1. Prepared by Dr. Syed Abdullah Gilani
Course: Phylogenetic Systematics I (BIOL471)
Tree Graphs
Prepared by
Dr. Syed Abdullah Gilani

2. Monophyly, Paraphyly, Polyphyly

3. Willi Hennig (1966:148) defined monophyly as groups based on synapomorphy 
paraphyletic groups are based on symplesiomorphy,
polyphyletic groups are based on convergence

4. Cladisitc Character State Definitions
Plesiomorphy: refers to the ancestral character state
Apomorphy: a character state different than the ancestral state, or DERIVED STATE
Synapomorphy: a derived character state (apomorphy) that is SHARED by two or more taxa due to inheritance from a common ancestor: these character states are phylogenetically informative using the parsimony or cladistic criterion
Autapomorphy: a uniquely derived character state

5. Character States
we will return
to this
After Page and Holmes 1998

6. Phylogeny and classification
Monophyletic group
Includes an ancestor
all of its descendants
A B C D
Paraphyletic group
Includes ancestor and
some, but not all of its
descendants
A B C D
Polyphyletic group
Includes two convergent
descendants but not their
common ancestor
A B C D
Taxon A is highly derived
and looks very different
from B, C, and ancestor
How could this happen?
Taxon A and C share
similar traits through
convergent evolution
Only monophyletic groups (clades) are recognized in cladistic classification

7. Phylogeny and classification
Monophyly
Each of the colored lineages
in this echinoderm phylogeny
is a good monophyletic group
Asteroidea
Ophiuroidea
Echinoidea
Holothuroidea
Crinoidea
Each group shares a common
ancestor that is not shared by any
members of another group

8. Paraphyletic groups Paraphyly Foxes
“Foxes” are paraphyletic with respect
to dogs, wolves, jackals, coyotes, etc.
This is a trivial example because
“fox” and “dog” are not formal
taxonomic units, but it does show
that a dog or a wolf is just a derived
fox in the phylogenetic sense
Lindblad-Toh et al. (2005) Nature 438:

9. Paraphyletic groups Monophyly Canids Note that canids are still a good
monophyletic clade within Mammalia
Each of the colored lineages within
canids is also a monophyletic clade
Lindblad-Toh et al. (2005) Nature 438:

10. Paraphyletic groups Paraphyly Lizards “Lizards” (Sauria) are
Fry et al. (2006) Nature 439:
Snakes are just derived,
limbless lizards
Lizards
Paraphyly
“Lizards” (Sauria) are
paraphyletic with respect
to snakes (Serpentes)
Serpentes is a monophyletic
clade within lizards
Squamata (lizards + snakes)
is a monophyletic clade
sister to sphenodontida

11. Paraphyletic groups Paraphyly Reptilia Birds are more closely related
to crocodilians than to other
extant vertebrates
Archosauria = Birds + Crocs
We think of reptiles as turtles,
lizards, snakes, and crocodiles
But Reptilia is a paraphyletic
group unless it includes Aves

12. Phylogenetic Trees 1. Stem-Based Trees 2. Node-Based Trees

13. Trees diagrams used in phylogenetics are tree graphs depicting the genealogical relationships of organisms.
Haeckel (1866) is usually regarded as the first evolutionary biologist to publish tree diagrams meant to show the evolutionary relationships among actual organisms.
In graph theory, a tree is any connected, acyclic graph. In general, tree corresponds fairly closely with the concept of hierarchy.
Cyclic graphs are not trees which may show reticulate relationships or may result in because of character ambiguities

14. Trees consist of two basic things
Vertices (singular vertex) also known as Nodes and
Edges also known as stems, lines, or internodes
A vertex with only one edge connection is termed a leaf.
Internal vertices (“ internodes ”) have two or more edges that connect them with other vertices.
stems, lines, or internodes
Or Node

15. Stem - Based Phylogenetic Trees
Node- Based Phylogenetic Trees

16. Stem-Based Trees
Phylogenetic Stem-based trees depicting the descent of species and monophyletic groups are actually directed acyclic graphs in which
the edges are taxa and
the nodes are speciation events
stem – based trees show some of the macroscopic historical processes of evolution that involve
cladogenesis of species or monophyletic groups of species.
the internal edges are ancestral species and the
terminal edges are either descendant species or descendant monophyletic groups represented by their ancestral species.
Stem - based trees may also be applied to show the descent relationships of individual organism or the genes of organisms.

17. Node-Based Trees Node - based trees are acyclic trees in which
vertices/nodes are taxa and
edges are statements of relationships or other properties shared by the taxa.
The arrows (arcs) do not represent lineages, ancestors, or any other kind of taxon.
Rather, they represent a concept: relationship.
In particular, they state that one vertex is the ancestor of (or parent of) another vertex.
i.e., the tail of the arc is the ancestor of the head of the arc.

18. Hennig (1966) frequently, but not consistently, symbolized
Arrows that point from only one entity to only one entity and in only one direction are characteristic of Hennig ’ s (1966) concept of hierarchical relationships and typical of directed acyclic graphs.
In the phylogenetic system, hierarchies represented as directed acyclic graphs are the markers of phylogenetic relationships.
Hennig (1966) frequently, but not consistently, symbolized
ancestral species as open circles at the nodes and
known, terminal, taxa with solid circles at the tips.
So, vertex B in Fig. 4.3 b is the ancestor of vertices D and E.
Vertex A is the ancestor of B and C and of the entire clade.
This is opposed to the nonhierarchical tokogenetic (and acyclic) relationships represented by graphs where two edges lead to a single entity in sexually reproducing species (Fig. 4.2 ) or two parents of a taxon of hybrid origin.

21. Hennig’s concept of the relationship between stem - based trees and node - based trees
In node-based trees,
The vertices at nodes symbolize the ancestral lineages of stem - based trees and
An edge does not represent a lineage or anything else occurring in nature. Rather, an edge simply
represents a phylogenetic relationship among two vertices
based on synapomorphies rather than similarity relationships.
In stem-based trees,
the nodes of stem – based trees represent lineage splitting.
Vertices represent speciation events.
Thus, the vertices of node - based trees do not represent lineage splitting, a speciation event, or any other process event; they simply represent the
objects of study, either sampled (leaf) or unsampled or unrecognized (vertex).

22. Cyclic Graphs

23. Fig. 4.1 d shows a cyclic graph with
Cyclic graphs can also be drawn in two configurations, somewhat analogous to stem and node - based trees
Fig. 4.1 d shows a cyclic graph with
two speciation events and
one hybridization event that leads to the origin of species N. Most of the edges are lineages, but the graph also shows a
tokogenetic event, with “ mating ” lines leading from the two parental species to the reticulate vertex at the base of the N edge.
The node - based tree is more straightforward (Fig. 4.1 e), stating that
N is equally related to its two ancestors M and O;
it is the child of both.

24. Stem - Based Phylogenetic Trees
Node- Based Phylogenetic Trees

25. Conclusion:
The haplotype map demonstrates that coalescence has not occurred among the haploptypes on this short segment of the mitochondrial gene cytochrome - b .
unobserved haplotypes of one mutation step.

26. Cladograms - Nelson Tree

27. The term cladogram is commonly used to describe phylogenetic tree graphs.
To many, a cladogram is simply a phylogenetic tree with unsampled ancestral species.
To others, it is a common ancestry tree, either stem or node based.
Gary Nelson ( 1979 ) explains it as any kind of acyclic graph where entities were clustered according to some property relationship.

28. According to Nelson cladograms (phylogenetic graphs by synapomorphy)
Nelson tree (Fig 4.3c):
According to Nelson cladograms (phylogenetic graphs by synapomorphy)
Nodes represent taxa, and
the edges are inclusion relationships.
all named taxa are displaced to the leaf position.
The topology of the Nelson tree in Fig. 4.3 c is different from stem-based and node-based trees
because the ancestral species A and B are displaced to a leaf position.

29. Gene Trees

30. Character evidence for descent of species may not always be the case.
Genes may have their own descent patterns that results in a gene tree that is different from a species tree.
For example,
Ruvolo (1997) found that among 14 DNA data sets, 11 support the hypothesis that chimps are the closest living sister species of humans but two supported the chimp – gorilla relationship and one supported the gorilla – human relationship.

31. Another common reason for mismatch between gene trees and species trees is the availability of
only short gene sequences and
incomplete lineage sorting.
Less common in eukaryotes and more common in prokaryotes is horizontal gene transfer.
The use of multiple unlinked genes may be employed to detect the mismatch between gene trees and taxon trees.