1. CHAPTER 26 TAXONOMY AND SYSTEMATICS Brenda Leady, University of Toledo
Prepared by
Brenda Leady, University of Toledo
Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

2. Taxonomy and systematics
Field of biology concerned with the theory, practice, and rules of classifying living and extinct organisms and viruses
Systematics
Study of biological diversity and the evolutionary relationships among organisms, both extinct and modern
Taxonomic groups are now based on hypotheses regarding evolutionary relationships derived from systematics

3. Taxonomy Hierarchical system involving successive levels
Each group called a taxon
Domain
Highest level
All of life belongs to one of 3 domains
Bacteria, Archaea, and Eukarya

6. Binomial nomenclature
Genus name and species epithet
Genus name always capitalized
Species epithet never capitalized
Both names either italicized or underlined
Rules for naming established and regulated by international associations

7. Domains similar but different
Scientists think all life originated from primordial prokaryotic cells between 4.0 and 3.5 bya
Soon after, 2 prokaryotic domains, Bacteria and Archaea, diverged
bya first unicellular eukaryotic species
Multicellular eukaryotes arose about 1.5 bya

8. Similarities DNA is used as the genetic material
All species use the same genetic code (with only a few rare codon exceptions)
Messenger RNA encodes the information to produce proteins
Transfer RNA and ribosomes are needed to synthesize proteins, using mRNA as a source of genetic information
All living cells are surrounded by a plasma membrane
Certain metabolic pathways, such as glycolysis, are found in all three domains

9. These traits are universal because all 3 domains evolved from a common ancestor
Dissimilarities exist because major evolutionary changes have occurred since the time that the three domains diverged

11. Domain Bacteria Domain Archaea Diverse collection of many species
So widespread only generalizations about their ecology
Key to success is metabolic diversity
Come in a myriad of shapes and sizes
Domain Archaea
Less diverse than Bacteria
Discovered in 1970s
Many found in extreme environments
Most are extreme halophiles, methanogens or hyperthermophiles
Not entirely restricted to extreme environments

13. Domain Eukarya
4 traditional kingdoms
Protista
Fungi
Plantae
Animalia

15. Kingdom Protista Simplest eukaryotes
Most unicellular but some are colonial or simple multicellular
Some photosynthesize while others eat bacterial or other protists
Most live in aquatic habitats
Leftover organisms not put in other 3 kingdoms

17. Kingdom Fungi Yeasts, molds, mushrooms
Present worldwide in aquatic and terrestrial environments
Many symbiotic with plants
Cell walls contain chitin
Most multicellular
Mass of hyphae combine to make mycelium

19. Kingdom Plantae Multicellular Almost all capable of photosynthesis
Mosses, ferns, conifers, flowering plants
Cell wall made primarily of cellulose

21. Kingdom Animalia Multicellular and eat others for food
More than 1 million species
Sponges, worms, insects, mollusks, fish, amphibians, birds, reptiles, mammals
Most ingest food and digest it in an internal cavity
Bodies composed of cells organized into tissues (except sponges)
Capable of complex and rapid movement
Nervous system
Lack a rigid cell wall

23. Systematics
Phylogeny – evolutionary history of a species or group of species
Gather morphological or molecular data
Use mathematical strategies to analyze data
Construct evolutionary trees
Molecular data has caused many revisions

24. Phylogenetic tree Diagram that describes phylogeny
A hypothesis of evolutionary relationships among various species
Based on available information
New species can be formed by
Anagenesis – single species evolves into a different species
Cladogenesis – a species diverges into 2 or more species

26. Monophyletic group or clade
Group of species, taxon, consisting of the most recent common ancestor and all of its ancestors
Smaller and more recent clades are subsets of larger clades
For larger taxa, common ancestor existed a long time ago (kingdom)
For smaller taxa, common ancestor more recent (family or genus)

28. Homology
Similarities among various species that occur because they are derived from a common ancestor
Bat wing, human arm and cat front leg
Genes can also be homologous

29. Morphological analysis
First systematic studies focused on morphological features of extinct and modern species
Convergent evolution (traits arise independently due to adaptations to similar environments) can cause problems

31. Molecular systematics/clocks
Analyzing genetic data to identify and study genetic homology and reconstruct phylogenetic trees
DNA sequences from closely related species are more similar to each other than to sequences from more distantly related species

32. Molecular clock
Favorable mutations rare and detrimental mutations eliminated
Most mutations are neutral
If neutral mutations occur at a constant rate they can be used to measure evolutionary time
Longer periods of time since divergence allows for a greater accumulation of mutations
Not perfectly linear
Not all organisms evolve at the same rate

34. Primate evolution example
Evolutionary relationships derived by comparing DNA sequences in a mitochondrial gene
3 branch points to examine (A,D, E)
A- common ancestor diverges into siamangs and other species
Gene in siamangs more different than the gene in the other 7 species
Humans and siamangs have more differences than humans and chimpanzees because there has been more time for them to accumulate differences
2 chimp species diverged recently and have very similar gene sequences

36. Cladistic approach
Reconstructs phylogenetic tree by considering various possible pathways of evolution and then proposing plausible tree
Phylogenetic trees or cladograms
Compares traits shared or not shared
Shared trait – shared primitive character or symplesiomorphy
Not shared – shared derived character or synapomorphy

37. Branch point – 2 species differ in shared derived characters
Ingroup – monophyletic group we are interested in
Outgroup – species or group of species that is most closely related to an ingroup
All traits shared by the outgroup and the ingroup must have arisen in a common ancestor that predates the divergence of the 2 groups

39. Cladogram can also be constructed with gene sequences
7 species called A- G
A mutation that changes the DNA sequence is analogous to a modification of a characteristic

41. Constructing a cladogram
Choose species
Choose characters
Determine order of character states
primitive or derived?
Group species (or higher taxa) based on shared derived characteristics

42. Build a cladogram based on
All species (or higher taxa) are placed on tips in the phylogenetic tree, not at branch points
Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified
All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once
Choose the most likely cladogram among possible options

43. Strategies for a likely cladogram
Challenge in a cladistic approach is to determine the correct order of events
May not always be obvious which traits are ancestral and came earlier, and which are derived and came later in evolution
Different approaches can be used to deduce the correct order
Analyze fossils and determine the relative dates that certain traits arose
Assume that the best hypothesis is the one that requires the fewest number of evolutionary changes (principle of parsimony)
Maximum likelihood and Bayesian analysis for gene sequence data

44. Example 4 taxa (A-D) A is the outgroup 3 potential trees
Has all the primitive states
3 potential trees
Tree 3 requires fewest number of mutations so is the most parsimonous

46. Ancient DNA analysis or molecular paleontology
Cooper and Colleagues Extracted DNA from Extinct Flightless Birds and Then Compared It with DNA from Modern Species to Reconstruct Their Phylogeny
Ancient DNA analysis or molecular paleontology
Under certain conditions DNA samples may be stable as long as 50,000 – 100,000 years
Discovery based sciences- gather data to propose a hypothesis
Sequences are very similar
New Zealand colonized twice by the ancestors of flightless birds
First by moa ancestor, then by kiwi ancestor

49. Ideal goal of taxonomy to place organisms in monophyletic groups

50. Many recent models propose several major groups, supergroups, as a way to organize eukaryotes into monophyletic groups
Shows that protists played a key role in the evolution of diverse eukaryote species

51. Due to Horizontal Gene Transfer, the Tree of Life Is Really a “Web of Life”
Vertical evolution involves changes in species due to descent from a common ancestor
Horizontal gene transfer is the transfer of genes between different species
Significant role in phylogeny of all living species
Still prevalent among prokaryotes but less common in eukaryotes
Horizontal gene transfer may have been so prevalent that the universal ancestor may have been a community of cell lineages