1. PHYLOGENY AND CLASSIFICATION
Module 2 Session 2

2. Evolution ACCOUNTS FOR LIFE’S diversity AND UNITY

3. TERMINOLOGY :
Classification is a very broad term which simply means putting things in classes
Taxonomy means giving names to organisms. It tends to go hand in hand with classification
Phylogeny traces the evolutionary history of species
Systematics is the process of trying to classify animals (or plants) according to their phylogeny.

4. Cladistics, also known as phylogenetic systematics.
It works by analyzing different taxa to find objective similarities and differences between them, and using those similarities and differences to derive a hierarchical structure showing which taxa are most similar to others
Cladistics groups organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants

5. TAXON: Each level of hierarchy represents a taxon.

7. LINKING CLASSIFICATION AND PHYLOGENY
. Classification and phylogeny do not always match New features may have emerged since last classified. DNA is a valuable tool used for classification. Classification does not reveal evolutionary history
Homo sapiens classification

8. exclusive inclusive Binomial Nomenclature: Use of Genus species names.
eg. Panthera pardus – leopard
exclusive
inclusive
Fig Taxonomic hierarchy

9. Phylum Chordata
Invertebrate chordates and vertebrate chordates including fish, sharks, amphibians, reptiles and mammals.
Derived characteristics

11. By studying inherited species' characteristics and other historical evidence, we can reconstruct evolutionary relationships and represent them on a "family tree," called a phylogeny. The phylogeny you see below represents the basic relationships that tie all life on Earth together.

12. ISSUES WITH classification (proposed by carolus linneaus)
DOES NOT REFLECT EVOLUTIONARY HISTORY DOES NOT SHOW EVOLUTIONARY RELATIONSHIP BETWEEN GROUPS PHYLOGENETIC TREES REFLECT EVOLUTIONARY RELATIONSHIPS

13. UNDERSTANDING PHYLOGENETIC TREES

14. where lineages diverge Taxon A
Branch point:
where lineages diverge
Taxon A
Taxon B
Sister
taxa
Taxon C
ROOTED
Taxon D
POLYTOMY
Taxon E
ANCESTRAL
LINEAGE
Taxon F
Figure 26.5 How to read a phylogenetic tree.
Basal
taxon
Taxon G
This branch point
represents the
common ancestor of
taxa A–G.
This branch point forms a
polytomy: an unresolved
pattern of divergence.
DIVERGED
EARLIER THAN
OTHERS

15. CREATING A PHYLOGENETIC TREE-ACTIVITY-
Molecular Phylogeny of Primates

16. What CAN WE and Cannot Learn from Phylogenetic Trees?
Phylogenetic trees show patterns of descent, not phenotypic similarity
Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage
It should not be assumed that a taxon evolved from thE taxon next to it, only that they shared a common
ancestor
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17. MORPHOLOGY AND MOLECULAR DATA ARE USED TO CONSTRUCT PHYLOGENETIC TREES

18. Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution
Convergent Evolution occurs when environmental conditions and natural selection produce similar adaptations in different species
Marsupial ,Mole
Eutheriam Mole
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19. 1 1 2 Deletion 2 1 2 Insertion 3 1 2 4 1 2 DNA ALIGNMENT USING
Figure 1 1
DNA ALIGNMENT USING
SOFTWARE HELPS
CONSTRUCT PHYLOGENETIC TREES 2
Deletion 2 1 2
Insertion 3 1
Figure 26.8 Aligning segments of DNA. 2 4 1 2

20. HOMOLOGOUS GENES

21. CONSTRUCTING PHYLOGENETIC TREES

22. HOMOLOGOUS CHARACTERISTICS ARE USEFUL IN CONSTRUCTING PHYLOGENETIC TREES AS THEY SHOW SHARED ANCESTRY

23. Cladistics is method of hypothesizing relationships among organisms; it is a method of inferring phylogeny from homologous characters Cladogram: diagram showing evolutionary relationship with respect to shared characters.
Cladogram

24. CLADE: INCLUDE ANCESTRAL SPECIES
AND ALL OF ITS DESCENDANTS

25. CLADES
MONOPHYLETIC: ANCESTRAL SPECIES AND DESCENDANTS POLYPHYLETIC GROUP: INCLUDES TAXA WITH WITH DIFFERENT ANCESTORS PARAPHYLETIC GROUP: ANCESTRAL GROUP WITH SOME BUT NOT ALL OF ITS DESCENDANTS

26. SHARED ANCESTRAL VS SHARED DERIVED CHARACTERS
CHARACTERS THAT ARE SHARED BY ORGANISMS AND RELATED TO AN ANCESTOR ARE SHARED ANCESTRAL CHARACTERISTICS CHARCTERS THAT ARE SHARED BY SOME ORGANISMS BUT NOT WITH THE ANCESTOR ARE REFERRED TO AS SHARED DERIVED CHARACTERS For eg Backbone in mammals and vertebrates is shared ancestral whereas hair is a derived character unique to mammals

27. PHYLOGENETIC TREES WITH PROPORTIONAL BRANCH LENGTHS
Figure 26.13
PHYLOGENETIC TREES WITH PROPORTIONAL BRANCH LENGTHS
MORE GENETIC CHANGES
In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
PALEOZOIC
MESOZOIC
CENOZOIC
542
251
65.5
Present
Millions of years ago
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28. From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: (Monera) (prokaryotes), (Protista), Plantae, Fungi, and Animalia
More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
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29. Eukarya Bacteria Archaea Figure 26.21
Land plants
Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi
Sulfolobus
Green
nonsulfur bacteria
Thermophiles
(Mitochondrion)
Figure The three domains of life.
Spirochetes
Halophiles
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
Bacteria
Methanobacterium
Cyanobacteria
Archaea
(Plastids, including
chloroplasts)

30. Why are there some similar genes in the three domains?
There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms
Horizontal gene transfer complicates efforts to build a tree of life

31. An Organism’s Evolution History is Documented in its Genome
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Species A
Species B
Orthologous genes
Orthologous Gene Families. The colored bands indicate regions of the gene where a mutation in the DNA sequence occurred.
(figure not in textbook)

32. Orthologous genes refer to homologous genes found in two different species that were inherited from a common ancestor.
Similarity or divergence in the DNA sequence between orthologous genes found in two species can be used to reveal phylogenetic relationships.
In the time since two species diverged from a common ancestor, random mutations create slight difference in DNA sequence.
The longer the time period since divergence from a common ancestor, the greater the variation in the DNA sequence of the orthologous genes.

33. Orthologous genes can extend over long evolutionary distances.
A comparison of the human and mice genomes reveals that > 90% of human genes are detectably orthologous to mice genes.
Comparing human genes to yeast (single-celled eukaryote) reveals that a large percentage of human genes are detectably orthologous to yeast genes, even though a billion years of evolution separate humans from yeast.
Examples of orthologous gene families include:
Hox genes – found in all animals, regulates embryonic development.
FOXP2 genes – found in all vertebrate animals, regulates the development of vocalization.