Taxonomy and Phylogeny
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Mason_UB3e_ch22_PPT_final_Accessible.pptxChapter 22 Lecture Outline
Understanding Biology
THIRD EDITION
Kenneth A. Mason
Tod Duncan
Jonathan B. Losos
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Systematics and Phylogeny
Chapter 22
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Systematics
All organisms share many characteristics:
Composed of one or more cells
Carry out metabolism
Transfer energy with ATP
Encode hereditary information in DNA
Tremendous diversity of life
Bacteria, whales, sequoia trees
Biologists group organisms based on shared characteristics and newer molecular sequence data
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Systematics versus Phylogeny
Since fossil records are not complete, scientists rely on other types of evidence to establish the best hypothesis of evolutionary relationships
Systematics
Reconstruction and study of evolutionary relationships
Phylogeny
Hypothesis about patterns of relationship among species
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Darwin’s Notebook
Darwin envisioned that all species were descended from a single common ancestor
He depicted this history of life as a branching tree
“Descent with modification”
(a): ©Letz/SIPA/Newscom
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Cladograms
Key to interpreting a cladogram
Looks at how recently species share a common ancestor based on branches
Does not look at the arrangement of species across the top of the tree
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Figure 22.1
Branching diagrams depict evolutionary relationships
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Early Predictions
Similarity may not accurately predict evolutionary relationships
Early systematists relied on the expectation that the greater the time since two species diverged from a common ancestor, the more different they would be
Rates of evolution vary
Evolution may not be unidirectional
Evolution is not always divergent
Convergent evolution
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Cladistics
Derived characteristic
Similarity that is inherited from the most recent common ancestor of an entire group
Ancestral
Similarity that arose prior to the common ancestor of the group
In cladistics, only shared derived characters are considered informative about evolutionary relationships
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Characters
Characters can be any aspect of the phenotype
Morphology
Behavior
Physiology
DNA
Characters should exist in recognizable character states
Example: Character “teeth” in amniote vertebrates has two states, present in most mammals and reptiles, and absent in birds and turtles
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Ancestral versus Derived Characters
Examples of ancestral versus derived characters
Presence of hair is a shared derived feature of mammals
Presence of lungs in mammals is an ancestral feature; also present in amphibians and reptiles
Shared, derived feature of hair suggests that all mammal species share a common ancestor that existed more recently than the common ancestor of mammals, amphibians, and reptiles
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Data for Constructing a Cladogram
| Traits: Organism | Jaws | Jaws | Amniotic Membrane | Hair | No Tail | Bipedal |
| Lamprey | 0 | 0 | 0 | 0 | 0 | 0 |
| Shark | 1 | 0 | 0 | 0 | 0 | 0 |
| Salamander | 1 | 1 | 0 | 0 | 0 | 0 |
| Lizard | 1 | 1 | 1 | 0 | 0 | 0 |
| Tiger | 1 | 1 | 1 | 1 | 0 | 0 |
| Gorilla | 1 | 1 | 1 | 1 | 1 | 0 |
| Human | 1 | 1 | 1 | 1 | 1 | 1 |
“1” = possession of derived character state
“0” = possession of ancestral character state
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Constructed Cladogram
The derived characters between the cladogram branch points are shared by all organisms above the branch points and are not present in any below them. The outgroup (in this case, the lamprey) does not possess any of the derived characters.
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Manual Cladistic Analysis 1
First step is to polarize the characters (are they ancestral or derived)
Example: polarize “teeth” means to determine presence or absence in the most recent common ancestor
Outgroup comparison used
Species or group of species that is closely related to, but not a member of, the group under study is designated as the outgroup
Outgroup species do not always exhibit the ancestral condition
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Manual Cladistic Analysis 2
When the group under study exhibits multiple character states, and one of those states is exhibited by the outgroup, then that state is ancestral and other states are derived
Most reliable if character state is exhibited by several different outgroups
Presence of teeth in mammals and reptiles is ancestral
Absence of teeth in birds and turtles is derived
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Clades
Cladogram
Depicts a hypothesis of evolutionary relationships
Clade
Species that share a common ancestor as indicated by the possession of shared derived characters
Evolutionary units and refer to a common ancestor and all descendants
Synapomorphy – derived character shared by clade members
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Synapomorphy
Simple cladogram is a nested set of clades, each characterized by its own synapomorphies
Amniotes are a clade for which the evolution of an amniotic membrane is a synapomorphy
Within that clade, mammals are a clade, with hair as a synapomorphy
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Ancestral States
Plesiomorphies – ancestral states
Symplesiomorphies – shared ancestral states
Character state “presence of a tail”
Exhibited by lampreys, sharks, salamanders, lizards, and tigers
Are tigers more closely related to lizards and sharks than apes and humans?
Symplesiomorphies reflect character states inherited from a distant ancestor, they do not imply that species exhibiting that state are closely related
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Homoplasy
Homoplasy – a shared character state that has not been inherited from a common ancestor
Convergent evolution
Evolutionary reversal
Systematists rely on the principle of parsimony, which favors the hypothesis that requires the fewest assumptions
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Figure 22.3
Based on the principle of parsimony, the cladogram that requires the fewest number of evolutionary changes is favored; in this case the cladogram in (a) requires four changes, whereas that in (b) requires five
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DNA Sequences for Cladogram Construction
Systematists increasingly use DNA sequence data to construct phylogenies because of the large number of characters that can be obtained through sequencing
Character states are polarized by reference to the sequence of an outgroup
Cladogram is constructed that minimizes the amount of character evolution required
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DNA Sequence Data
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Cladogram Based on DNA
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Other Phylogenetic Methods
Some characters evolve rapidly and principle of parsimony may be misleading
Stretches of DNA with no function have high rates of evolution of new character states as result of genetic drift
Only 4 character states are possible (A, T, G,C) so there is a high probability that two species will independently evolve the same derived character state at any particular base position
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Molecular Clock
Statistical approach
Start with an assumption about the rate at which characters evolve
Fit the data to these models to derive the phylogeny that best accords (that is, “maximally likely”) with these assumptions
Molecular clock
Rate of evolution of a molecule is constant through time
Divergence in DNA can be used to calculate the times at which branching events have occurred
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Systematics and Classification 1
Classification
How we place species and higher groups into the taxonomic hierarchy
Genus, family, class, etc.
Monophyletic group
Includes the most recent common ancestor of the group and all of its descendants (clade)
Paraphyletic group
Includes the most recent common ancestor of the group, but not all its descendants
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Systematics and Classification 2
Polyphyletic group
Does not include the most recent common ancestor of all members of the group
Taxonomic hierarchies are based on shared traits, should reflect evolutionary relationships
Birds as an example
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Monophyletic Group
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Paraphyletic Group
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Polyphyletic Group
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Plant Phylogenetics
The traditional classification included two groups that we now realize are not monophyletic: the green algae and bryophytes
New classification of plants does not include these groups
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Species Concepts
Biological species concept (BSC)
Defines species as groups of interbreeding populations that are reproductively isolated
Phylogenetic species concept (PSC)
Species is a population or set of populations characterized by one or more shared derived characters
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PSC versus BSC
PSC solves two BSC problems
BSC cannot be applied to allopatric populations – would they interbreed?
PSC looks to the past to see if they have been separated long enough to develop their own derived characters
BSC can be applied only to sexual species
PSC can be applied to both sexual and asexual species
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PSC Still Controversial
Critics contend it will lead to the recognition of even slightly different populations as distinct species
Paraphyly problem
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Taxonomy
Taxonomy is a quest for identity and relationships
The science of classifying living things
Linnaeus instituted the use of binomial descriptive names
Genus and specific together constitute the species name
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Common Names
Common names make poor labels. In North America, the common name “bear” brings a clear image to mind, but the image is very different for someone in Australia.
(left): ©Moodboard/Image Source; (right): ©John White Photos/Getty Images
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Taxonomic Hierarchy
Shifted from emphasis on identifying and naming organisms to constructing evolutionary hypotheses to explain the relatedness of species
Organisms grouped into eight levels
Domain, kingdom, phylum, class, order, family, genus, and species
Other categories assist with classification
Each hierarchal level is called a taxon
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Gray Squirrel Classification 1
Hierarchical system used in classifying the eastern gray squirrel
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Gray Squirrel Classification 2
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Honeybee Classification
Each taxon groups organisms by a set of characteristics
For example, the European honeybee
Species level: Apis mellifera, meaning honey-bearing bee
Genus level: Apis, a genus of bees
Family level: Apidae, a bee family. All members of this family are bees—some solitary, some living in colonies as A. mellifera does.
Order level: Hymenoptera, a grouping that includes bees, wasps, ants, and sawflies—all of which have wings with membranes
Class level: Insecta, a very large class that comprises animals with three major body segments, three pairs of legs attached to the middle segment, and wings
Phylum level: Arthropoda. Animals in this phylum have a hard exoskeleton made of chitin and jointed appendages.
Kingdom level: Animalia. The animals are multicellular heterotrophs with cells that lack cell walls.
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Limitations of the Hierarchy
Many higher taxonomic ranks are not monophyletic and do not represent natural groups
Taxonomic groups may not represent clades that originated at the same
Differences across a single taxon limits the usefulness making evolutionary predictions
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Domains
Domains are the largest taxon
Molecular data support the existence of three domains
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Eukarya Are Grouped into Four Kingdoms
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Bacteria
Most abundant organisms on Earth
Play critical roles throughout the biosphere
Carbon and sulfur cycling
Extract nitrogen from air
Photosynthesis
12 to 15 major groups of bacteria
Based on ribosomal RNA sequences
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Archaea 1
Typically live in extreme environments
Diverged early from bacteria
More closely related to eukaryotes than to bacteria
Based on genes that encode ribosomal RNAs
Swapped genetic information via horizontal gene transfer (HGT) with other microorganisms
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Archaea 2
All archaea share certain key characteristics
Grouped into three general categories
Methanogens
Extremophiles
Nonextreme archaea
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Eukarya
Eukaryotes have compartmentalized cells
Appear in fossil record about 2.5 bya
Their structure and function allowed multicellular life to evolve
The roots of the eukaryotic tree remain elusive
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Three Domains
TABLE 22.1 Features of the Three Domains of Life
| Feature | Archaea | Bacteria | Eukarya |
| Amino acid that initiates protein synthesis | Methionine | Formyl-methionine | Methionine |
| Introns | Present in some genes | Absent | Present |
| Membrane-bounded organelles | Absent | Absent | Present |
| Membrane lipid structure | Branched | Unbranched | Unbranched |
| Nuclear envelope | Absent | Absent | Present |
| Number of different RNA polymerases | Several | One | Several |
| Peptidoglycan in cell wall | Absent | Present | Absent |
| Response to the antibiotics streptomycin and chloramphenicol | Growth not inhibited | Growth inhibited | Growth not inhibited |
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Compartmentalization
Compartmentalization of cells enabled the advent of eukaryotes
Bacteria and archaea are distinct from eukaryotes in that they lack compartmentalization
Eukaryotes developed extensive endomembrane system
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Endomembrane
Evolution of the endomembrane system
Nuclear membrane, not found in bacteria and archaea, accounts for increased complexity in eukaryotes
Physical separation of transcription and translation adds additional levels of gene expression
Golgi apparatus and endoplasmic reticulum facilitate intracellular transport
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Endosymbiosis
Endosymbiosis and the origin of eukaryotes
Mitochondria and chloroplasts entered early eukaryotic cells by endosymbiosis
Mitochondria are the descendants of relatives of purple sulfur bacteria and the parasite Rickettsia
Chloroplasts are derived from cyanobacteria.
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Chloroplast Origins
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Multicellularity Leads to Cell Specialization
Unicellular body plan tremendously successful
Unicellular prokaryotes and eukaryotes constituting about half of the biomass on Earth
Single cell has limits with cell specialization
Multicellularity allowed organisms to deal with environment in novel ways through differentiation
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Sexual Reproduction
Eukaryotic species as a group carry out sexual reproduction
Some interchange of genetic material occurs in bacteria
It is not regular and predictable
Reproduction occurs only occasionally in many unicellular phyla
First eukaryotes were probably haploid
Diploids arose on separate occasions
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Constructed Cladogram - Text Alternative
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There is a common ancestor at the branch separating lampreys into an outgroup. The trait of jaws are acquired before the next branch separating sharks from the other animals. The trait of lungs are acquired before salamanders are separated. Next amniotic membranes are acquired before lizards separate. The hair leads to tigers followed by tail loss before gorillas. The final branch of this cladogram is humans which are separated because they are bipedal.
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Synapomorphy - Text Alternative
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From the base of the cladogram, the first synapomorphy is jaws. The outlier is lamprey, but includes sharks, salamanders, lizards, tigers, gorillas and humans. The next synapomorphy is lungs and excludes sharks. The next synapomorphy is amniotic membrane and excludes salamanders. The next synapomorphy is hair and excludes lizards. The next synapomorphy is tail loss and excludes tigers. The final synapomorphy is bipedal and excludes gorillas.
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Figure 22.3 - Text Alternative
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One cladogram might show frogs being closely related to salamanders with a derived trait of tail loss. Another possible cladogram could show frogs as closely related to primates with derived characteristics of hair loss and amniotic membrane loss. That means that ancestors before frogs would have gained amniotic membranes and hair while also losing tails. Then frogs would have lost hair and the amniotic membrane. The first cladogram is more simple and more likely.
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DNA Sequence Data - Text Alternative
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Comparing 5 species of trees by the D N A sequence of 10 nucleotides reveals similarities in the nucleotide sequences which indicates evolutionary relationships or homoplasy. The principle of parsimony is used to analyze the data and find the most likely evolutionary relationships.
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Cladogram Based on DNA - Text Alternative
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The outgroup branches off first. The change at site 2 from t to c occurs before all of the other species. The next branch is for species b which had changes at site 4, t to g and site 8, t to c. Then changes at site 6, c to g and 9, a to g occurs before the remaining species separate. Species d separates next because site 10 changes from t to g. Site one changes from a to g and site 5 changes from c to a before species a and c arose. Species a separated from c at site 8 which changes from t to c. Site 8 is an example of homoplasy.
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