1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. Overview: Investigating the Tree of Life
Phylogeny - the evolutionary history of a species or group of related species
Systematics - an analytical approach to understanding the diversity and relationships of organisms (current and extinct)
uses morphological, biochemical, and molecular comparisons to infer evolutionary relationships

3. Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence
To infer phylogenies, systematists gather information about morphologies, development, and biochemistry of living organisms
They also examine fossils to help establish past relationships between living organisms

4. LE 25-4 Leaf fossil, about 40 million years ago
Petrified trees in Arizona, about 190
million years old
Insects preserved whole in amber
Dinosaur bones being
excavated from sandstone
Casts of ammonites, about
375 million years old
Boy standing in a 150-million-year-old
dinosaur track in Colorado
Tusks of a 23,000-year-old mammoth, frozen whole
in Siberian ice

5. Morphological and Molecular Homologies
More similar = more recent common ancestor
Need to distinguish whether a similarity is the result of homology or analogy ( due to convergent evolution)

6. Sorting Homology from Analogy
In constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution

7. Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

8. LE 25-6
Computer programs and mathematical tools are used when analyzing DNA segments from different organisms 1 2
Deletion 1 2
Insertion 1 2 1 2

9. Concept 25.2: Connecting classification with evolution
Taxonomy is the division of biology that sorts organisms into categories based on similarities and differences
Phylogenetic trees - depict evolutionary relationships though branches
Each branch point represents the divergence of two species
“Deeper” branch points represent progressively greater amounts of divergence

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

11. Concept 25.3: Creating Phylogenetic Trees
Cladistics studies resemblances among clades
Clade is a group of species that includes an ancestral species and all its descendants – 3 types: Monophyletic, paraphyletic, polyphyletic
Cladogram depicts patterns of shared characteristics among taxa, shows RELATIVE times of change

12. A valid clade is monophyletic signifying that it consists of the ancestor species and all its descendants

13. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

14. A polyphyletic grouping consists of various species that lack a common ancestor

15. How the clades are determined:
A shared primitive character is a character that is shared beyond the taxon we are trying to define
A shared derived character is an evolutionary novelty unique to a particular clade

16. Outgroups
An outgroup is a (monophyletic) group of organisms that serves as a reference group to determine the evolutionary relationship between three or more monophyletic groups of organisms.
Conclusion is that the outgroup branched from the parent group before the other two groups branched from each other.
Assumes that shared homologies must be primitive characters that predate the divergence of both groups from a common ancestor
helps focus on characters derived at various branch points in the evolution of a clade

17. LE 25-11 TAXA (outgroup) Salamander Lancelet Lamprey Leopard Turtle
Tuna
Turtle
Hair
Amniotic (shelled) egg
CHARACTERS
Four walking legs
Hinged jaws
Vertebral column
(backbone)
Character table
Leopard
Turtle
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram

18. Phylograms
In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage

19. Ultrametric Trees
Branching in an ultrametric tree is the same as in a phylogram, but all branches traceable from the common ancestor to the present are equal length

20. Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set
The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters (novelties)
The principle of maximum likelihood uses the rules regarding DNA change over time to reflect the most likely sequence of evolutionary events

21. LE 25-14 Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip
30%
40%
Mushroom
40%
Tulip
Percentage differences between sequences
25%
15%
15%
20%
15%
10% 5% 5%
Tree 1: More likely
Tree 2: Less likely
Comparison of possible trees

22. Molecular Changes
The most efficient way to study hypotheses is to consider the most parsimonious hypothesis, the one requiring the fewest molecular changes

23. Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
Sometimes the best hypothesis is not the most parsimonious

24. Concept 25.4: Much of 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
Studies include:
Gene Duplications and Gene Families
Orthologous genes
Paralopgous genes

25. Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes

26. Genes found in a single copy in the genome
LE 25-17a
Orthologous Genes
Genes found in a single copy in the genome
They can diverge only after speciation occurs
Ancestral gene
Speciation
Orthologous genes

27. Genome Evolution
Orthologous genes are widespread and extend across many widely varied species
The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions

28. 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, often adding new functions
Ancestral gene
Gene duplication
Paralogous genes

29. Molecular Clocks – have to extend what we know to fill in gaps
Provides a way to measure absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates

30. Neutral Theory
States that a lot of evolutionary change in genes and proteins has no effect on fitness, therefore is not influenced by Darwinian selection
It states that the rate of molecular change in these genes and proteins should be regular like a clock

31. However…..
The molecular clock does not run as smoothly as neutral theory predicts
Irregularities DO result from natural selection in which some DNA changes are favored over others
Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty

32. 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