1. LECTURE 1: Phylogeny and Systematics

2. What is Phylogeny? the evolutionary history of a species
Evolutionary biology is about both process and history
A major goal of evolutionary biology is to reconstruct the history of life on earth
To reconstruct phylogeny, scientists use SYSTEMATICS
The study of biodiversity in an evolutionary context

3. How are Phylogenies Constructed?
The Fossil Record
Morphological similarities
Homologous Structures (remember those?)
Molecular similarities
DNA
Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences

4. How can Scientists determine whether structure are Homologous or Analagous?
HOMOLOGY is similarity due to SHARED ANCESTRY
ANALOGY is similarity due to CONVERGENT EVOLUTION
CONVERGENT EVOLUTION: two organisms develop similarities as they adapted to similar environmental challenges – not because they evolved from a common ancestor
EXAMPLE: both birds and bats have adaptations that allow them to fly
However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb than to a bird’s wing
Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors
Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing

5. HOW DO THESE ORGANISMS DISPLAY EXAMPLES OF CONVERGENT EVOLUTION?

6. How would you compare the fins in these 2 organisms?

7. What are Homoplasies?
Analogous structures or molecular sequences that evolved independently
Example: the four-chambered heart of birds & mammals is analogous

8. What are Molecular Homologies?
Systematists compare long stretches of DNA and even entire genomes to assess relationships between species
If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous
In closely related species, sequences may differ at only one or a few base sites
Distantly related species may have many differences or sequences of different length

9. How is Phylogeny linked with Classification?
Systematists explore phylogeny by examining various characteristics in living and fossil organisms
They construct branching diagrams called PHYLOGENETIC TREES to depict their hypotheses about evolutionary relationships
The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups

10. LE 25-9 Panthera pardus (leopard) Mephitis mephitis (striped skunk)
Lutra lutra
(European
otter)
Canis
familiaris
(domestic dog)
Canis
lupus
(wolf)
Species
Genus
Panthera
Mephitis
Lutra
Canis
Family
Felidae
Mustelidae
Canidae
Order
Carnivora 10

11. Each branch point represents the divergence of two species
LE 25-UN497
Leopard
Domestic cat
Each branch point represents the divergence of two species
Common ancestor
Wolf
Leopard
Domestic cat
“Deeper” branch points represent progressively greater amounts of divergence
Common ancestor 11

12. LE 25-13 Drosophila Lancelet Amphibian Mouse Fish Bird Human Rat
Cenozoic
65.5
Mesozoic
251
Paleozoic
542
Neoproterozoic
Millions of
years ago 12

13. What is Cladistics?
classifying organisms based on RESEMBLANCES among clades
Determining which similarities between species are relevant to grouping the species in a clade 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
CLADISTICS enables us to identify the sequence of the evolution of derived characteristics

14. What is a Cladogram?
depicts patterns of shared derived characteristics among taxa
Synapomorphies
the chronological sequence of branching during the evolutionary history of a set of organisms
This chronology DOES NOT indicate the TIME of origin of the species that we are comparing, only the groups to which they belong
A cladogram is NOT a phylogenetic tree
To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared

15. What is a Clade? THREE TYPES OF CLADES: MONOPHYLETIC PARAPHYLETIC
a group of species that includes an ancestral species and all its descendants
THREE TYPES OF CLADES:
MONOPHYLETIC
single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram
PARAPHYLETIC
members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion
POLYPHYLETIC
lacks the common ancestor that would unite the species; does not meet cladistic criterion

16. Grouping 1 Monophyletic
LE 25-10a
Grouping 1
A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
Monophyletic 16

17. Grouping 2 Paraphyletic
LE 25-10b
Grouping 2
A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
Paraphyletic 17

18. Grouping 3 Polyphyletic
LE 25-10c
Grouping 3
A polyphyletic grouping consists of various species that lack a common ancestor
Polyphyletic 18

20. How are Cladograms Constructed?
In cladistic analysis, clades are defined by their evolutionary features (novelties)
A CHARACTER
any feature that a particular taxon possesses
A SHARED DERIVED CHARACTER (SYNAPOMORPHIES)
an evolutionary novelty unique to a particular clade
A SHARED PRIMITIVE CHARACTER
found not only in the clade being analyzed, but also in older clades
Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters

21. SHARED DERIVED CHARACTERISTICS
Need to differentiate between shared primitive characters and shared derived characters
ANALOGIES
All similar characters
PRIMITIVE (ANCESTRAL)
HOMOLOGIES
DERIVED (UNIQUE TO A CLADE) 21

22. SHARED PRIMITIVE & SHARED DERIVED CHARACTERISTICS
EXAMPLE: the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.
It is a shared derived character that uniquely identifies mammals
However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.
Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates
SHARED DERIVED CHARACTERS ARE USEFUL IN ESTABLISHING A PHYLOGENY, BUT SHARED PRIMITIVE CHARACTERS ARE NOT 22

23. How are Cladograms built Using Outgroups?
OUTGROUP COMPARISON
used to differentiate shared primitive characters from shared derived ones
OUTGROUP
a species or group of species that is closely related to the INGROUP (the various species being studied)
ASSUMPTION: homologies shared by the outgroup and ingroup must be a primitive character that predate the divergence of both groups from a common ancestor

24. PERFORMING OUTGROUP COMPARISON
What is the shared primitive characteristic?
DOES NOT MEAN THAT TURTLES EVOLVED MORE RECENTLY THAN SALAMANDER 24

25. 25

26. BUILDING A CLADOGRAM 26

27. THE CHARACTER TABLE: 27

28. THE RESULT: 28

29. 29

30. AND SOMETIMES THE SIMPLEST EXPLANATION IS NOT THE BEST…
Parsimony does not always work, nature does not always take the simplest course 30

31. Much of an organism’s evolutionary history is documented in its genome31

32. What are Gene Duplications and Gene Families?
increases the number of genes in the genome, providing more opportunities for evolutionary changes
GENE FAMILIES
groups of related genes within an organism’s genome
Like homologous genes in different species, duplicated genes have a common genetic ancestor
There are two types of homologous genes: ORTHOLOGOUS genes and PARALOGOUS genes 32

33. TWO REMARKABLE FACTS ABOUT GENE FAMILIES
All living things share many biochemical and development pathways
The number of genes seems not to have increased at the same rate as phenotypic complexity
Humans have only five times as many genes as yeast, a simple unicellular eukaryote, although we have a large, complex brain and a body that contains more than 200 different types of tissues
Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues 33

34. What are Orthologous Genes?
genes found in a single copy in the genome
They can diverge only after speciation occurs
i.e. The ß hemoglobin genes in humans and mice are orthologous
Orthologous genes are widespread and can extend over enormous evolutionary distances
Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast

35. What are Paralogous Genes?
result from gene duplication, so they are found in more than one copy in the genome
They can diverge within the clade that carries them, often adding new functions
i.e. Olfactory receptor genes have undergone many gene duplications in vertebrates
Humans and mice each have huge families of more than 1,000 of these paralogous genes

36. Ancestral gene Speciation Orthologous genes
LE 25-17a
Ancestral gene
Speciation
Orthologous genes 36

37. Ancestral gene Gene duplication Paralogous genes
LE 25-17b
Ancestral gene
Gene duplication
Paralogous genes 37

38. What are Molecular Clocks?
The MOLECULAR CLOCK is a yardstick for measuring absolute time of evolutionary change
They are based on the observation that some regions of the genome evolve at constant rates
For these regions, the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the two species last shared a common ancestor
In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated
Proteins and mitochondrial genomes have constant rate of change over time 38

39. APPLYING A MOLECULAR CLOCK: THE ORIGIN OF HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way 39