1. Systematics and the Phylogenetic Revolution
Chapter 25

2. Outline
The Classification of Organisms
Systematics
Analogy versus Homology
Kingdoms
Domains
Viruses
Impact of Molecular Cladistics
Protists

3. The Classification of Organisms
Classification - multilevel grouping of individuals
organisms first classified by Aristotle over 2,000 years ago
Eventually groups started to be formed and referred to as genera (singular, genus).
Starting in the middle ages, names began to be systematically written down using Latin.

4. The Classification of Organisms
Classification scheme of the Middle Ages (polynomial system) was replaced with a binomial system by Linnaeus about 250 years ago.
polynomial - strings of Latin words and phrases containing up to 12 words
binomial - two-part name for each species

5. Species Names
Taxa - group of organisms at a particular level in a classification system (taxonomy)
By convention:
first word of binomial name is genus and is always capitalized
second word refers to particular species and is not capitalized
together form scientific name, written in italics

6. The Taxonomic Hierarchy
Species
Genus
Family
Order
Class
Phylum
Kingdom
Domain

8. Evolutionary Relationships
Systematics - reconstruction and study of evolutionary relationships
construct phylogeny by looking at similarities and differences between species
Cladistics - distinguishes ancestral from shared characters
only shared derived characters are considered in determining evolutionary relationships

9. Cladistics
Outgroup comparison is used to assign polarity.
A species or group of species closely related to, but not a member of, the group under study is designated an outgroup.
Character states exhibited by the outgroup are assumed ancestral, and other states are considered derived.

10. Cladistics
A cladogram is constructed that depicts hypothesis of evolutionary relationships
Species that share derived characters belong to a clade.
A derived character shared by clade members is a synapomorphy of the clade.
Each node represents a hypothetical ancestral species.

11. Cladogram

12. Cladogram
Plesiomorphies - ancestral states
Symplesiomorphies - shared ancestral states
Homoplasies - derived characters that are lost as species re-evolve the ancestral state
Principle of parsimony favors the hypothesis that requires the fewest assumptions

13. Cladogram
Systematics and classification
A monophyletic group includes the most recent common ancestor of the group and all of its descendants.
A paraphyletic group includes the most recent common ancestor of the group, but not all of its descendents.
A polyphyletic group does not include the most recent common ancestor of all the members.

16. Analogy Versus Homology
Examination of the characters on a cladogram can provide insight on how they evolved, how many times they evolved, and how complex characters evolved.

17. The Kingdoms of Life
Most biologists use a six-kingdom system.
Animalia
Plantae
Fungi
Protista
Archaebacteria
Bacteria
Domains - taxonomic level above kingdoms

18. Classifying Living Organisms

19. Tree of Life

20. Domain Archaea
Share key characteristics:
cells wall lack peptidoglycan
possess unusual lipids and ribosomal RNA
Three general categories
methanogens - obtain energy using hydrogen gas to reduce carbon dioxide to methane gas

21. Domain Archaea
extremophiles - grow under extreme conditions
thermophiles (heat)
halophiles (salt)
pH tolerant
pressure tolerant
nonextreme archaebacteria - grow in same environment as eubacteria

22. Domain Bacteria
most abundant organisms on earth
most taxonomists recognize major groups
as different from archaebacteria as from eukaryotes

23. Domain Eukarya
Appear in fossil record only about 1.5 billion years ago.
complex cellular organization
Fungi, Plants, and Animals are well-defined evolutionary groups.
largely multicellular
Diversity among protists is much greater than within or between Fungi, Plants, and Animals.

24. Domain Eukarya
With few exceptions, all modern eukaryotic cells possess energy-producing organelles (mitochondria).
Some protist phyla have also acquired chloroplasts and are photosynthetic.
Mitochondria and chloroplasts are both believed to have entered early eukaryotic cells by endosymbiosis.

25. Domain Eukarya
Key characteristics
Compartmentalization
Discrete compartments provide evolutionary opportunities for increased specialization within the cell.
Multicellularity
Activities of individual cells are coordinated and the cells themselves are in contact.

26. Domain Eukarya
Key characteristics
Sexuality
alternate between syngamy and meiosis

27. Viruses: A Special Case
Viruses do not satisfy the basic criteria of life, thus are not living organisms.
cannot logically be placed in any of the kingdoms
appear to be fragments of nucleic acids originally derived from genome of a living cell
infect organisms at all taxonomic levels

28. Viral Diversity

29. Impact of Molecular Cladistics
Traditional classification systems are based on similar traits, but do not take into account evolutionary relationships.
no clear basis for determining relative importance of traits
Systematic phylogenetics is based on evolutionary relationships using cladistics.
Each clade has a single common ancestor.

30. Impact of Molecular Cladistics
Molecular systematics labels protists as paraphyletic.
Land plants are members of Streptophyta.
Segmentation may have arisen twice.
Insects may be a sister group of crustaceans.
Eutherian mammals may be reclassified.

31. Fall of Kingdom Protista

32. Major Mammalian Groups

33. Summary
The Classification of Organisms
Systematics
Analogy versus Homology
Kingdoms
Domains
Viruses
Impact of Molecular Cladistics
Protists