1. Molecular Systematics
Systematics - the science of identifying, naming, and classifying living organisms into groups
A natural activity of the human brain
Aristotle - Scala Naturae, or “Chain of Life,” which consisted of God, man, mammals, oviparous with perfect eggs (e.g., birds), oviparous with nonperfect eggs (e.g., fish), insects, plants, and non-living matter.
Dominated for ~2000 yrs but made no real attempt at an orderly, consistent classification
Lineaus and others – downward classification
Dividing larger groups into smaller ones via dichotomies
Actually a method of ‘identification’ not ‘classification’
Highly dependent on the order in which the dichotomies were investigated
Upward classification –
Grouping organisms with similar characteristics
Still, all of this was influenced heavily by the idea of archetypes, distinct types or kinds of organisms that are unchanging
This was an attempt to find a ‘natural’ system. But, what is the basis for this ‘natural’ system?

2. Molecular Systematics
Enter The Origin of Species
Provided the rationale for a coherent system
Common descent as the basis for classification
Phylogenetic Systematics
Classifying organisms based on evolutionary relationships
“The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of Nature” - Charles Darwin
Therefore, 2 goals for phylogenetics
(1) reconstruct life's geneology
(2) use geneology as basis for classification.

3. Molecular Systematics
What can we do with molecular phylogenies?
Classify organisms according to evolutionary history
bring order to the chaos of living things
There is only one "fundamental law" in biology: life evolves. That's it. The messiness comes because life is an emergent property of chemistry and physics. Just like a grain of sand acts differently than a pile of sand, so too do physics and chemistry act differently than biology - the amount of interacting forces that happen in biology are orders of magnitudes more than in physics and chemistry

4. Molecular Systematics
What can we do with molecular phylogenies?
Determine evolutionary patterns and processes in organisms
evolutionary rates among organisms (speciation, extinction, morphological change)
identification of key adaptations
correlations between traits or characters
FOXP2 in bats and other mammals

5. Molecular Systematics
What can we do with molecular phylogenies?
Determine evolutionary patterns and processes in genomes

6. Molecular Systematics
What can we do with molecular phylogenies?
Inform conservation efforts 8 9 x
Tabasco
Peten

7. Molecular Systematics
What can we do with molecular phylogenies?
Inform medical and forensic genetics

8. Molecular Systematics
What can we do with molecular phylogenies?
Investigate population histories and demography

9. Molecular Systematics
Tree – a mathematical model of a proposed evolutionary history of organisms or some aspect of organisms
The ultimate goal of phylogenetics is to recover an accurate tree of life

10. Molecular Systematics
(OTU)

11. Molecular Systematics
Levels of resolution

12. Molecular Systematics
Polytomies

13. Molecular Systematics
Cladograms, phylograms, phenograms, etc…
Cladogram – illustrates evolutionary relationships of organisms via relative common ancestry
branch lengths are meaningless and arbitrary
Phylogram – illustrates relationships of organisms with branch lengths proportional to time or similarity
a subset of cladograms
Phenogram – illustrates relative amounts of similarity or difference (NOTE: intent is not necessarily to represent common ancestry)
more on this distinction later
Cladogram
Phylogram

14. Molecular Systematics
Rooted vs. unrooted trees
Rooted trees have a node from which all other nodes have descended
It is directional
Allow for the inference of ancestor-descendant relationships
Unrooted trees lack a root, direction and indications of ancestral relationships

15. Molecular Systematics
Rooted vs. unrooted trees
Rooted trees have a node from which all other nodes have descended A B C
Root D
Rooted tree C D
Root A B

16. Molecular Systematics
Rooted vs. unrooted trees
Two major ways to root a tree
By outgroup:
Use taxa (the “outgroup”) that are known to fall outside of the group of interest (the “ingroup”). Requires prior knowledge about the relationships among the taxa.
outgroup
By midpoint:
Roots the tree at the midway point between the two most distant taxa in the tree, as determined by branch lengths. Assumes that the taxa are evolving in a clock-like manner. A
d (A,D) = = 18
Midpoint = 18 / 2 = 9 10 C 3 2 B 2 5 D

17. Molecular Systematics
Rooted vs. unrooted trees
Most phylogenetic methods infer unrooted trees
Thus, choosing a root is an extremely important decision
5 potential roots to this one unrooted tree
each one has a different interpretation

18. Molecular Systematics
Rooted vs. unrooted trees
Numbers of rooted and unrooted trees
Possible Number of
Number
of OTU’s
Rooted trees
Unrooted trees 2 1 1 3 3 1 4 15 3 5
105 15 6
945
105 7
10395
945 8
135135
10395
Log # trees 9
135135 10
OTU’s

19. Molecular Systematics
More terminology
Tree -phyly
Monophyletic groups – a group on a tree that includes one ancestor and the all terminal taxa that arose from it.
Paraphyletic groups – A group of terminal taxa and ancestor(s) that excludes one or more members
Polyphyletic – A completely unnatural grouping of terminal taxa

20. Molecular Systematics
More terminology
Tree -phyly
Monophyletic – Archosauria, Lepidosauria
Paraphyletic – “reptiles”, “dinosaurs”
Polyphyletic – “ homeotherms”

21. Molecular Systematics
Gene trees vs. species trees
We usually assume that trees inferred from molecular data (sequences) reflect the history of the organisms. What happens when we assume? A B C A B C A B C A B C A B C + A B C

22. Molecular Systematics
Incomplete lineage sorting
We usually assume that trees inferred from molecular data (sequences) reflect the history of the organisms. What happens when we assume?
Salem et al. 2003, PNAS

23. Molecular Systematics
More terminology
Characters and character states
Organisms comprise sets of features
A particular feature that is heritable is a “character”
a nucleotide position, the shape of a bone, presence or absence of a bone
When taxa differ with respect to a feature (e.g. the presence or absence or difference of a base at a particular locus) the different conditions are called “character states”
Character states can be discrete or continuous, reversible or nonreversible, ordered or non-ordered, ancestral or derived (polarity)
Character
Possible states
Nucleotide position
A, T, C, G, gap
TE insertion
Presence, absence
Amino acid
Polar, nonpolar, acid, base, etc
Mandibular symphysis
Unfused, partially fused, ossified

24. Molecular Systematics
Homology assignment
All phylogenetic methods (molecular and morphological) assume that you are comparing homologous loci/structures
Homologous – sharing a common ancestor
Two loci are either homologous or not, there is no such thing as 95% homologous – 95% similar, yes; 95% homologous, no
Homology comes in two flavors
Paralogy – loci originating from a duplication event recent enough to reveal their common ancestry
Orthology – loci that share ancestry via lineage divergence
One must be able to discern the two a priori

25. Molecular Systematics
More terminology
Homoplasy
Similarity that is not homologous (not due to common ancestry)
Can be the result of convergence, parallelism, reversals of state
Can provide misleading evidence of phylogenetic affinity (if interpreted incorrectly as homology)
Common in DNA sequence data

26. Molecular Systematics
Challenges to inferring trees with molecular data
Paralogy

27. Molecular Systematics
Challenges to inferring trees with molecular data
Gene conversion

28. Molecular Systematics
Challenges to inferring trees with molecular data
Varying rates of mutation

29. Molecular Systematics
Challenges to inferring trees with molecular data
Horizontal gene transfer

30. Identity by Descent/State
Identity By State
time
Species A
Species A
ATGGTCC
Species B
ATGATCC
mutation
insertion
Species A
Species A
ATGGTCC
Species B
Species A’
Species B