1. Lesson 3: Phylogeny & Modern Taxonomy
Recall that the fundamental unit of biodiversity is the species
Today’s lesson focuses on:
Methods to define a species
Defining and using phylogenies to classify and organize species

2. Classification of species is a difficult task partly because there is no one clear-cut way to single handily define a species.
Furthermore, as new species are being identified, we need to find ways to determine how closely related it is to other species
There are different ways to categorize a species

3. Identifying Species: Using the Species Concept
Morphological Species Concept
2. Biological Species Concept
3. Phylogenetic Species Concept

4. 1. Morphological Species Concept
Focus on the morphology of an organism
Morphology refers to: body size, shape, and other structural features
Organisms are compared and scientists decide whether similar organisms represent different species

5. 1. Morphological Species con’t
ADVANTAGE:
Simple to use
Most widely used by people in general
DISADVANTAGE:
Too much variation within a species

6. Problems with Morphological based classification

7. 2. Biological Species Concept
Focus on similar characteristics AND the ability of organisms to interbreed in nature and produce viable, fertile offspring

8. 2. Biological Species con’t
ADVANTAGE:
It is widely used by scientists
DISADVANTAGE:
Can’t be applied for species that reproduce asexually
Uncertain for populations that are physically separated and don’t have the opportunity to breed naturally
Can’t be applied to fossil species, which are no longer reproducing

9. 3. Phylogenetic Species Concept
Focus on evolutionary relationships among organisms
A species is defined as a cluster of organisms that is distinct from other clusters and shows a pattern of relationship among organism
Ex: when a prehistoric species branches into two species over time, it becomes two different phylogenetic species. Ie: bacteria and archaea are two different phylogenetic species that branched from a common ancestor. As more DNA analysis becomes available, this is becoming the more popular concept.

10. 3. Phylogenetic Species con’t
ADVANTAGES:
Can be applied to extinct species
Considers information about relationships among organisms learned from DNA analysis
DISADVANTAGE:
Evolutionary histories are not known for all species

11. Phylogeny....we need to know a bit about evolution
Evolution: the scientific theory that describes changes in species over time and their shared ancestry.
All living things are descended from a common ancestor.
When scientists say that two species are closely related, it means that they share a common ancestor in their recent, evolutionary, history.

12. Which are more closely related?

14. More About Phylogeny
Phylogeny refers to the evolutionary history of a species
Phylogenies are determined through:
Developmental Traits (Embryology)
Structural Traits (Homology)
Molecular Traits (Genetics & Molecular Biology)
How do we determine if two species have a shared phylogeny? Use anatomical, physiological and DNA evidence and interpret it to make hypotheses about evolutionary history.

15. Organisms likely share a common ancestry if:
Phylogeny con’t:
Organisms likely share a common ancestry if:
They show similar stages of embryological development
They have similar anatomical structures, regardless of function
They are genetically similar

16. Embryological Similarities
Evidence of common ancestry:
Embryological Similarities
It has been observed that the early stages of embryo development are similar in closely related species
All vertebrate embryos go through a state in which they have gill pouches similar to those of fish and a postanal tail.

17. Recapitulation Theory:
History:
Recapitulation Theory:
Theory proposed by embryologists in the 19th century (Ernst Haeckel)
The notion that “ontogeny recapitulates phylogeny” is an overstatement. Some scientists proposed that the stages of embryonic development was a replay of its evolutionary history. This is generally not accepted; however, what recapitulation does occur is a replay of embryonic states, not a sequence of adultlike states of ever more advanced vertebrates
Ontogeny: the development of an individual organism
Phylogeny: evolutionary history of the species
Recapitulates: replay

18. If ontogeny recapitulates phylogeny, then the embryonic development of a chick would look like the above picture. This is not the case. Instead, we see it more like below. The early embryos of the chick will be similar to the early embryos of reptiles or fish at points in its development, but it does not recapitulate the adult forms of ancestors. .

19. Anatomical Similarities - Homology
Evidence of common ancestry:
Anatomical Similarities - Homology
Homologous Structures: structures of different organisms that are similar in form
Even though each animal uses its forelimbs for different functions, it’s bone structures are similar.

20. Molecular Similarities
Evidence of Common Ancestry:
Evolutionary relationships among species are reflected in DNA and proteins
Two species that have matching gene and protein sequences would share a common ancestor
Humans and
chimpanzee share 99.9%
identical DNA sequence

21. International Barcode of Life Project
Paul Herbert of the U of Guelph started the IBL project in 2010 to catalogue every species using a DNA barcode
Applications of Barcoding
iBOL

22. Traditional Method of Classification

23. MODERN TAXONOMY:
Phylogenetic Tree
Phylogenetic Tree: a diagram depicting the evolutionary relationships between different species or groups (previously called cladogram)

24. Phylogentic trees can be used for extinct species as well!

26. Phylogenetic Trees differ from Dichotomous keys because Dichotomous keys focus on catagories based on morphology (physical features) and Phylogenetic trees focus on catagories based on common ancestors (evolution).

27. Clades
Clades: a taxonomic group that includes a single common ancestor and all its descendants. Each clade on a phylogenetic tree can be thought of as a branch on the tree of life.

28. Importance of Classification
Drugs – narrow your search for pharmaceuticals to closely related species that produce valuable proteins/chemicals
Disease – trace the transmission of diseases; disease spread more rapidly between species that share common genetics
Agriculture – increase crop yield and resistance by cross-breeding related species; biological control of natural predators, parasites, disease
Conservation – ex: In 2001 African forest elephant, Loxodonta cyclotis was declared a different species from African bush elephant, Loxodonta africana; only Loxodonta africana was protected
Why do we care about how species are evolutionarily related?

29. Thinking Question
In northwestern Ontario, there are two similar-looking garter snakes: the red-sided garter snake and the eastern garter snake. The two interbreed successfully in nature in that part of Ontario, producing offspring that have a mix of physical traits of the two. The eastern garter snake also co-exists in southern Ontario with another very similar snake, the eastern ribbon snake. However, these two snakes are not known to interbreed successfully. Infer whether these three snakes are the same species or not. Explain your reasoning.

30. Complete the Tutorial on How to Read a Phylogenetic Tree