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Macroevolution:
Phylogeny and Systematics
• Debates in Systematics
• Molecular Techniques
• Cladistics
• Domains and Kingdoms
Systematics
• Study of biological diversity and its
classification.
• Done by taxonomists
• Group organisms into more inclusive
categories
• Goal since Darwin’s time – have
classification reflect evolutionary
connections among species.
• Genera are
grouped
into progressively
broader
categories:
family, order,
class, phylum,
kingdom
and domain.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 25.7
Phylogentic Trees• Depict hypotheses about the evolutionary
history of species.
http://insects.eugenes.org/DroSpeGe/
Morphological and Molecular
Homologies
• 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
Sorting Homology from Analogy
• A potential misconception in constructing a
phylogeny
– Is similarity due to convergent evolution, called
analogy, rather than shared ancestry
• Analogous structures or molecular
sequences that evolved independently
– Are also called homoplasies
• Determining which similarities between species are relevant to grouping the species is a challenge.
• It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.
– These two desert plantsare not closely relatedbut owe theirresemblance toanalogousadaptations.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 25.10
• Shared derived characters are useful in
establishing a phylogeny, but shared primitive
characters are not.
• The status of a character as analogous versus
homologous or shared versus primitive may
depend on the level at which the analysis is
being performed.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Primitive Characters
Contrasting with derived characters, they are the more
common shared characters of a given group of organisms.
Like derived characters, they also have the same structure
and function. The evolutionary interpretation is that these
characters evolved earlier than derived characters.
Derived Characters
Among a given group of organisms, the shared derived
characters are generally the less common characters. The
evolutionary interpretation is that these characters of
organisms are more recently evolved. They are contrasted
with primitive characters. Shared derived characters
should have the same structure and function.
http://www.cals.ncsu.edu/course/ent425/library/tutorials/systematics_taxonomy/phylogenetic_trees.html
Character Rivet Nail Screw Bolt
Head notch 0 0 1 0
Rounded head 0 0 1 0
Hex head 0 0 0 1
Threaded shaft 0 0 1 1
Tapered shaft 0 0 1 0
Pointed tip 0 1 1 0
Thick diameter 0 0 1 1
Rivet Nail Screw Bolt
Rivet - 6 1 4
Nail - 2 3
Screw - 2
Bolt -
If the phenetic approach is used to classify
these fasteners, they are compared with one
another by counting the total number of
shared character states (both primitive and
derived).
Phenetic Comparison
(Total of all shared states)
Rivet Nail Screw Bolt
Rivet - 0 0 0
Nail - 1 0
Screw - 2
Bolt -
If the cladistic approach is used, the
comparison is based only upon the number of
derived character states shared.
Cladistic Comparison
(Total of derived states only)
• A phylogeny is determined by a variety of
evidence including fossils, molecular data,
anatomy, and other features.
• Most systematists use cladistic analysis,
developed by a German
entomologist Willi Hennig
to analyze the data
• A phylogenetic diagram or
cladogram is constructed
from a series of dichotomies.
Modern phylogenetic systematics is
based on cladistic analysis
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Analyzing the taxonomic distribution of
homologies enables us to identify the
sequence in which derived characters
evolved during vertebrate phylogeny.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 25.11
• Systematists can use cladograms to place
species in the taxonomic hierarchy.
– For example, using turtles as the outgroup,
we can assign increasing exclusive clades to
finer levels of the hierarchy of taxa.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 25.12
• The application of molecular methods and data for
comparing species and tracing phylogenies has
accelerated revision of taxonomic trees.
– If homology reflects common ancestry, then comparing genes and proteins among organisms should provide insights into their evolutionary relationships.
– The more recently two species have branched from a common ancestor, the more similar their DNA and amino acid sequences should be.
• These data for many species are available via the internet.
Systematists can infer phylogeny
from molecular evidence
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The rates of change in DNA sequences
varies from one part of the genome to
another.
– Some regions (e.g., rRNA) that change
relatively slowly are useful in investigating
relationships between taxa that diverged
hundreds of millions of years ago.
– Other regions (e.g., mtDNA) evolve relatively
rapidly and can be employed to assess the
phylogeny of species that are closely related
or even populations of the same species.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
The rate of nucleotide substitution varies in different gene components and
gene-associated sequences
On the basis of the above substitution rates and the
observation that an average mammalian coding DNA
sequence comprises 400 codons, the coding DNA of
an average human gene would be expected to
undergo about one or two substitutions every million
years. UTR, untranslated region. Redrawn from Li and
Graur (1991) Fundamentals of Molecular Evolution.
Applying a Molecular Clock: The
Origin of HIV
• Phylogenetic analysis shows that HIV
– Is descended from viruses that infect
chimpanzees and other primates
• A comparison of HIV samples from
throughout the epidemic
– Has shown that the virus has evolved in a
remarkably clocklike fashion
• The molecular clock approach has been
used to date the jump of the HIV virus
from related SIV viruses that infect
chimpanzees and other primates to
humans.– From their analysis, they
project that the HIV-1M
strain invaded humans in
the 1930s.
– Investigators calibrated
their molecular clock by
comparing DNA sequences
in a specific HIV gene
from patients sampled
at different times.Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Linnaeus divided all living things into five
major groups, or kingdoms. (1707-1778)
The characteristics that Linnaeus used to divide all organisms into one of the five
groups included:
1) how many cells made up their bodies
2) if they can move on their own
3) if they could make their own food, or had to eat other
creatures to survive
4) if their cells were very simple or had complex parts
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
Figure 25.18
Bacteria Eukarya Archaea4 Symbiosis of
chloroplast
ancestor with
ancestor of green
plants
3 Symbiosis of
mitochondrial
ancestor with
ancestor of
eukaryotes
2 Possible fusion
of bacterium
and archaean,
yielding
ancestor of
eukaryotic cells
1 Last common
ancestor of all
living things
4
3
2
1
1
2
3
4
0B
illio
n y
ears
ago
Origin of life
Carl Woese (1928-)
The End
