Evolutionary Trees

literally the root of the node

Represents
ancestral taxon
and splitting
point

a point between roots

line between nodes

It's the tip, where the images are sometimes

The cat phylogeny includes some of the evolutionary modifications, or transitions, that occurred as the various cat lineages diverged.

Modifications from node ancestors to the tips

(Node and
everything above;
also a monophyletic
group)

Two clades or taxa that
share a common
ancestor

The line Darwin labeled “1” represents the root of the tree, the species that is
the common ancestor of species A, B, C, and D

The node of the first tree that was drawn, the image is on the book

Cladogram or Phylogeny can be depicted in many ways
with the same basic topology

Only under extremely rare circumstances do we know the evolutionary history
of populations or species by direct observation. These usually involve lineages
maintained and managed in laboratories (see, for example, Hillis et al. 1992). The
rest of the time, history is unrecorded and we are left to infer it from what clues
we can gather and piece together. We consider data and methods used to infer
phylogenies shortly. But it bears emphasizing that an evolutionary tree is virtually never a revealed truth. Instead, it is a hypothesis based on a particular data set
that has been analyzed with a particular technique.

Because they infer clues to pierce together the trees. They don't know the completely accurate history.

Example:

Consider the cat phylogeny, assembled by Werdelin and Olsson, that we have
looked at in this section. Neither Werdelin and Olsson, nor we, nor anyone
else, knows the true evolutionary history of the leopard and its kin. Not only do
we not know the true history of coat colors, we do not know the true pattern
of branching on the tree from the common ancestor to today’s cats. The best
Werdelin and Olsson could do was use the available evidence to identify the
most plausible scenarios

First we note which of the evolutionary novelties, also known as derived
characters, are unique to one species and which are shared

Now we look at the shared derived characters. Note that orange wing tips are
shared by exactly two species. This evidence identifies the orange-tipped birds
as sister species, and tells us that orange tips must have evolved after the lineage
leading to the orange-tipped species diverged from the lineages leading to the
other species. Otherwise, other species would have orange tips too.
That masks are shared by the two orange-tipped birds and the long-billed bird
tells us that these three species are more closely related to each other than any of
them is to the remaining species. And the fact that all four species have tail bars
tells us that this trait must have evolved before any of the lineages leading to the
four birds diverged from each other.

Depending on their shared derived characters, draw the tree.

In an ideal case, we can infer
the evolutionary history of a
set of species from their nested
sets of shared evolutionary
innovations.

We have used nested sets of shared
derived characters to reconstruct the history of diversification among lineages.
That is, we have used shared derived characters to infer a phylogeny.

Continuing to draw our tree backward in time,

So by timing they refer to bulding the tree backwards in time.

An apomorphy is a feature that was not present in the common ancestor of two or more groups of organisms, but has evolved and been retained in all descendants of a particular group. It is a unique trait that distinguishes one group of organisms from another. In other words, it's a shared derived characteristic.

A derived character state. This is anything that is an innovation along an evolutionary linage. So anything that is different from the ancestral character state. For example, within the phylum Chordata, the evolution of a vertebral column, which is something lineages that branched off earlier in Chordate evolution do not have and so is new in the Class Vertebrata, would be an apomorphy.

A plesiomorphy is a characteristic that is shared by two groups of organisms, but is not unique to one group. It is a trait that was present in their common ancestor and has been retained in all descendants. In other words, it's an ancestral trait.

An ancestral character state. This is any trait that was inherited from the ancestor of a group. For example, reptiles are exothermic, they do not maintain a constant internal body temperature. They have this characteristic because the ancestor of all reptiles was exothermic. This differs from a synapomorphy because some descendants of the first reptiles are not exothermic (birds are endothermic). In other words, this trait is ancestral, but is shared by some, but not all, of that ancestors; descendants.

There are two groups. By that I mean that they don't have the same common ancestor, but they have one that is much, much further apart. Now, they retained this ancestral train (so it's obvious that the distance ancestor has it as well) from their distant node

A synapomorphy is a characteristic that is shared by two or more species but is not present in their common ancestor. It is a trait that evolved in one species and was then inherited by all its descendants, making it a unique characteristic of that particular group of organisms.

Derived trait (not ancestral so new), the entire clade has the trait

A monophyletic group, also known as a clade, consists of an ancestor and
all of its descendants.

Shared derived traits identify
monophyletic groups—sets of
taxa that include an ancestor
and all of its descendants.

A group consisting of an ancestor and
some, but not all, of its descendants, such as the light-tailed birds and their lighttailed common ancestor in Figure 4.9c, is described as paraphyletic.

Paraphyletic groups have a shared single ancestor and most descendants, but there are some descendants that aren't included in the group.

A group
that contains some, but not all, of an ancestor’s descendants, and that also excludes
the ancestor, such as the living masked light tails, is called polyphyletic.

Polyphyletic groups have many different lineages without a clear single ancestor.

Polytomy refers to a situation where two or more lineages share a common ancestor, but it is not possible to determine the branching pattern between them. This is due to incomplete information or lacking evidence to determine the ancestry. In this situation, the tree topology is not resolved and may need further research to identify the true evolutionary history.

Uses Discrete
Characters (like mutations, or
some heritable trait)
Select the tree with the
minimum number of
character-state transitions
summed across all characters

Under parsimony analysis, we prefer the hypothesis that requires the fewest
evolutionary changes in the characters of interest (see Felsenstein 2004). We
evaluate each character on each possible tree, looking for the simplest evolutionary scenario that can explain the distribution of the character states among the
species at the tips

One criterion
is parsimony—the minimum
amount of evolutionary change
implied by a tree.

Uninformative characters refer to those anatomical, molecular, or behavioral characters that contain little or no useful information about the evolutionary history of a particular organism or group of organisms.

These characters are often difficult to interpret, and their presence alone does not provide enough information to determine the evolutionary relationships between different taxa. Uninformative characters can be seen as a result of homoplasy, which is the independent evolution of similar structures or traits in unrelated groups.

Because of this lack of information, uninformative characters do not usually contribute much to the formation of phylogenies that aim to establish the evolutionary relationships between organisms. Instead, they may be used to study other aspects of the biology or ecology of a particular organism or group of organisms.

Because the simplest scenarios require the same number of changes
under all three hypotheses, striped legs and spotted rumps are uninformative
characters for our analysis.

Basically uninformative characters aren't useful for building a tree

occurs when characters are simliar but are not derived from a common ancestor

any similarity between characters that is due to their common ancestor

Reversal may occur when formerly adaptive derived characters are lost because environmental changes have rendered them more costly than beneficial

Example: Other reversals include the loss of eyes in cave-dwelling animals,
of teeth in birds, and of body armor in freshwater threespine sticklebacks.

In the tree frog, caerulein is encoded by a locus that arose as a duplication of the gastrin gene. In the clawed frog, caerulein is encoded by a locus that
arose as a duplication of the cholecystokinin gene. Production of the same toxin
in these frogs is not a synapomorphy, but a stunning example of convergence.

In still other cases, unfortunately, homoplasy can be discovered only by reconstructing a phylogeny and finding that the distribution of some characters cannot
be explained without convergence, reversal, or both (Wake et al. 2011). In other
words, homoplasy is a fact of life in phylogeny inference. It represents “noise”
in the data sets used to reconstruct evolutionary history. Homoplastic traits are
analogous to the faulty or misleading measurements that are present in almost
every data set used in science. The best way to avoid being misled by the noise
of homoplasy is to analyze many independent characters in reconstructing evolutionary relationships instead of just one or a few.

Phylogeny of fossil sand dollars estimated by
parsimony analysis Most of
the anatomical characters used to
infer this evolutionary tree have
two possible states; a few have
three. The string of numbers next
to each sand dollar lists its state
for each character. Redrawn from
Mooi et al. (2000).

Cetacea is identified as a monophyletic group by a number of synapomorphies in
the skull

Cetaceans have an enlarged, thickened, and dense
auditory bulla, a bony shell at the base of the skull that surrounds the structures
of the ear. This is thought to be an adaptation for hearing underwater

teeth in line with the cheek teeth (the premolars and molars), instead of in an
arc across the front of the mouth as in most mammals.

EXAMPLE:
Two hypotheses
on the origin of whales
(a) Whales are artiodactyls.
(b) Whales are kin to artiodactyls.

When biologists began using formal parsimony analysis of morphological
characters to address the question, their results tended to support the hypothesis
that cetaceans are close kin to, but not members of, the Artiodactyla
This shape allows the foot to rotate in a wide arc
around the end of the ankle and contributes to the long stride and strong running
ability observed in many artiodactyls. Living whales, of course, have no ankles.
The shape of their astragalus cannot be assessed.
As we have already noted, some fossil cetaceans have hindlimbs.
In others, the known specimens were, until recently, too fragmentary to support definitive conclusions about whether whales’
ankles qualify them as artiodactyls
We can infer evolutionary trees
using molecular characters,
such as nucleotide or amino
acid sequences, in addition to
morphological characters.
The first step in reconstructing
evolutionary history using
sequence data is to align the
sequences. We then compare
alternative phylogenetic
hypotheses using any of several
criteria, including parsimony.
When we encountered conflict among morphological characters, we turned
to parsimony analysis. We can do the same with sequence data (Felsenstein 1988).
We consider all possible trees as hypotheses, determine the minimum amount of
evolution required to explain the distribution of nucleotides at each site on each
tree, and seek the tree that requires the least change overall.
Using a computer program (Felsenstein 2009) to find the most parsimonious
among all 10,395 trees for all 60 characters, we learn that the tree in Figure 4.23a
is the winner, requiring 41 substitutions. The tree in Figure 4.23b requires 47.
Whale + hippo wins
All of our trees point to the
same conclusion. Whales are not merely kin to artiodactyls, they are artiodactyls
And our analyses provide some support for the hypothesis that whales and hippos
are sister taxa. A close relationship between hippos and whales has a certain intuitive charm because hippos are semiaquatic and whales fully so.

Which method is best? Neighbor joining is not quite as good as the others,
although its speed makes it a useful adjunct to the other methods. Parsimony,
maximum likelihood, and Bayesian inference all have strengths and weaknesses
(Felsenstein 1978; Kolaczkowski and Thornton 2005). For this reason researchers often use a variety of methods and check whether the trees they produce are
consistent with each other (Huelsenbeck and Hillis 1993; Hillis et al. 1994).

Parsimony: Minimize # steps – use synapomorphy
Statistical Methods:
• Maximum Likelihood: Probability of the data given the
tree
• Bayesian: Probability of the tree given the data

Uses Discrete
Characters (like mutations, or
some heritable trait)
Select the tree with the
minimum number of
character-state transitions
summed across all characters

Maximum Likelihood (R.A. Fisher)
Probability of the data given the tree
• This is a “Frequentist” method: one true
answer (one true tree)
• Draw from the data (probability distribution of
DNA sequence data) to find the true tree
• Choose the tree (x, y axis) that maximizes the
probability of the observed data (z axis)

Draw from the data (probability distribution of
DNA sequence data) to find the true tree
vs
Select the tree with the
minimum number of
character-state transitions
summed across all characters

Typically, evolutionary biologists will use a variety of
methods to reconstruct a phylogeny.
• Maximum likelihood and Bayesian methods are
considered more robust.

Tree is only as good as the data. Having many
homoplastic characters (due to convergent evolution,
reversals, etc.) will make the reconstruction less robust
• Standard to use Bootstrapping and Bayesian
Posterior Probabilities to assess the validity of the
tree