1. Phylogeny and the Tree of Life
Chapter 19
Phylogeny and the Tree of Life

2. why isn't it a snake? -no fused eyelid -no highly mobile jaw
Fig. 26-1
why isn't it a snake?
-no fused eyelid
-no highly mobile jaw
-no short tail
Figure 26.1 What is this organism?
some lizerds have lost the limbs
this condition is found in burrowers
that live in grasslands
adaptation

3. Overview: Investigating the Tree of Life
Phylogeny is the evolutionary history of a species or group of related species
The discipline of systematics classifies organisms and determines their evolutionary relationships
Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

4. Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms

5. The two-part scientific name of a species is called a binomial
Carolus Linnaeus published a system of taxonomy: 2 key features of his system remain useful today: two-part names for species and hierarchical classification
The two-part scientific name of a species is called a binomial
The first part of the name is the genus
The second part, called the specific epithet, is unique for each species within the genus
The first letter of the genus is capitalized, and the entire species name is italicized or underlined
Both parts together name the species

6. Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories
The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
A taxonomic unit at any level of hierarchy is called a taxon

7. Figure 26.3 Hierarchical classification
Species:
Panthera
pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Figure 26.3 Hierarchical classification
Phylum: Chordata
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea

8. Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees
Linnaean classification and phylogeny can differ from each other
Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents

9. Canis lupus Order Family Genus Species Felidae Panthera Pantherapardus
Fig. 26-4
Order
Family
Genus
Species
Felidae
Panthera
Pantherapardus
Taxidea
Taxidea
taxus
Carnivora
Mustelidae
Lutra lutra
Lutra
Figure 26.4 The connection between classification and phylogeny
Canis
latrans
Canidae
Canis
Canis
lupus

10. Polytomy: more than 2 groups emerge
Fig. 26-5
Branch point
(node)
Taxon A
Taxon B
Sister
taxa
Taxon C
ANCESTRAL
LINEAGE
Taxon D
Taxon E
Figure 26.5 How to read a phylogenetic tree
Taxon F
Common ancestor of
taxa A–F
Polytomy: more than 2 groups emerge

11. What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees do show patterns of descent
Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage
It shouldn’t be assumed that a taxon evolved from the taxon next to it
Applications: whale meat sold illegaly in Japan

12. Sorting Homology from Analogy
Homology is similarity due to shared ancestry like between a wolf and a coyote
Analogy is similarity due to convergent evolution, similar conditions/adaptations
Australian "mole"
Look alike, but evolved
independantly from each
other
North American mole

13. Fig. 26-8 1
Systematics use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms
Deletion 2
Types of mutations that
notmally occur
Insertion 3
Figure 26.8 Aligning segments of DNA
Orange sections no longer align 4
only with addition of gaps
will they align

14. It is also important to distinguish homology from analogy in molecular similarities
Mathematical tools help to identify molecular homoplasies, or coincidences
Molecular systematics uses DNA and other molecular data to determine evolutionary relationships

15. Shared characters are used to construct phylogenetic trees
Cladistics groups organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants
A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
A polyphyletic grouping consists of various species that lack a common ancestor

16. Includes all descendants
Fig
Includes all descendants A A A B
Group I B B C C C D D D E E
Group II E
Group III F F F G G G
Figure Monophyletic, paraphyletic, and polyphyletic groups
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group

17. Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics
A shared ancestral character is a character that originated in an ancestor of the taxon
A shared derived character is an evolutionary novelty unique to a particular clade
A character can be both ancestral and derived, depending on the context, it is useful to know in which clade a shared derived character first appeared

18. Fig
TAXA
Lancelet
(outgroup)
(outgroup)
Lancelet
Salamander
Lamprey
Leopard
Lamprey
Tuna
Turtle
Vertebral column
(backbone)
Tuna 1 1 1 1 1
Vertebral
column
Hinged jaws 1 1 1 1
Salamander
Hinged jaws
CHARACTERS
Four walking legs 1 1 1
Turtle
Four walking legs
Amniotic (shelled) egg 1 1
Amniotic egg
Leopard
Hair 1
Hair
(a) Character table
(b) Phylogenetic tree
An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics
Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor
Figure Constructing a phylogenetic tree

19. Phylogenetic Trees with Proportional Branch Lengths
In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage
In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

20. Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set
Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely
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

21. (a) Percentage differences between sequences
Fig
Human
Mushroom
Tulip
Human
30%
40%
Mushroom
40%
Tulip
(a) Percentage differences between sequences
15% 5% 5%
Figure Trees with different likelihoods
15%
15%
10%
20%
25%
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees

22. Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendants
This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles

23. Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Fig
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Saurischian
dinosaurs
lFigure A phylogenetic tree of birds and their close relatives
Birds

24. An organism’s evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history
DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
mtDNA evolves rapidly and can be used to explore recent evolutionary events

25. Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
Like homologous genes, duplicated genes can be traced to a common ancestor
Orthologous genes are found in a single copy in the genome and are homologous between species
They can diverge only after speciation occurs
Paralogous genes result from gene duplication, so are found in more than one copy in the genome
They can diverge within the clade that carries them and often evolve new functions

26. Genome Evolution
Orthologous genes are widespread and extend across many widely varied species
Gene number and the complexity of an organism are not strongly linked
Genes in complex organisms appear to be very versatile and each gene can perform many functions

27. From Two Kingdoms to Three Domains
More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes

28. EUKARYA BACTERIA ARCHAEA Fig. 26-21 Land plants Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
(Mitochondrion)
Figure The three domains of life
Spirochetes
Halophiles
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
BACTERIA
Methanobacterium
Cyanobacteria
ARCHAEA
(Plastids, including
chloroplasts)

29. Eukarya Bacteria Archaea The End Fig. 26-23
Figure A ring of life
The End

30. Things to keep straight….
Evidence of evolution (method of classifying, organizing, tracking change)
Mechanisms of evolution, cause of change (hardy Weinberg equilibrium when these do NOT happen)
Condition of natural selection
Types of natural selection
Preconditions for change (natural selection)
Mechanisms of speciation
Pre and post zygotic isolation
Methods of speciation (allopatric and sympatric)

31. Evidence of Evolution
The theory of evolution is supported by evidence that can found in
1.  The Fossil Record: traces the history of life
2.  Biogeography: study of range and distribution of plants and animals  
3.  Anatomy: homologous, vestigial structures
4.  Embryology: all vertebrates have the same basic pattern of development 
5.  Biochemistry: DNA, amino acids are similar I related organisms, all life of same few elements

32. 5 Agents of evolutionary change
Mutation
Gene Flow
Non-random mating
Genetic Drift
Natural Selection

34. Hardy Weinberg (non-evolving) population
Evolution = change in allele frequencies in a population
hypothetical: what conditions would cause allele frequencies to not change?
Hardy Weinberg (non-evolving) population
REMOVE all agents of evolutionary change
no genetic drift -very large population size
no migration (no gene flow in or out)
no mutation (no genetic change)
random mating (no sexual selection)
no natural selection (everyone is equally fit)
Real populations rarely meet all five conditions.

35. These are three preconditions for natural selection.
1. The members of a population have random but heritable variations.
2. In a population, many more individuals are produced each generation than the environment can support.
3. Some individuals have adaptive characteristics that enable them to survive and reproduce better.

36. REPRODUCTIVE ISOLATING MECHANISMS
PREZYGOTIC Isolation: prevent a zygote from forming
Habitat Isolation
Temporal Isolation
Behavioral Isolation
Mechanical Isolation
Gamete isolation
POSTZYGOTIC Isolation: prevent reproduction after zygote formation
Zygote mortality
Hybrid sterility
F2 fitness (reduced fitness level)

37. MODES OF SPECIATION
2. Sympatric Speciation
Sympatric speciation would occur when members of a single population develop a difference without geographic isolation
Ex. Apple Maggot flies choosing a particular type of apple (Sympatric Speciation)
Ex. Mate preference
Allopatric Speciation: Populations separated geographically
Variations accumulate
Reproductive isolation
separates the population