Phylogenetics.
 Phylogenetic Trees.
1. Represent presumed
terns of descent.
pat-
2. Analogous to family trees.
3. Resolve taxa, e.g., species,
into clades each of which
includes an ancestral taxon and all its descendants.
4. In the figure at the right, we
can define three non-trivial
clades.1
a. A (A+C+K), P (P+Y+S)
and G (G+A+P).
Family trees and phylogb.
enies. In a. your aunt,
A and P are nested with- parent and grandparent
may still be alive. In b.
in G.
and c., species A, P and
G are extinct.
1
Trivial clades are those consisting of a single taxon, in the present case, C
and K (nested within A) and, Y and S (nested within P).
1
 Terminology.
1. Nodes are branch or
terminal points.
a. Internal nodes are
points of lineage
splitting, i.e., speciation events.
b. Terminal nodes are
contemporaneous
taxa.
2. “Taxa” can be species or higher taxonomic groups. In
the figure, they are labeled A, B, etc.
3. A pair of taxa that have a common ancestor not
shared by any other taxon are called sister taxa,
e.g., A and B.
4. F is called the outgroup.
a. Outgroup inclusion “completes the tree” by identifying character states that are ancestral and
hence a presumptive common ancestor.
2
b. This is called rooting the tree.
c.
Typically, one chooses a taxon that, on other
grounds, is believed to be
 Closely related to taxa of interest, but
 Less closely related to any of them than they
are to each other.
d. Example. If one were
constructing a cladogram for birds, the
outgroup could be
 Dromaeosauridae
(includes Velocraptor and Deinonychus) if fossils are
used.
 Crocodilians if only
living species used.
3
 Questions.
1. (2 pts) The node marked with a single asterisk in the
figure on page 2 represents the most recent common
ancestor of _______; the node marked with two asterisks represents the most recent common ancestor of
_______.
2. (5 pts) Identify the non-trivial clades by circling the appropriate nodes.
3. (2 pts) Among the tip taxa, identify sister taxa in addition to A and B.
4
4. (4 pts) Consider the mammalian cladogram below. Indicated are the following: Class Mammalia, which is divided into Prototheria (monotremes) and Theria (mammals
that bear their young alive), and Theria, which is divided
into Metatheria (marsupials) and Eutheria (placental
mammals). Indicate on the diagram, appropriate outgroup(s) for Eutheria and Theria.
5
 Determining Relatedness.
1. Two approaches.
a. Phenetic – infers relatedness from overall similarity.
b. Cladistic –
 Distinguishes ancestral from derived characters.
 Infers relatedness from the presence of shared
derived characters called synapomorphies.
2. In the table below,
a. Two groups of species can be defined by presence
or absence of character 2.
b. Presence of characters 1, 3, 4 in all four species is
uninformative.
Trait
Species
A
B
C
D
1
+
+
+
+
2
+
+
6
3
+
+
+
+
4
+
+
+
+
 Questions. (# 5-7 relate to the preceding example.)
5. (6 pts) Assuming that characters 1, 3 and 4 are ancestral, and bearing in mind that characters can be lost as
well as gained, draw two phylogenetic trees. Indicate on
each where traits are acquired and lost.
6. (3 pts) Draw an additional tree assuming that characters
1, 3 and 4 are not ancestral.
7. (6 pts) Suppose now that you have an outgroup, O, for
which characters 1-4 are present and distinguished by a
fifth character not found in species A-D. Assume that
trait 5 is derived. Draw two phylogenies corresponding
to your answers to Question 5 above. Which is more
likely? Why?
7
8. (4 pts) Assume that none of the “trait absent” characters
in the table below reflect evolutionary reversals. Draw a
phylogenetic tree. Which characters is (are) ancestral?
Trait
Species
Platypus
Echidna
Kangaroo
Dog
Lemur
Four
Limbs
+
+
Live
Birth
-
+
+
+
8
Milk
Pouch
+
+
-
+
+
+
+
+
+
+
-
 Principle of Parsimony.
1. In Question 7, you encountered the Principle of Parsimony: The most the plausible phylogeny is that
which necessitates
a. The fewest evolutionary reversals.
b. Fewest independent character acquisitions.
2. An evolutionary reversal is the re-acquisition of
an ancestral trait or the loss of a derived trait.
3. Fundamental point:
a. Evolutionary history,
H, uniquely determines character distribution, D. But …
b. D does not uniquely An infinite number of evoludetermine H.
tionary histories are compatic.
Statistics required ble with a given distribution of
characters.
to determine the relative likelihood of alternative phylogenies – especially when characters
are easily reversed, e.g., nucleotide sequences.
9
 Homology.
1. Similarity by virtue of
common descent.
a. The synapomorphies
that define clades
are homologies.
b. Often used in the
context of organs
that
have
been
modified to different
ends in different
species.
2. Serial homology (duplication and modification
of parts in different
ways) was first discussed
by the poet, J. W. von
Goethe, with reference The modified forelimbs of
to flower parts which he men, cats, whales and bats
correctly believed were are homologous.
modified leaves –“foliar theory” of the flower.
10
Spirally-arranged floral organs illustrating serial homology in basal
angiosperms. A: Magnolia watsoniana. B: Nymphaea caerulea;
C: Nymphaea gigatea var. Perry´s Baby; D: Nymphaea odorata.
Note the gradual transition between petals and stamens. Bars indicate scale: A-C: 1.5cm; D: 600μm. From Dornelas and Dorneias
(2005).
11
Homology of head appendages in Onychophora and Arthropoda..
Abbreviations as follows: at, antenna; at1, first antenna; at2,
second antenna; ch, chelicera; jw, jaw; le, leg; md, mandible; mx,
maxilla; pp, pedipalp; sp, slime papilla. From Mayer et al (2013).
12
 Homoplasy – Similarity by
independent acquisition.
1. Convergent evolution:
acquisition of similar
traits by distant lineages.
2. Parallel evolution: acquisition of similar traits
by closely related lineages.
Famous example of convergent
evolution.
3. Distinguishing between
homology and convergence requires appeal to other traits.
Despite their superficial similarity (and the fact that ichthyosaurs gave birth to their young alive!), the two taxa are separable on the basis of other characters such as skull morphology.
13
4. Convergent or parallel? Distinction hinges on
a. What one means by “closely related” vs. “distantly
related".
b. Level you’re looking at:
i.
At the morphological
level, vertebrate and
cephalopod eyes are
convergent.
ii.
At genetic level, parallel – the same regulatory genes determine
their development.
5. Homologous or homoplastic? Depends on one’s
point of view. Pterodactyl,
bat, bird wings are
a.
Wings of flying vertebrates are homologous
Homologous if viewed or homoplastic dependas forelimbs;
ing on one’s viewpoint.
b. Homoplastic if viewed as wings.
14
 Homology vs. Homoplasy in Mammal Dentition.
1. Four mammalian tooth types:
a. incisors,
b. canines,
c. premolars,
d. molars.
2. In living carnivores, P4, and
M1, specialized for slicing.
a. Called carnassials –
b. A synapomorphy defining order Carnivora.
c.
Creodonts (now extinct)
a. Independently evolved Carnassial pair, P4 (blue)
/ M1 (red) in a saber
carnassials, but,
b. Carnassial pair
M1/M2 or M2/M3.
c.
was
Convergent evolution if
ref. is to which cheek
teeth modified; parallel, if just cheek teeth.
15
tooth “tiger.” Note the
extreme reduction (observed in all felids) of
the
remaining
postcanine dentition that
consists primitively of
four
pre-molars
and
three molars.
 When Data Conflict – a Whale of a Tale.
1. Old theory: Whales descended from extinct carnivores.
2. New theory: Whales descended from artiodactyls
– “even-toed” ungulates.2
3. Molecular evidence suggests that whales descended
from artiodactyls.
4. Conflicts with morphological
Foot bones of an Eocene
evidence: whales lack dou- artiodactyl. Its two articuble pulley astragalus (DPA). lar surfaces (shaded red
a.
and blue) allow the
DPA (ankle bone) is the astragalus to articulate
synapomorphy that dis- with the tibia (above) and
tinguishes
artiodactyls the os navicular (below).
In most mammals, there
from other ungulates.
is only one such surface.
b. The term “double pulley” refers to the presence of
two articular surfaces – one with the tibia (leg
bone), the other with the os navicular (another
foot bone).
2
Hoofed mammals.
16
5. Deriving whales from artiodactyls necessitates an evolutionary reversal: DPA gained, then lost.
6. Whales from carnivores more parsimonious.
17
 So which is it?
1. Fossil evidence: primitive
whales had a double pulley
astragalus.
2. In this case, paleontology
confirms molecular biology;
in other cases, e.g., putative
derivation of amphibians
from lungfish, not.
3. Fossils always trump anatomy, genetics, etc., of living
organisms.
Ankle bones of fossil whales
(left, right) and a living
pronghorn (center). Note
the double pulley astragalus
in all three.
Restoration of a paddling proto-whale, Rodhocetus kasrani. Forelimbs
were probably folded against the body during rapid swimming by pelvic paddling and caudal undulation when submerged. On land, Rodhocetus supported itself on hoofed digits II, III, and IV of the hands
and the undersides of the feet. From Gingerich et al. (2001).
18
Astragalus anatomy in a typical mammal (left) and cetaceans
/ artiodactyls (right)
19
6. Types of Taxa.
1. Monophyletic.
a. Includes the most recent
common (MRCA) ancestor
and all its descendants.
b. Monophyletic taxa called
clades.
c.
E.g., Mammals, birds.
2. Paraphyletic.
a. Includes the MRCA, but
not all descendants.
b. E.g., Reptiles.
3. Polyphyletic.
a. Does not include MRCA.
b. E.g., Flying vertebrates – MRCA ancestor walked.
20
 Question.
9. (4 pts) Historically, terrestrial vertebrates were divided into four classes: Amphibia, Reptilia, Mammalia and Aves
(birds). Below is a cladistic analysis that accords with the
fact that birds evolved from small, carnivorous dinosaurs.
The four terrestrial vertebrate clades are shown in blue
and their division into more familiar groups in black at the
right. a. What are Tuataras and squamates. b. Which of
the familiar groups are “reptiles?” c. If we lump these
groups together, resulting class, Reptilia, is paraphyletic.
Explain why. Be specific.
21
 Reading Evolutionary Trees.
1. Unless otherwise indicated, branch length is
arbitrary.
2. Order of tip taxa also
arbitrary.
a. The only information contained
in a cladogram is
the
order
of
branching
that
defines the clades
b. In particular, internal nodes can
be rotated with no
consequence
to These two cladograms look
the clades defined. different, but contain exactly
c.
the same information. You
It follows that evo- can verify this by circling the
clades in each.
lutionary relations
cannot be inferred by reading across the tips.
22
 Question.
10. (6 pts) Three of the evolutionary trees below are equivalent. Which is different?
23