AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
Macroevolution attempts to explain how major adaptive characteristics came into existence. These
characteristics would be the basis for creating new taxa above the species level.
Phylogeny: the evolutionary history of a species – based on common ancestries inferred from:
– Fossil records
– Morphological & biochemical resemblances
– Molecular evidence
Systematics: the study of biological diversity in an environmental context, encompassing taxonomy and
involving the reconstruction of phylogenetic history.
Sedimentary Rocks are the richest source of fossils.
The fossil record is a substantial, but incomplete, chronicle of evolutionary history.
– The history of life on Earth is punctuated by mass extinctions
– Biologists draw on the fossil record which provides information about ancient organisms
– Sedimentary rocks are deposited into layers called strata
– The fossil record is based on the sequence in which fossils have accumulated in such strata
– Fossils reveal ancestral characteristics that may have been lost over time
FIGURE 26.7 - Systematics: connecting classification and phylogeny.
In addition to fossil organisms phylogenetic history can be inferred from certain morphological and molecular
similarities among living organisms
– In general, organisms that share very similar morphologies or similar DNA sequences are likely
to be more closely related than organisms with vastly different structures or sequences
A potential misconception in constructing a phylogeny is similarity due to convergent evolution, called analogy,
rather than shared ancestry
– It is important in phylogeny to sort HOMOLOGY from ANALOGY.
• Homologous structures INFER common
ancestry
• Analogous structures INFER convergent
evolution by similar environmental
pressures
– Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages
• Analogous structures or molecular
sequences that evolved independently
are also called homoplasies
AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
FIGURE 26.4 - Taxonomy employs a hierarchical system of classification.
Phylogenetic systematics connects classification with evolutionary history:
• Taxonomy is the ordered division of organisms into categories based on a set of characteristics used
to assess similarities and differences
• Binomial nomenclature
– Is the two-part format of the scientific name of an organism
– Was developed by Carolus Linnaeus
– The binomial name of an organism or scientific epithet
– Is latinized
– Is the genus and species
• Linnaeus also introduced a system for grouping species in increasingly broad categories
– Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
• Systematists depict evolutionary relationships in branching phylogenetic trees.
FIGURE 26.5 & 26.10 - Cladistic Analysis is the basis for modern phylogenetic systematics.
A phylogentic diagram based on cladistics is called a cladogram. Each branch point represents the divergence
of two species
• Deeper” branch points represent progressively greater amounts of divergence
Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics
• A cladogram is a depiction of patterns of shared characteristics among taxa
– A clade within a cladogram is defined as a group of species that includes an ancestral species and
all its descendants
– Cladistics is the study of resemblances among clades
Clades can be nested within larger clades, but not all groupings or organisms qualify as clades
– A valid clade is monophyletic signifying that it consists of the ancestor species and all its
descendants
– A paraphyletic clade is a grouping that consists of an ancestral species and some, but not all, of the
descendants
– A polyphyletic grouping includes numerous types of organisms that lack a common ancestor
Phylogenetic trees are constructed to reflect the hierarchial classification of taxonomic groups nested within
more inclusive groups.
• Today, most systematists practice cladistics.
AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
•
•
•
A phylogenetic diagram based on cladistics is called a cladogram – and a valid cladogram is
monophyletic.
The term “character” is referring to any feature that a particular taxon possesses.
2 Types:
– Shared Primitive Characters: a homology common to a taxon more inclusive than the one being
defined.
– Shared Derived Characters: an evolutionary novelty unique to a particular clade (also called
synapomorphies).
– The sequence of branching in a cladogram represents the sequence in which SHARED DERIVED
CHARACTERS evolved.
FIGURE 26.11 - Performing Outgroup Comparisons: as a key step in cladistic analysis, systematists use a
method called outgroup comparison.
Systematists use a method called outgroup comparison to differentiate between shared derived and shared
primitive characteristics
• As a basis of comparison we need to designate an outgroup
– which is a species or group of species that is closely related to the ingroup, the various species
we are studying
Outgroup comparisons are based on the assumption that homologies present in both the outgroup and ingroup
must be primitive characters that predate the divergence of both groups from a common ancestor
• The outgroup comparison enables us
to focus on just those characters that
were derived at the various branch
points in the evolution of a clade
FIGURE 26.15 - Parsimony: Systematists narrow the possibilities for a phylogenetic tree by applying the
principles of maximum parsimony and maximum likelihood.
Among phylogenetic hypotheses the most parsimonious tree is the one that requires the fewest evolutionary
events to have occurred in the form of shared derived characters
• The principle of maximum likelihood states
that, given certain rules about how DNA
changes over time, a tree can be found that
reflects the most likely sequence of
evolutionary events.
AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
FIGURE 26.19 - Molecular Clocks help track evolutionary time.
The molecular clock is a yardstick for measuring the absolute time of evolutionary change based on the
observation that some genes and other regions of genomes appear to evolve at constant rates
• Neutral theory states that
– Much evolutionary change in genes and proteins has no effect on fitness and therefore is not
influenced by Darwinian selection
– And that the rate of molecular change in these genes and proteins should be regular like a clock
– The molecular clock does not run as smoothly as neutral theory predicts
FIGURE 26.21 - The Universal Tree of Life
The tree of life is divided into three great clades called domains: Bacteria, Archaea, and Eukarya
• The early history of these domains is not yet clear.
AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
FIGURE 26.16 – Arranging the diversity of life into the highest taxa is a work in progress. New information
has revised our understanding of the tree of life.
The first taxonomic schemes divided organisms into plant and animal kingdoms.
1.
2.
3.
4.
5.
384 – 322 B.C. Aristotle - 2 Kingdom Broad Classification (Plants or Animals)
1735 - Carl Linnaeus - 2 Kingdom Multi-Divisional Classification (Kingdom, Phylum, Class, Order, Family Genus,
Species)
Evolutionary Classification (After Darwin) - Group By lines of Evolutionary Descent
5 Kingdom System (Whittaker) – 1950s – Plantae, Fungi, Animalia, Protista, Monera
3 Domain System – late 1990s – Bacteria, Archaea, Eukarya
The Five Kingdom System described classification as:
1.
2.
3.
4.
5.
6.
Plantae, Fungi, Animalia, Protista, Monera
recognizes only 2 types of cells: prokaryotic and eukaryotic
sets all prokaryotes apart from eukaryotes
prokaryotes are in their own kingdom (Monera)
distinguished 3 kingdoms of eukaryotes based on mode of nutrition
protista were all eukaryotes that did not fit the definition of plants, fungi, or animals
AP Biology
LECTURE NOTES: Chapter 26
Phylogeny and the Tree of Life
The most recent proposed reorganization of the phylogenetic system of classification includes the Domain, a
new taxonomic category higher (and more inclusive) than the 5 Kingdom System. This classification scheme
presents 6 different conclusions about the relationship among living organisms than those presented by the
previous five-kingdom system of classification seen below:
1.
2.
3.
4.
5.
6.
Not all prokaryotes are closely related (not monophyletic)
Prokaryotes split early in the history of living things (not
all in one lineage)
Archaea are more closely related to Eukarya than to
Bacteria
Eukarya are not directly related to Eubacteria
There was a common ancestor for all extant organisms
(monophyletic)
Eukaryotes are more closely related to each other (than prokaryotes are to each other)
The following modes of evidence were used to develop the 3 Domain taxonomic scheme:
Description
Differences
Habitat - mostly extreme (halophilic,
thermophilic, acidic)
Reproduction
Multicellularity exists
Nucleus
Membrane-bound organdies
Microtubules/ microfilaments
Cell walls with peptidoglycan
Chromosomes:
Shapes
Number
Histories present
Structure of tRNA
RNA polymerase
Introns
Operon organization of genes
Can be pathogens
Response to antibiotics
Explanations
Eukaryotes
Mitosis/meiosis
+
+
+
+
-
Archaea
+
Binary
fission
-
Eubacteria
Binary fission
+
Linear
More than
one
+
Circular
One
+
Circular
One
-
Similar
Multiple
types
Present
+
-
Unique
Multiple
types
Some
+
-
Similar
Single type
None
+
+
+