Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
BIOLOGY—101
Professor: Dr. Thomas R. Sawicki
Text: Biology 8th ed. (Campbell and Reece Chapters 19, 26 and 27)
The diversity of the living world is one of the most interesting and challenging aspects of nature. – Page | 1
Ernst Mayr
Lecture # 1 Phylogeny and Systematics
Systematics is the study of the diversity of organisms and their natural relationships. There are three
sub-disciplines within the field of systematics that are fundamental to the derivation of reconstructing
“natural relationships”: 1) Taxonomy; 2) Phylogenetics; 3) Biogeography. It is important to note that each
of the sub-disciplines is fundamentally interconnected and interdependent. They cannot exist without the
other and that is why all three are subfields of systematics.
Taxonomy
Naming and Classifying
Taxonomists are biologists who name and classify organisms. The goal of taxonomy is to name and
classify organisms relative to their evolutionary=phylogenetic relationships. The scientific naming
system is based on binomial nomenclature—using two scientific names. The binomial itself is based on
the overall scientific classification of the organism. This infers then that naming a species is part of its
overall classification and of course the classification is based on its phylogeny! I mention this to reinforce
the interconnectedness between the sub-disciplines of systematics and if you don’t fully understand yet
don’t worry, we will cover this again as we move along.
The system of naming species we currently use is almost exactly the same as it was originally conceived
by Carolus Linnaeus (1707-1778). Taxonomists and all biologists use binomial nomenclature handed
down to us by Linnaeus. The binomial naming system is a two part Latin name. The first name is the
genus to which the species belongs. The second is the specific epithet, i.e. the species name. In
other words, closely related species will all be classified i.e., named, within the same genus.
For instance, the scientific name of a house cat is Felis catus. Now you know where Felix the cat got his
name. The scientific name of a wild cat is Felis sylvestris. Now you know where Sylvester the cat got his
name! The fact that both species are within the same genus indicates their close relatedness, i.e. the
individual species are named in accordance to their defined evolutionary relationships.
Notes on how to write scientific names
Bio 102 Notes: Dr. Thomas R. Sawicki
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
When typing a scientific name the genus and species names are italicized like so: Felis sylvestris. They
can also be underlined like so: Felis catus. BUT NOT BOTH UNDERLINED AND ITALICIZED!! Notice
how the space between the names is NOT underlined!! Underlining is usually done when writing
scientific names by hand. Note also that the genus name is capitalized Felis but the species name catus
is not.
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Scientists often discuss species without saying both the genus and species names. For instance, I could
write: “The Bahadzia living in Cuba have extremely large gills.” I also could have said: “Bahadzia
patilarga and Bahadzia yagerae, which live in caves in Cuba, have extremely large gills.” But because I
am speaking generally about all the species within a given genus living in Cuba and not referring to one
of the species in particular, it is correct and simpler to refer only to the genus in this case. Again note that
both species are placed within the same genus denoting there close evolutionary relationship.
Finally, the first time you mention a particular species in a paragraph you MUST use the entire name.
Once it has been completely spelled out, each additional time it is mentioned, it can be abbreviated. For
instance: “Because no males were found during the expedition, only the female for the new species
Hadzia spinatus was described. It is noteworthy that H. spinatus females have extremely large, heavily
spined, almost male-like gnathopods. ”Notice that once the scientific name was spelled out the first time,
the second time I could refer to this species by only abbreviating the generic name. Some species are
better known by their abbreviation, for instance the bacterium E. coli is short for Escherichia coli.
Taxonomy—Classification
After Darwin’s thesis on The Origin of Species, scientists attempted to classify organisms based on their
hypothesized evolutionary relationships NOT just on superficial behavioral or morphological similarities.
For instance, both bats and birds can fly and both are warm-blooded. But just because they both have
wings and are warm blooded does not mean they merit the same taxonomic classification.

Bats have mammary glands, fur and give birth to live young.

Birds have feathers, no mammary glands, and lay eggs.

Bats have more shared, derived characters (sometimes called synapomorphies) with other
mammals (mammary glands, fur and live births) than with birds (wings and warm blooded).
In addition the wings of bats and birds are NOT homologous, they are analogous.

Analogous structures have a similar structure and function but only superficially—they are
derived independently and NOT from a common ancestor.

Homologous structures are similar in position, morphology, embryology and evolutionary
origin—they are derived from a common ancestor.
o
As we will see homologous structures can either be apomorphic—recently inherited
from a common ancestor; or they can by pleisiomorphic—derived from a common
ancestor in the distant past.
Bio 102 Notes: Dr. Thomas R. Sawicki
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
Thus bats and birds are classified within completely different taxonomic hierarchical classifications: birds
traditionally within Class Aves and bats in Class Mammalia. Although as we will learn later on many
taxonomists feel that birds should be classified within the Class Reptilia.
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Another example, which may be less obvious, may help us better understand how scientists classify
organisms. The scientific name of a lion is Panthera leo and the scientific name of a tiger is Panthera
tigris. Notice that these two large cats are given a name that classifies them within the genus Panthera.
This clearly denotes that the tiger and lion share a more recent common ancestor with each other than
they do with either a house cat (Felis catus) or a wild cat (Felis sylvestris); however, the house cat, wild
cat, lion and tiger are all cats and are therefore all classified within the family Felidae—the cat family
(review figure 26.3 and 26.4 and the corresponding text). This indicates that all cats share a more recent
common ancestor with each other than they do with dogs that are classified within the family Canidae.
However, cats and dogs are classified together in the order Carnivora indicating that they share a more
recent common ancestor with each other than they do with other orders found within class Mammalia
such as the order Primates (apes, monkeys and humans) or Probiscidea (elephants) etcetera. This
example demonstrates how systematists use the hierarchical classification scheme to classify organisms
based on their evolutionary relationships.
As noted above, the hierarchical classification scheme was originally developed by Carolus Linnaeus.
Classically, there were seven levels within the hierarchy as written below:
Kingdom
Phylum
Class
Order
Family
Genus
Species
As one goes down this classification system from kingdom to species you are discussing groups
hypothesized to have a more and more closely derived evolutionary heritage. In other words, organisms
within a single genus share a common ancestor more recently in the past than organisms classified within
the same family and so on.
As noted above, the broadest classification level was the Kingdom. Until very recently there were five
kingdoms: Animalia, Plantae, Fungi, Protista and Monera. This five kingdom level of organization was
proposed by Robert H. Whittaker in 1969. This five kingdom scheme was based on three multicellular
eukaryotic Kingdoms (Plantae, Fungi and Animalia). These kingdoms were separated mostly upon their
means of nutrition. In other words it was inferred that means of obtaining energy is a very fundamental
and thus anciently derived trait from which broad classifications could be made.
Bio 102 Notes: Dr. Thomas R. Sawicki
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27

Kingdom Plantae—autotrophic, specifically photoautotrophic

Kingdom Fungi—saprophages, i.e. they are heterotrophic organisms that are decomposers.
Fungi secrete digestive enzymes into dead organisms and absorb small organic molecules.

Kingdom Animalia—heterotrophic by means of ingesting food and digesting it within a special
body cavity.
There was one other kingdom of eukaryotic organisms:

Kingdom Protista—any eukaryotic organism that did not readily fit into any of the other three
eukaryotic kingdoms (Plantae, Animalia or Fungi) were placed into Protista. It has often been
called a “trash-bin” kingdom. Dr. Michael Gable at Eastern CT State University used to say
regarding the protistans, “Tissue is the issue.” In other words, if you did not have readily defined
tissues but were a eukaryotic organism, you were classified in the kingdom Protista. So all
SINGLE CELLED eukaryotic organisms are protistans. This should make very intuitive sense. If
your whole being is a single cell then by definition you don’t have any tissues, e.g. Paramecium
and Amoeba. Also, algae were placed into kingdom Protista as they do not have truly
differentiated tissues and to some extent behave much like colonial single-celled organisms;
however, this has recently been changed and as we will see the algae have now been split and
are either classified within kingdom Plantae or within a new kingdom, the Chromista.
Finally the last kingdom was prokaryotic:

Kingdom Monera—this kingdom included all the bacteria, i.e. all prokaryotic organisms.
Today, we have added an eighth, and broadest, category to the classification hierarchy: Domains. This
has happened only within the last decade or so (figure 26.3). The kingdom Monera (the bacteria) is an
extremely diverse group of organisms (all prokaryotic) and relatively recent discoveries have found
prokaryotes that can live in extremely harsh environments, e.g. hot springs. These prokaryotes—
collectively called archaea for ancient—appear to be genetically different from other more common
prokaryotes—the bacteria (see table 27.2 for a list of biochemical and other characteristics that
differentiate these two groups of prokaryotic cells).
The differences between the archaea and the more common strains of bacteria—often called eubacteria
where eu is from the Greek for true—have resulted in the new hierarchical classification: Domain.
We now use a 3 Domain system:

Domain Archaea—prokaryotic organisms, which include methanogens (which produce
methane), thermoacidophilic bacteria (phil from Greek meaning love; thermo=hot and
acido=acidic), and halophilic bacteria (halo Greek meaning salt). Note: these various prokaryotic
Bio 102 Notes: Dr. Thomas R. Sawicki
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Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
organisms have only relatively recently been discovered. They live in environments that, not too
long ago, most scientists thought were impossible for life to survivie.

Domain Bacteria—obviously also prokaryotic organisms, the majority of prokaryotes are
classified under this Domain. These are the typical, common types of bacteria, e.g. the kind for
which you must take antibiotics. Cyanobacteria (sometimes incorrectly called blue-green algae)
are also within this domain. Cyanobacteria are photosynthetic bacteria.

Domain Eukarya—these organisms have true, membrane bound nuclei as the name suggests.
Plants, animals, fungus and single celled eukaryotes (read protistans) and the new kingdom
Chromista are placed into this Domain.
To sum this up, the kingdom level is no longer the highest (or broadest) level of classification. For
instance the kingdom Plantae and kingdom Animalia are now both classified within the domain Eukarya.
As noted above table 27.2 shows some of the major differences between the Archaea, Bacteria and
Eukarya. Interestingly, the domains Eukarya and the Archaea appear to be more closely related (that is
to say they share the more recent common ancestor) than the domains Archaea and Bacteria. Thus
eukaryotes (all plants, animals, protists, fungi and chromistans) appear to share a common ancestry with
prokaryotic like organisms which live in more extreme environments than do the bacteria. This phylogeny
is based both on genetic studies first conducted by Carl Woese starting in the late 1970’s and also on
morphological characters noted in table 27.2 (see also figure 27.16).
Because of this ground breaking work, the new hierarchical classification scheme, including the level
Domain is as follows:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
In addition, each of the individual classification levels e.g., class or order can themselves be subdivided
as so:
Domain
Kingdom
Superkingdom
Phylum
Subphylum
Superclass
Class
Subclass
Superorder
Order
Bio 102 Notes: Dr. Thomas R. Sawicki
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Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
Suborder
Superfamily
Family
Subfamily
Genus
Species
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Further divisions are possible and we will discuss these later in the course.
In addition to the adding of a new hierarchical level of classification, there are other changes happening at
the kingdom level. As noted above, kingdom Protista is a very diverse group and an active debate is
underway on how to correctly classify this “kingdom.” For instance, based on a large amount of genetic,
morphological and biochemical data the green and red algae, once placed in the kingdom Protista, are
now classified within the kingdom Plantae (many botanists place the red and green algae within a
completely separate kingdom which is denoted to be closely aligned with the plants). Some of the
evidence for this change in classification includes:
o
Homologous chloroplasts, red and green algae use chlorophyll b and beta-carotene like
plants.
o
Biochemical similarities in the cell walls of plants and red and green algae.
o
Mitosis and cytokinesis are similar between the two groups.
o
Sperm ultrastructure is similar.
o
Genetic similarities—multiple lines of genetic evidence points to a close relationship between
green and red algae and plants.
In addition, taxonomists have introduced a new kingdom, Chromista, for (almost) all other “algal” groups.
So now domain Eukarya has (at least) five kingdoms: Protista, Chromista, Plantae, Fungi and Animalia.
This will surely change as more data comes to light and scientists reach a consensus.
Another important field of systematics is biogeography. Biogeography is the study of the distribution of
organisms in space, both past and present and how distribution correlates with variation in biological
characteristics e.g. morphological, behavioral or molecular differences. These patterns of distribution
within a defined space are correlated with historical geology, i.e. geological changes that have occurred
over time. For instance, have you ever asked yourself why only the continent of Australia has a great
diversity of extant (living) groups of marsupial mammals? Understanding the geology of plate tectonics
allows us to understand continental drift and derive plausible hypotheses regarding current macro
distributions of plant and animal fauna (see figures 25.12, 25.13 and the corresponding text for a brief
description of plate tectonics and continental drift). We can use historical geology and biogeography, in
combination with molecular genetics and paleontology to “read” the evolutionary history of a species or
groups of species.
Bio 102 Notes: Dr. Thomas R. Sawicki
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
As we now can see by using morphological, behavioral and molecular differences and correlating these
differences to geographical distributions, and historical geology, systematists can derive phylogenies. A
phylogeny is a hypothetical evolutionary relationship between extant (living) and or extinct organisms
within a lineage. This leads us to the third major field of systematic:
Phylogenetics
Phylogenetic systematics (cladistics) is the field of systematics that uses morphological, behavioral,
molecular (or other) characters to infer hypothetical evolutionary relationships between organisms (extinct
or extant). Evolutionary relationships derived in cladistics are usually based on the idea of allopatric
speciation—speciation that occurs when gene flow between populations of a given species is interrupted
due to some geological, climatological or other event.
The basic assumption we use to derive phylogenies based on allopatric speciation is that the more recent
a split occurred, the more shared-derived characters should be observed. What does shared-derived
character mean? Simply that two species (or other taxonomic groups) share characters in common that
are NOT found in ancestral forms. The more shared-derived characters that different groups share, the
more closely related they are inferred to be.
Characters can be morphological, molecular, behavioral, biochemical or a combination of these. These
characters are distributed in a matrix and then a computer program is used to determine the relationships
based on these characters. A couple of very common computational methodologies for determining
relatedness are maximum parsimony and maximum likelihood.
Maximum parsimony—is based on the concept of Occam’s Razor (the simplest explanation is usually
the correct one). In the case of assigning relatedness based on character states, maximum parsimony
assumes that the fewest number of character changes needed will most likely reflect the correct
phylogeny. In order to more fully understand how this works we need to learn some new terminology:

Character—Any heritable attribute or feature that distinguishes one thing, individual or group
from another.

Homologous characters—characters derived by two taxa because they share a common
ancestor and thus inherited that character from the common ancestor.

Apomorphic—the most derived (more recently evolved) state in an evolutionary sequence of
homologous characters. For instance, pine trees and oak trees share the character of vascular
tissue. However, oak trees are more closely related to tulips than to pine trees because oak trees
and tulips share the more derived apomorphy (apomorphic character)—flowers.

Plesiomorphic—the ancestral character state in an evolutionary sequence of homologous
characters. In the above example, vascular tissue is the plesiomorphic character.
Bio 102 Notes: Dr. Thomas R. Sawicki
Page | 7
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27

Analogous character (Homoplasy)—a phenomenon in which two taxonomic groups, e.g., two
species, share a similar character, but NOT because it was inherited from a common ancestor.
Homoplasies are often the result of convergent evolution (also called parallelism when it
occurs amongst closely related groups), e.g. both birds and bats have wings but the character is
not homologous it is a homoplasy because birds and bats do NOT share the MOST RECENT
common ancestor and thus did not inherit their wings from a common ancestor.

Cladogram—a diagram that depicts the hypothetical phylogeny of different taxonomic groups
based on the number of shared derived characters.

Clade—a taxonomic group that includes the most recent common ancestor and its descendents.

Monophyletic clade—a taxonomic group whose members are ALL descended from the nearest
common ancestor. Systematists agree that a hierarchical classification system should be
monophyletic.

Paraphyletic—a taxonomic group that does not include ALL the descendents of a common
ancestor. For instance, Class Reptilia is a paraphyletic clade if it does not include the birds.

Polyphyletic—any taxonomic group, the members of which have not originated from the nearest
common ancestor. For instance, if class Reptilia included frogs, it would be polyphyletic.
Figure 26.5 and the corresponding text provides information on how to read “phylogenetic
trees”=cladograms and figure 26.10 provides diagrammatical examples of monophyletic, paraphyletic and
polyphyletic cladograms.
How does one determine which characters are apomorphic and which are pleisomorphic? The answer is
via an out-group analysis. A taxon which is outside of the study group, preferably a sister group is
studied and its characters described; next characters found in the “in-group” i.e., the group of interest are
studied and described. Those characters found in the “in-group” but are not found in the out-group are
considered to be apomorphic homologies—derived from a common ancestor that led to the taxa of the
in-group. Characters found in both the in-group and the out-group are considered pleisiomorphic
homologies. As you might guess, this is a time consuming and tedious process and means the
researcher must fundamentally understand the organisms being studied.
Maximum parsimony is very commonly used for morphological data. Using “parsimony” will allow us to
determine what characters are homologies and what characters are homoplasies. The character matrix
below is a real character matrix used to determine the phylogenetic relationship of a number of different
amphipod genera. Can you see how a phylogeny could be derived from this matrix? Note genus X is the
out-group. For a bonus on your first exam, see if you can convert this data matrix into a cladogram. I will
begin the process in class. I ask you to do this because I believe by working through the matrix you will
get a better idea of the idea of apomorphic vs. pleisiomorphic homologous characters and homoplasious
characters.
Bio 102 Notes: Dr. Thomas R. Sawicki
Page | 8
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
Table 1. Distribution of character states for 22 characters among 9 genera (A - I) of
amphipod crustaceans—X = out-group; 0 = plesiomorphic; 1 = apomorphic
1
2
3
4
5
6
7
8
9 10
11 12 13 14 15 16 17 18 19 20 21 22
A
0
0
1
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
B
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
1
0
0
C
1
1
0
0
0
0
0
0
0
1
1
0
0
1
0
0
0
1
0
0
1
0
D
1
1
0
0
0
0
0
0
0
1
1
0
0
1
0
0
0
1
0
0
1
0
E
1
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
1
0
0
1
0
F
1
1
1
1
0
0
0
1
0
0
0
0
1
0
1
0
1
1
0
0
0
0
G
1
1
1
1
0
1
0
1
0
0
0
0
1
0
1
0
1
1
0
0
0
0
H
1
1
1
1
0
0
1
0
0
0
0
0
1
0
0
1
1
1
1
0
0
1
I
1
1
1
1
0
0
0
0
1
0
0
0
1
0
0
1
1
1
1
0
0
1
X
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
To better understand the characters (1-22) listed across the top of the matrix, below is a table describing
each of the characters. I will discuss a few of these during class. Of course you are not expected to
learn and understand each of these characters. The point is to help you learn how we determine which
characters are apomorphic and which plesiomorphic.
Table 2. Descrption of characters used to analyze the phylogenetic relationship among nine genera (A-I)
of a monophyletic group of amphipod crustaceans.
Character
Plesiomorphic State
Apomorphic State
1.
Accessory flagellum of antenna 1
2-4 segments
1 segment of vestigial
2.
Mandibular palp
Present
Absent
3.
Mandibular molar seta
On right and left
On right only
4.
Lacinia mobilis of right mandible
Present
Absent
5.
Number of apical setae on inner plate of
Few to 25
40
7-11
15
10-50
100
maxilla 1
6.
Number of spines on outer plate of
maxilla 1
7.
Number of facial setae in oblique row on
inner plate of maxilla 2
8.
Inner plate of maxilliped
Normal
Greatly expanded
9.
Palm of gnathopod 1
Short and transverse
Relatively long, oblique
10.
Posterior margin of segment 5 of
Without distinct lobe
With distinct lobe
gnathopod 1
Bio 102 Notes: Dr. Thomas R. Sawicki
Page | 9
Lecture #1: Systematics; Campbell and Reece Chapters 19, 26 and 27
11.
Segment 4 of gnathopod 1
Enlarged, with lobe
Not enlarged, without
lobe
12.
Sexual dimorphism of gnathopod 2
Male enlarged with lobe
Male not enlarged,
without lobe
13.
Coxal plate of pereopod 4
Expanded, with posterior
Reduced, excavation
excavation
shallow or obsolete
14.
Bases of periopods 3 and 4
Narrow, not expanded
Broadly expanded
15.
Pereopods 5, 6, and 7
Not attenuate
Attenuate, especially
bases
16.
Setae on segment 5 of pereopod 6
Short
Elongate
17.
Number of setae on anterior margin of
1
3-8
1
2-4
dactyls of pereopods 5, 6, and 7
18.
Number of basofacial spines on
peduncle of uropod 1
19.
Size of basofacial spines
Small
Enlarged
20.
Rami of uropod 3
With spines and setae
With spines only
21.
Lobes of telson
Separated or nearly so
Partly fused
22.
Telson (overall)
Lightly spinose
Heavily spinose
Maximum likelihood—is modeling technique used to derive phylogenies, which is commonly used for
molecular data, specifically DNA sequences. Specific genes are sequenced and the amount of
differences (percent differences) between the species is examined. In order for maximum likelihood to
work one needs to have a model of how DNA is assumed to evolve. The simplest model is to assume
that genes mutate at a relatively constant rate. By having the assumption of constant rates of mutation
within genes of different taxa over time, a computer program can work out the most likely phylogenetic
arrangement (see figure 26.14 and the corresponding text for a description of maximum likelihood).
Today, the derivation of phylogenies is based on multiple lines of evidence. The derived phylogenies are
then used to help create the classification of organisms. In Biology 102 you will be learning the
taxonomic classification of almost all major groups of organisms known to exist on earth. You will also
learn their major morphological and physiological characteristics. In other words, by learning the
shared morphological and physiological characters of different groups you will begin to
understand how and why organisms are classified.
Bio 102 Notes: Dr. Thomas R. Sawicki
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