1. Binomial Nomenclature vs. Phylogenetic Tree
Taxonomy vs. Systematics
Binomial Nomenclature vs. Phylogenetic Tree

2. What are Taxonomy and Systematics?
Why is it essential?
• It helps us make sense of the bewildering patterns of variation we see in nature
• It improves our ability to predict things about organisms without having to
study them all in detail
• It enables us to interpret their origins and historical relationships
• It gives us the compass to make an informed decision to preserve our Earth.
What are Taxonomy and Systematics?
Taxonomy: the theory and practice of classification (e.g. naming, grouping)
Systematics: the study of biodiversity and the relationships among organisms
(e.g. evolutionary relationship, ecology, eco-system)

3. Carolus Linnaeus (18th century):•
Developed the modern classification system
Used the generalized 6 kingdoms & John Ray’s idea of genera and species to
formulate the two-name system called binomial nomenclature
The six (6) kingdoms are very general with each further specify into a series of
smaller group called taxa:
 Animalia
 Fungi
 Plantae
 Bacteria
Protista
Archaea bacteria
Seven (7) taxa are used to further organize organisms:
Kingdom  Phylum  Class  Order  Family  Genus  Species
e.g. Animalia Chordata Mammalia Carnivora Canidae Canis familiaris
“Kings Play Chess on Fine Green Sand”

4. • A two-word name system to name each species
• 1st word in the name is the genus, with the first letter capitalized
• 2nd word is the name of the species, not capitalized eg. Felis domesticus
The genus contains multiple species so more than one (1) species has a name with
the same genus:
e.g. Lynx canadensis (lynx)
e.g. Lynx rufus (bobcat)
In addition to this nomenclature, organisms are also called by common names
e.g. nutmeg = Myristica fragrans
Common names are misleading because:
 A species can have multiple names e.g. N.A. cougar = panther = mountain lion
 Starfish and jellyfish are not part of the same phylum

5. When a new species is discovered, taxonomist:
 Describe accurately the characteristic features of the species
 Determine its affinities to other known species that share similar traits
 To give the new species a unique binomial name
While it is possible to classify organisms in many different ways depending
on our objectives, the most widely accepted approach to modern
classification is to develop classification systems that consider evolutionary
relationships – that is, they reflect the phylogeny or root of the organisms.

6. • Based on evidence of evolutionary relationships among organisms
Phylogenetic tree:
• Based on evidence of evolutionary relationships among organisms
• These evidence include a wide range of characters such as:
 morphological
 developmental
 structural
 biochemical
 molecular data
• Account degree of difference between species
Cladistics tree: •
Similar to phylogenetic tree, but do not account the degree of difference
between species
Depicts evolutionary relationships by showing the points at which lineages
diverged from common ancestral forms using ancestral and derived traits
Ancestral traits – a trait shared with a common ancestor
Derived traits – a trait that differs from the ancestral trait within a lineage

7. Ancestral traits – a trait shared with a common ancestor
Derivedtraits – a trait that differs from the ancestral trait within a lineage

8. Phylogeny
A hypothesis about the evolutionary relationships among groups of species
Phylogenies can be based on morphology
e.g., comparative anatomy such as homologous structures (arm of a person, wings of a bird, flipper of a whale)
Most recent phylogenies are based on molecular similarities
e.g., similarities of mitochondrial DNA (mtDNA) sequences, amino acid sequences of the protein hemoglobin
The proposed relationships between the species are shown in a phylogenetic tree
Phylogeny is a history that indicates hypothesized evolutionary paths!

9. Phylogenetic Tree is like a family tree…
Roots or base  common ancestor
primitive characteristics: general characteristics that are shared by all the species that evolved from it
Forks in each branch  2 new species
derived characteristics: additional traits that create new species who have evolved from the common ancestor
shared derived characteristics: specific traits shared by groups of organisms
Upper ends of branches  present-day descendant species
The more derived characteristics organisms share, the closer the evolutionary relationship!
Phylogenic trees show the relationships between different organisms that are thought to have a common ancestry. The common ancestor at the base of the tree has general characteristics that are shared by all the species that evolved from it. These features are called primitive characteristics. New species that evolve from the common ancestor have a new feature called derived characteristics.

10. Cladistics
A scientific classification scheme that is based on phylogeny.
It only identifies and considers those characteristics of organisms that are evolutionary innovations - new characteristics that arise as lineages evolve over time.
Each new group of related species has one common ancestor, and organisms retain some ancestral characteristics.

11. Species A, B, C & D all exist in modern times
Recent
time
Past
DELETE???
Species A, B, C & D all exist in modern times 11

13. Species A, B, and C are extinct.
Species C & D shared a common ancestor more recently than B & D.
Species D will display the most advanced morphological characteristics.
Species D is most closely related to Species A.
Species D evolved from Species C.
DELETE???
Sp A
Sp B
Sp C
Sp D 13

14. Illustrating Phylogeny - Cladograms
patterns of shared characteristics.
diagram that shows the evolutionary relationships among a group of organisms 14

15. classify organisms according to the order in time at which branches arise along its phylogenetic tree
What shared derived character is common to the salmon, lizard, and rabbit, but not the lamprey?

16. Outgroup Analysis
Determines which characteristics in a given group of taxa are primitive or which are derived
An outgroup is usually a taxon that represents the primitive condition.
The amphioxus (figure on previous slide) is the outgroup because it is a chordate without vertebrae. Also because of evidence based on the fossil record, and development.
All other taxa are grouped according to shared derived characters.
The more derived structures two organisms share, the closer is their evolutionary relationship -- that is, the more recently their common ancestor lived.
Close relationships are shown by a recent fork from the supporting branch – the closer the fork in the branch between two organisms, the closer their relationship.

17. Determining which similarities between species are relevant to grouping the species in a clade is a challenge.
It is important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.
These two desert plants are not closely related but owe their resemblance to analogous adaptations to very
similar environments.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

18. For example, based on the number of heart chambers alone, birds and mammals, both with four chambers, appear to be more closely related to each other than lizards with three chambers.
But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.
The four chambered hearts are analogous, not homologous, leading to a misleading cladogram.

19. As a general rule, the more homologous parts that two species share, the more closely related they are.
Also, the more complex two structures are, the less likely that they evolved independently.
For example, the skulls of a human and chimpanzee are composed not of a single bone, but a fusion of multiple bones that match almost perfectly.
It is highly improbable that such complex structures matching in so many details could have separate origins.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

20. Analyzing the distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.

21. Systematists can use cladograms to place species in the taxonomic hierarchy.
For example, using turtles as the outgroup, we can assign increasing exclusive clades to finer levels of the hierarchy of taxa.
Fig
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

22. Cladistic Analysis
As a general rule, the more homologous characters shared by two species, the more closely they are related
Sequences of DNA & RNA (nucleotides) and proteins (amino acids) are used as characters; as a general rule, the more recently two species shared a common ancestor, the more similar their sequences

23. All similar characters
Cladistic Analysis
Shared Primitive Characters (ancestral)
Analogies
All similar characters
Homologies
This flowchart summarizes types of similarities among species…
Shared Derived Characters(unique to a clade)
The sequence of branching in a cladogram then represents the sequence in which evolutionary novelties (shared derived characters) evolved

24. Ingroup = the group whose relationships we are trying to resolve
Cladistic Analysis
Ingroup vs. Outgroup
Ingroup = the group whose relationships we are trying to resolve
Fig

25. Cladistic Analysis Ingroup vs. Outgroup
Outgroup = a species (or group) known to have an older most recent common ancestor with the ingroup than the ingroup’s most recent common ancestor
Fig

26. Cladistic Analysis Ingroup vs. Outgroup
An outgroup helps identify shared ancestral and shared derived characters (unique to a clade)
Fig

27. Cladistic Analysis
The most parsimonious tree is the one that requires the fewest evolutionary events (appearance of shared derived characters)
Fig

28. Cladistic Analysis Parsimony
On this most parsimonious cladogram, each key character originated (evolved) once
Fig