fission
○ DNA uncoils and duplicates → cell grows in size → DNA moves to the poles of
the cell → cell pinches in and divides → two identical daughter cells created
○ There is no opportunity for recombination in binary fission (genetic diversity
doesn’t result from fission)
● Horizontal gene transfer:
○ Transformation - uptake of DNA from the environment
○ Transduction - bacteriophage (virus) transfers DNA between cells
○ Conjugation - direct DNA transfer via cell-to-cell contact
○ This is different from sexual reproduction because it only goes one way and only
transfers small amounts of genes
● Prokaryotic evolutionary rates:
○ Reproduction is fast, so there is more opportunity for mutation and evolution
○ High genetic diversity
○ Can respond to selective pressures very quickly (ex: “superbugs”)
Prokaryotic metabolism & role in the ecosystem
● Bacteria and archaea are able to live in a wide variety of environments
○ Extreme environments (ie. no light, high/low pH, high/low temperatures)
○ They have a variety of ways to produce energy
● Metabolism requires an energy source (either chemical bonds or sunlight) and a carbon
source
○ Phototrophs - use sunlight
○ Chemotrophs - break chemical bonds
○ Autotrophs - get inorganic carbon via CO2
○ Heterotrophs - get organic carbon via C–H bonds
● Photoautotroph (plants, algae, cyanobacteria)
● Photoheterotroph (only bacteria and archaea)
● Chemoheterotrophs (animals, fungi, bacteria, and archaea)
● Chemoautotrophs (only bacteria and archaea)
● Carbon cycle:
○ Photo- and chemo- autotrophs convert CO2 to organic carbon
○ Prokaryotes and fungi are the main decomposers that break down organic matter
to be reused, making organic compounds available to other organisms
● Nitrogen cycle:
○ Nitrogen is a very important element to life
○ Plants can’t directly take in N2 gas from the atmosphere
○ Nitrogen fixation: when gaseous nitrogen is transformed/fixed into more readily
available forms such as ammonia
