Augustin Augier’s detailed tree of
life for plants in 1801
Jean-Baptiste Lamarck
sketchy diagram for animals
in 1809.
Vestiges of the Natural History of
Creation, anonymously published by
Robert Chambers in 1844, had an
even sketchier one, where fish,
reptiles, and birds are represented
by branches from a path leading to
mammals.
in 1858, just a year before the
Origin of Species, Heinrich Georg
Bronn published a hypothetical
phylogenetic tree labeled with
letters.
“Paleontological chart” from Edward Hitchcock’s Elementary Geology, first published in 1840.
Reading a Phylogenetic Tree
Outgroup
Node
•
•
A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set
of organisms or groups of organisms, called taxa (singular: taxon).
Because no one was present to observe the splitting of taxa from a common ancestor,
many evolutionary biologists consider a phylogenetic tree to be a hypothesis of those
relationships
Understanding a phylogeny is a lot like
reading a family tree. The root of the
tree represents the ancestral lineage,
and the tips of the branches represent
the descendants of that ancestor. As
you move from the root to the tips, you
are moving forward in time.
When a lineage splits (speciation), it is
represented as branching on a
phylogeny. When a speciation event
occurs, a single ancestral lineage gives
rise to two or more daughter lineages.
Phylogenies trace patterns of shared
ancestry between lineages. Each lineage
has a part of its history that is unique to
it alone and parts that are shared with
other lineages.
Similarly, each lineage has ancestors that are unique
to that lineage and ancestors that are shared with
other lineages — common ancestors.
Character state – One of the variant conditions of a character (e.g. melanic or typical
moth color. Or presence and absence of a trait. ).
Derived character state - same as apomorphy; a derived character / trait is inferred to
be a modified version of a more primitive condition of that character and
therefore inferred to have arisen later in the evolution of the clade.
Clade - a group of organisms that share a common ancestor; lineage; a monophyletic
group.
Monophyletic group - terms applied to a group of organisms that includes an
ancestral species and all of its descendants; e.g. Aves, Mammalia. This group is a
complete branch of the tree of life, the phylogeny of life. Such a branch is called a
clade.
A clade is a grouping that includes a common
ancestor and all the descendants (living and extinct)
of that ancestor. Using a phylogeny, it is easy to tell if
a group of lineages forms a clade. Imagine clipping a
single branch off the phylogeny — all of the
organisms on that pruned branch make up a clade.
Taxonomically, an organism accumulates all the names
of all the clades to which it belongs.
A member of the most recent clade is also a member
of all the ancestral (preceding clades).
Evo. Edu. Outreach (2009) 2:303-309
Phylogenetic thinking – birds are dinosaurs.
• Birds evolved from dinosaurs.
• Cannot clip a branch that includes
• a) dinosaurs and b) more dinosaurs without
including c) birds.
• Q: Using tree thinking, are all reptiles coldblooded? Is this a good definition of reptiles?
Evo. Edu. Outreach (2009) 2:303-309
Using tree thinking and the concept of clades, we
can see that Ostriches belong to every clade
preceding them (their ancestors).
Conclusion – Birds are descendants of dinosaurs.
Evo. Edu. Outreach (2009) 2:303-309
Depending on how many branches of the tree you are
including however, the descendants at the tips might be
different populations of a species, different species, or
different clades, each composed of many species.
Aristotle's vision of a Great Chain of
Being, above. We now know that
this idea is incorrect.
Reading Phylogenetic Trees
Although mosses branch off early on
the tree of life and share many
features with the ancestor of all land
plants, living moss species are not
ancestral to other land plants. Nor
are they more primitive. Mosses are
the cousins of other land plants.
University of California Museum of Paleontology's
Understanding Evolution (http://evolution.berkeley.edu).
So when reading a phylogeny, it is important to keep three things in mind:
1. Evolution produces a pattern of
relationships A B C D among lineages
that is tree-like, not ladder-like.
2. Just because we tend to read
phylogenies from left to right,
there is no correlation with level
of "advancement."
3. For any speciation event on a
phylogeny, the choice of which
lineage goes to the right and
which goes to the left is arbitrary.
The phylogenies at left are
equivalent
University of California Museum of Paleontology's
Understanding Evolution (http://evolution.berkeley.edu).
Paraphyletic group – a group that is monophyletic, except some
descendant(s) have been removed.
Synapomorphies – A derived character state that is shared by two or
more taxa and is postulated to have evolved in (been modified by)
their common ancestor.
Synapomorphies are integral to studying phylogenetic trees because:
a) they identify evolutionary branch points
b) they are nested. As you proceed from the base of the tree to the tips, each branching event adds one
or more shared, derived traits.
A shared derived character is one that two lineages
have in common, and a derived character is one that
evolved in the lineage leading up to a clade and that
sets members of that clade apart from other
individuals.
Four limbs is a shared derived character inherited
from a common ancestor that helps set apart this
particular clade of vertebrates.
However, the presence of four limbs is not useful for determining
relationships within the clade in green above, since all lineages in
the clade have that character.
Homologous characters — characters in different
organisms that are similar because they were inherited
from a common ancestor that also had that character.
An example of homologous characters is the four limbs
of tetrapods. Birds, bats, mice, and crocodiles all have
four limbs . Sharks and bony fish do not. The ancestor of
tetrapods evolved four limbs, and its descendents have
inherited that feature — so the presence of four limbs is
a homology.
The structural dissimilarities between a
bird wing and bat wing suggests that they
were not inherited from a common
ancestor with wings.
Independent evolution of a character – the wing.
Bird and bat wings are analogous — that is, they
have separate evolutionary origins, but are
superficially similar because they have both
experienced natural selection that shaped them to
play a key role in flight.
Analogies are the result of convergent evolution.
In what way are bird and bat wings homologous?
A reversal – When a derived trait can revert to an ancestral trait either
through a mutation, or selection.
3 Assumptions to Cladistics
1. Change in characteristics occurs in
lineages over time.
2. Any group of organisms is related by
descent from a common ancestor.
3. There is a bifurcating, or branching,
pattern of lineage-splitting.
What about primitive and derived characters?
The use of the term “primitive” have inaccurate
connotations.
Often the original (or plesiomorphic) character
state is more complex than the changed (or
apomorphic) state.
For example, as they have evolved, many
animals have lost complex traits (like vision and
limbs). In the case of snakes, the plesiomorphic
characteristic is "has legs" and the apomorphic
characteristic is "doesn't have legs."
Reconstructing trees: A step by step method
1. Choose the taxa whose evolutionary relationships interest you.
2. Determine the characters and examine each taxon to determine the character states.
Use homologies, not analogies.
3. Determine the polarity of characters — in other words, figure out the order of
evolution for each character.
•
For example, did the beetle species under consideration all evolve from an ancestor with five
antennal segments — and only later did six evolve, or was it the other way around?
4. Group taxa by synapomorphies, not by symplesiomorphies.
•
Synapomorphies are derived or "changed" character states shared by two taxa.
•
Symplesiomorphies An ancestral character state (i.e., a plesiomorphy) shared by two or more
lineages in a particular clade.
Synapomorphy versus symplesiomorphy
Reconstructing trees: A step by step method
1. All taxa go on the endpoints of the tree, never at nodes.
2. All nodes must have a list of synapomorphies, which are common to all taxa above
the node (unless the character is later modified).
3. All synapomorphies appear on the tree only once unless the character state was
derived separately by evolutionary parallelism.
Using Parsimony to Recreate Phylogenetic Trees
Parsimony - choose the simplest scientific explanation that fits the evidence.
Hypothesis 1 requires six evolutionary changes.
Hypothesis 2 requires seven evolutionary changes,
with a bony skeleton evolving independently, twice.