Higher Classification groupings (ranks) above the species level
species
supraspecific taxon
natural taxon
biological classification
Biological Classification is the ordered grouping of organisms
according to their similarity and consistency with

1/19/16
Species and Modes of Speciation
What are species and their variants at the species boundary?
How does speciation take place?
Schuh and Brower 2009
Species Concepts
What is a species?
[ Species - Latin for "kind" (type) ]
Species represents the ba

Systematics 112
TA: Austin Baker
email: bakerau73@gmail.com or abake005@ucr.edu
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
EAST
Entomol

SYSTEMATICS (BIOL 112, BPSC 112, ENTM 112) Winter 2016
Class Meetings:
Lectures
Tues. and Thur. at 11:10 AM -12:30 PM in Sproul Hall 2340
Discussion
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)
I

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
nature

Finding the Shortest Tree!
Graphical Representation of Phylogeny!
Tree Basics!
Finding the Shortest
Tree with Maximum
Parsimony and the
Fitch Algorithm!
Search Strategies!
Newick Format!
FigTree 1.3.1 Software!
(Arctic_fox, Kit_fox),(Ruppell's_Fox, Red

1. An unrooted tree is shown below
hyrax
tapir
cow
a
j
d
c
l
e
f
b
dolphin
sloth
g
rabbit
i
m
k
armadillo
h
pika
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

Systematics 112
W3: Speciation, Species Concepts,
Homology
Name these modes of geographic
speciation:
1.
Sympatry - distribution pattern of two or more
broadly overlapping geographic areas.
Sympatric speciation
Species occurs in one area
Stable polymorp

Maximum Likelihood
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!
4
6
5
Measuring Reliability in Statistics!
Suppose that we are interested in the average and
error for a variable of interest
Carry out meas

Systematics 112
W7: Tree Building continued
Metric Distances
Metric: 4 conditions
d(A,A)=0
d(A,B)=d(B,A)
Distances are non-negative
d(A,B)d(A,C)+d(B,C)
What does it mean if distances
are metric?
The data fits to one or more
trees.
A
A
A
B
C
B
C
Metric

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

Discussion 2
Systematics 112
Name:
Due: January 21, 2015
Section No./Time:_
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

Systematics 112
W2: Nomenclature and Trees
Tree Concepts
Monophyletic
Paraphyletic
Polyphyletic
Apomorphy
Pleisomorphy
Group of organisms that
include all of the descendents
of a common ancestor (usually
refers to supraspefic taxa
(more that one species o

Systematics 112
W6: Tree Building Continued
Fitch Algorithm
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

Discussion 3
Systematics 112
Name:
Due: January 28, 2015
Section No./Time:_
1) What types of dendrograms (tree diagrams) are used by each of the following philosophical schools when
constructing a classification system? (1 point)
Cladistics: _
Phenetics:

Systematics 112
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?
i.
ii.
i.
ii.
iii.
iv.
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
time reversible?
2. Relative rate parameters for different models of sequence
evolution are shown below. Which model has two rates for
transit

1. The true tree for four hypothetical taxa is shown below.
C
2. The tree below has branches a-l. Which of the following is
not a condition of ultrametricity for this tree?
a b d
f
c
e
A
4
B
2
10
a. Construct a matrix of pathlength distances for taxa A-D.

Systematics 112
W8: Fossils and Geology
Geology concepts to review before final
Relative dating
Stenos laws
James Hutton: rock cycles
Cross-cutting relationships
Inclusions
Fossils and correlation
Absolute dating
Rates of sediment deposition
Lord Kelv