Higher Classification groupings (ranks) above the species level
Biological Classification is the ordered grouping of organisms
according to their similarity and consistency with
Species and Modes of Speciation
What are species and their variants at the species boundary?
How does speciation take place?
Schuh and Brower 2009
What is a species?
[ Species - Latin for "kind" (type) ]
Species represents the ba
TA: Austin Baker
email: firstname.lastname@example.org or email@example.com
Office hours: ENT135 Tuesday 1:00-2:00 or by appointment
When emailing me please title email with course number and name.
ex: ENT112 Jane Doe help with assignment
SYSTEMATICS (BIOL 112, BPSC 112, ENTM 112) Winter 2016
Tues. and Thur. at 11:10 AM -12:30 PM in Sproul Hall 2340
Fri. at 12:10 pm-1:00 pm in OLMH 1133 (section 021)
Fri. at 1:10 pm-2:00 pm in Spieth 1222 (section 022)
Taxonomic characters (morphological or molecular) are the
essence of systematics, both for recognition and identification
(taxonomy) and for discovery of relationships (phylogenetics).
any morphological or genetic evidence that relates to the
Finding the Shortest Tree!
Graphical Representation of Phylogeny!
Finding the Shortest
Tree with Maximum
Parsimony and the
FigTree 1.3.1 Software!
(Arctic_fox, Kit_fox),(Ruppell's_Fox, Red
1. An unrooted tree is shown below
a. Draw a rooted tree that is rooted on branch i.
b. How many rooted, bifurcating trees are there for the unrooted tree shown above?
c. In rec
W3: Speciation, Species Concepts,
Name these modes of geographic
Sympatry - distribution pattern of two or more
broadly overlapping geographic areas.
Species occurs in one area
Calculating the Likelihood for a Tree
ML is an optimality criterion method
Likelihood is the probability of observing the data given a hypothesis,
i.e., Prob (D H); this is not the same as the probability of a hypothesis
given the dat
Assessing the Reliability of Phylogenetic Trees!
Statements about relationships reside in the internal branches!
Measuring Reliability in Statistics!
Suppose that we are interested in the average and
error for a variable of interest
Carry out meas
W7: Tree Building continued
Metric: 4 conditions
Distances are non-negative
What does it mean if distances
The data fits to one or more
Dating Evolutionary Events: I. Fossils and
Principles of Geology
days, weeks, months, years, and even decades
How do we measure time?
We all have personal experience pertaining to the passing of
seconds, minutes, hours!
It is more difficult to comprehend
Due: January 21, 2015
Viewing the tree
1) Trees and associated terminology (1 point)
A is most closely related to B. C is most closely related to D. The group A+B is most closely related
to the group C
Bonus Assignment (15 points)
1. Your name
2. Your organism (provide binomen)
3. Draw rooted phylogeny for your organism and four other species. Label each tip
(leaf) with binomen.
4. Label internal nodes 1 through 4 on your tree.
5. Annotate your phylogen
Geologic Dating II: Absolute Dating and
the Age of the Earth
How Old is the Earth?
Geologists in the 17th, 18th, and 19th centuries developed a
geologic time scale based on relative dating methods.
What about absolute ages? What is the absolute age of the
W2: Nomenclature and Trees
Group of organisms that
include all of the descendents
of a common ancestor (usually
refers to supraspefic taxa
(more that one species o
W6: Tree Building Continued
Used in parsimony reconstruction
Only for unordered characters
Shortcuts when using the Fitch algorithm:
1. Invariant sites (such as AAAAA) can be dropped from
the analysis without affecting tr
Due: January 28, 2015
1) What types of dendrograms (tree diagrams) are used by each of the following philosophical schools when
constructing a classification system? (1 point)
W8: Likelihood methods
Pairwise Distance Methods
E is the error of fitting distances to a tree
E=0 if distances are additive (perfect fit)
is either 1 (absolute values) or 2 (least squares)
In simple terms: the error equals the sum of the
Posterior Probability of Fair Versus Biased Die with Bayes Theorem
Start with 1000 dice [400 fair: Pr(1, 2, 3, 4, 5, or 6) = 1/6 for each outcome; 600
biased: Pr(6) = 1/2, Pr(1, 2, 3, 4, or 5) = 1/10 for each outcome
Pick one die at random and roll twice,
1. Suppose that you randomly select one die from a bag of dice that contains 4000 fair
dice and 1000 unfair dice, each of which has a 7/12 chance of rolling a 6 and a 1/12
chance of rolling each of the other numbers (1, 2, 3, 4, 5). Now suppose that you r
1. Which statement is true?
2. Which statement is true?
The law of superposition is one of Stenos laws
The law of original continuity states that sedimentary strata are
deposited in horizontal layers
iii. Correlation uses fossils or
1. Relative rate parameters for different models of sequence
evolution are shown below. Which model is not fully
2. Relative rate parameters for different models of sequence
evolution are shown below. Which model has two rates for
1. The true tree for four hypothetical taxa is shown below.
2. The tree below has branches a-l. Which of the following is
not a condition of ultrametricity for this tree?
a b d
a. Construct a matrix of pathlength distances for taxa A-D.
W8: Fossils and Geology
Geology concepts to review before final
James Hutton: rock cycles
Fossils and correlation
Rates of sediment deposition