~Phylogenetics~

Hey yall! Today we will be talking about phylogenetics. Phylogeny is the evolutionary history of
a species or group of species. A phylogeny for snakes and lizards, for example, indicated that
the scaly-foot, a legless lizard in Australia, originates from a different legged lizard than snakes
did despite their phenotypic similarities. Their legless conditions evolved independent of one
another. To construct a phylogeny, biologists utilize systematics, a discipline focused on
classifying organisms and determining evolutionary relationships.

Taxonomy is used to more specifically classify organisms. Taxonomy is the scientific discipline
of how organisms are named and classified. Organisms are classified binomially meaning that
their genus and species name are used to identify the species. Latin is used in the classification
of these species so there is a universal name for each species. The classification of each
species is done in a hierarchical system beginning with domain and
ending in species. (figure). The taxon or taxa, is the named taxonomic
unit at any level of the hierarchy. For a leopard, Panthera is a taxon at
the genus level.

When constructing a phylogenetic tree, a branching diagram in which

the evolutionary history of a group of organisms is displayed, it is
important to remember that the tree represents a hypothesis about
evolutionary relationships. These relationships are often depicted as
branch points. (show
branch points). Branch
points show the divergence of
two evolutionary lineages
from a common ancestor.
Sister taxa (show) are two organisms that share an
immediate common ancestor and are each others
closest relatives.

Phylogenetics is studied because a species

phylogeny provides an enormous amount of
information. For example, by analyzing the genes of
corn, or maize, researchers were able to identify two living relatives of maize that can be used
to genetically modify the maize. In 2001, phylogenetics was used to identify the strain of anthrax
bacterium sent to politicians and journalists so that the authorities could track the anthrax back
to the terrorist.

To infer phylogeny, systematists must first gather information regarding biochemistry, genes,
and morphology. Biologists must determine if characteristics that two species share are due to
homology or analogy. Homologies are similarities due to shared ancestry whereas analogies are
similarities due to convergent evolution. Analogous structures occur due to environmental
pressures and natural selection and the two species end up developing similar structures while
evolving from two different species. The Australian mole and American mole look similar
phenotypically but when looking at their phylogenies, the Australian mole is really a marsupial
whose young completes their embryonic development in a pouch outside of the mothers body.
The American mole is a eutherian and their young complete embryonic development in the
uterus of the the mothers body. The common ancestor of these two moles lived approximately
140 million years ago and their lineages diverged at about this time. The analogous
characteristics evolved independently of the other mole lineage and the two species developed
the characteristic as they became adapted to similar lifestyles. Analogous structures that arose
independently are also called homoplasies which means to mold in the same way in Greek.

Homologies are characteristics two species have in common due to shared ancestry. Molecular
systematics is the discipline that uses DNA and other molecular data to determine evolutionary
relationships. To determine whether two species have homologous or analogous structures,
biologists most sequence and compare sequences of nucleic acids of organisms to determine
the most likely cause of the similar characteristics. If two species are very closely related, the
sequences differ at only a few sites, but if the species are distantly related, there will likely be
different bases at many sites and may have differing sequence lengths because insertions and
deletions have occurred over long periods of time. Two sequences that resemble each other at
many points along their length most likely are homologous.

Cladistics is the approach to systematics in which common ancestry is the primary criterion
used to classify organisms. Biologists place species into groups or clades which includes an
ancestral species ad all its descendants. Clades can be the same thing as taxa only if the clade
is monophyletic meaning that the clade includes the ancestral species and all its descendants.
Taxa and clades differ if the clade only includes the ancestral species and some, but not all, of
its descendants, which is called a paraphyletic group, or by polyphyletic groups which are
groups that include taxa with different ancestors.

Clades are defined by analyzing the difference between shared ancestral characters and shared
derived characters. Shared ancestral characters are those that originated in an ancestor of the
taxon. For example, all mammals have a backbone but the backbone does not distinguish
mammals from all vertebrates because all vertebrates have a backbone. The backbone
predates the branching of the mammalian clade from other vertebrates. In contrast, shared
derived characters are characteristics that are unique to a particular clade. In mammals, hair is
considered a shared derived character because all mammals have hair but hair is not found in
their common ancestors. Phylogenies are developed using derived characters. The outgroup, or
a species or group of species from an evolutionary lineage that is known to have diverged
before the lineage of the ingroup, is the first species or group of species to diverge from the
common ancestor. This group will not have the same derived characters as the ingroup. The
ingroup is the species or group of species that we are studying. By comparing the members of
the ingroup, we can determine what characters are
derived and then develop the phylogeny.

Now, when creating a phylogenetic tree, branch

length does matter.branch lengths are
proportional to the amount of evolutionary change or to the times at which particular events
occurred. Even though the branches on a phylogenetic tree may be different lengths, among
organisms alive today, all the different lineages that descend from a common ancestor have
survived for the same number of years. The lengths of the branches differ because of the
number of genetic changes that have occurred since two lines diverged. In the figure below, in
the time since the fly and mouse diverged from a common ancestor, more genetic change has
occurred in the fly than in the mouse.

There are two principles used to narrow the possibilities and create the most accurate
phylogenetic trees possible. Maximum parsimony is the idea that one should investigate the
simplest explanation that is consistent with the facts whereas maximum likelihood is the idea
that given certain rules about how DNA changes
over time, a tree can be found that reflects the most
likely sequence of evolutionary events. In maximum
parsimony, you look at only the facts you absolutely
need in order to create the phylogenetic tree. With
maximum likelihood, you look at all the facts and
determine from the gathered information what is
important for the phylogenetic tree.
Phylogenetic bracketing is used to predict that
features shared by two groups of closely related
organisms are present in their common ancestor
and all its descendants, unless independent data
indicates otherwise. (Figure) The tree shows how
the birds and saurischian dinosaurs are the most
closely related of the species shown and how the two species share a common ancestor with
the ornithischian dinosaurs.

Using Phylogenetics:
Phylogenetics was used to split the original plant and
animal kingdoms into what is now three domains and
six kingdoms. The domains became Eukarya, Bacteria,
and Archaea as biologists began to realize that bacteria
could be further classified. Kingdom Protista separated
from the animal kingdom recently for this reason too
and in the future, will likely split into animal-like and
plantlike protists. (Figure 26.22)
Horizontal gene transfer, which is a process in which
genes are transferred from one genome to another
through mechanisms such as exchange of
transportable elements and plasmids, viral infection, and perhaps fusions of organisms, was
used to figure all of this out (figure 26.23)
Phylogenetic Vocab
Phylogeny: the evolutionary history of a species or group of species
Systematics: a discipline focused on classifying organisms and determining evolutionary relationships
Taxonomy: the scientific discipline of how organisms are named and classified
Binomial: the two-part format of the scientific name
Taxon: the named taxonomic unit at any level of the hierarchy
Phylogenetic Tree: the branching diagram in which the evolutionary history of a group of organisms is
displayed
PhyloCode: names groups that include a common ancestor and all of its descendants
Branch Point (AKA Dichotomy): the divergence of two evolutionary lineages from a common ancestor
Sister Taxa: groups of organisms that share an immediate common ancestor and are each others
closest relatives
Rooted: a branch point within the tree, usually the branch to the farthest left, represents the last common
ancestor of all the taxa in the tree
Polytomy: a branch point from which more than two descendent groups emerge
Analogy: similarity due to convergent evolution
Homology: similarity due to shared ancestry
Homoplasies: analogous structures that arose independently
Molecular Systematics: the discipline that uses DNA and other molecular data to determine evolutionary
relationships
Cladistics: approach to systematics where common ancestry is the primary criterion used to classify
organisms
Clades: groups of species that include an ancestral species and all of its descendants
Monophyletic: a clade that consists of an ancestral species and all of its descendents: the only way a
taxon is equivalent to a clade
Paraphyletic: a group that consists of an ancestral species and some, but not all, of its descendents
Polyphyletic: a group that includes taxa with different ancestors
Shared Ancestral Character: a character that originated in an ancestor of the taxon
Shared Derived Character: a novelty unique to a particular clade
Outgroup: a species or group of species from an evolutionary lineage that is known to have diverged
before the lineage of the ingroup
Ingroup: a species or group of species whose evolutionary relationships we seek to determine
Maximum Parsimony: investigate the simplest explanation that is consistent with the facts
Maximum Likelihood: given certain rules about how DNA changes over time, a tree can be found that
reflects the most likely sequence of evolutionary events
Phylogenetic Bracketing: used to predict that features shared by two groups of closely related
organisms are present in their common ancestor and all of its descendents, unless independent data
indicates otherwise
Horizontal Gene Transfer: a process in which genes are transferred from one genome to another
through mechanisms such as exchange of transportable elements and plasmids, viral infection, and
perhaps fusions of organisms

Review sheet
Need to own!
Difference between clades and taxa
Instances when phylogenetics can be used in real life
Difference between homology and analogy
Shared ancestral characters vs shared derived characters
Branch length, branch points, sister taxa
Maximum parsimony vs maximum likelihood
Phylogenetics used in classification of animals; how have the classification groups
changed recently?