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  1. 1. Classification
  2. 2. The Need for Order <ul><li>Evolution has produced enormous diversity </li></ul><ul><ul><li>1.4 million species described </li></ul></ul><ul><li>Scientists need a method to order organisms logically, to understand relationships between organisms </li></ul><ul><li>Taxonomy : </li></ul><ul><ul><li>The science of classifying organisms on the basis of their similarities </li></ul></ul>
  3. 3. Systematics <ul><li>The study of biological diversity in an evolutionary context. </li></ul><ul><ul><li>Connects classification to phylogeny </li></ul></ul><ul><ul><li>Classification based on evolutionary history </li></ul></ul><ul><li>Traditional taxonomy employed a hierarchical system of classification </li></ul><ul><li>Modern phylogenetic systemics is based on cladistic analysis </li></ul><ul><li>Systematics allows us to infer phylogeny from molecular data </li></ul>
  4. 4. The History of Taxonomy <ul><li>Aristotle, a Greek philosopher, proposed one of the first systems - 350 B.C. </li></ul><ul><li>Divided living thing into 2 groups: </li></ul><ul><ul><li>plants & animals </li></ul></ul><ul><ul><li>Further divided animals by habitat and behavior & plants by size and structure </li></ul></ul><ul><li>This system was used for 2000 years </li></ul><ul><ul><li>Produced many errors based on what we know now </li></ul></ul><ul><li>By mid-1700’s naturalists were discovering many new life forms. </li></ul><ul><ul><li>Because different scientists used different principles to classify, understanding & communication was difficult </li></ul></ul>
  5. 5. Linnaeus <ul><li>Carolus Linnaeus </li></ul><ul><ul><li>a Swedish Botanist </li></ul></ul><ul><ul><li>mid 1700’s </li></ul></ul><ul><ul><li>proposed a system of classification </li></ul></ul><ul><li>Organisms with similar structures should be placed in the same taxonomic group. </li></ul><ul><li>We still use Linnaeus’s basic system </li></ul><ul><li>Linnaean system has 2 main features: </li></ul><ul><ul><li>A 2 part name for each species </li></ul></ul><ul><ul><li>A hierarchical classification into broader & broader groups. </li></ul></ul>
  6. 6. Binomial Nomenclature <ul><li>Use of common names can lead to confusion </li></ul><ul><li>Examples: </li></ul><ul><ul><li>mountain lion, puma, cougar = same animal </li></ul></ul><ul><ul><li>starfish, jellyfish, silverfish = misleading relationships </li></ul></ul><ul><li>Linnaeus suggested use of scientific names </li></ul><ul><li>Scientific name = genus + species </li></ul><ul><ul><li>genus is capitalized, species is not </li></ul></ul><ul><li>Called binomial nomenclature </li></ul><ul><ul><li>bi=2 </li></ul></ul><ul><li>Genus and species names are generally Latin </li></ul>
  7. 7. The Species <ul><li>Linnaeus’s smallest taxonomic group was the species </li></ul><ul><li>Similar species were grouped in a larger category, genus . </li></ul><ul><ul><li>Similar genera were grouped into a family , then order , class , phylum , kingdom </li></ul></ul><ul><li>Example: </li></ul><ul><ul><li>dogs, wolves & jackals are different species, but the same genus </li></ul></ul>
  8. 8. Defining a Species <ul><li>The most basic grouping used in biological classification. </li></ul><ul><li>A species differs from other similar organisms in at least one characteristic </li></ul><ul><li>Cannot interbreed freely with other species to produce fertile offspring. </li></ul><ul><li>Species evolve and change, so definition is not always sharp </li></ul>
  9. 9. Linnean Taxonomy <ul><li>Created a hierarchy </li></ul><ul><li>As we move from species to kingdom, each category contains more organisms, and the organisms are less similar. </li></ul>
  10. 10. The Linnaean Hierarchy <ul><li>MOST SPECIFIC FEWEST ORGANISMS Species </li></ul><ul><ul><li> Genus </li></ul></ul><ul><ul><li> Family </li></ul></ul><ul><ul><li> Order </li></ul></ul><ul><ul><li> Class </li></ul></ul><ul><ul><li> Phylum </li></ul></ul><ul><ul><li> Kingdom </li></ul></ul><ul><ul><li> [Domain] </li></ul></ul><ul><li>LEAST SPECIFIC MOST ORGANISMS </li></ul>
  11. 11. <ul><li>Dogs, wolves, coyotes are separate species, but have similar characteristics. </li></ul><ul><li>All are genus Canis. </li></ul><ul><ul><li>Dog = Canis familiaris ; Wolf = Canis lupus ; Coyote = Canis latrans </li></ul></ul><ul><li>Family: Canidae </li></ul><ul><ul><li>also includes foxes - genus Vulpus </li></ul></ul><ul><li>Order: Carnivora </li></ul><ul><ul><li>includes other meat eaters such as cats, bears </li></ul></ul><ul><li>Class: Mammalia </li></ul><ul><ul><li>includes rodents, monkeys, many others that produce milk </li></ul></ul><ul><li>Phylum: Chordata </li></ul><ul><ul><li>all fish, birds, reptiles & other animals with a spinal cord </li></ul></ul><ul><li>Kingdom: Animalia </li></ul><ul><ul><li>all living things we think of as animals </li></ul></ul>
  12. 12. The Kingdom <ul><li>Often the first level of classification </li></ul><ul><ul><li>The Domain is an even broader taxonomic level now embraced by many scientists </li></ul></ul><ul><li>Linnaeus proposed a system with 2 kingdoms: </li></ul><ul><ul><li>Autotrophs </li></ul></ul><ul><ul><li>organisms that produce their own food (the plant kingdom) </li></ul></ul><ul><ul><li>Hetertrophs </li></ul></ul><ul><ul><li>organisms that depend on others for food (animal kingdom) </li></ul></ul><ul><li>As we have been able to explore the microscopic world and examine cell structure this was not sufficient </li></ul>
  13. 13. Cell Types <ul><li>All living things are made of cells </li></ul><ul><li>Cells help us understand relationships between organisms </li></ul><ul><li>Based on cell structure, organisms were classified as prokaryotes or eukaryotes </li></ul><ul><li>Prokaryotes : </li></ul><ul><ul><li>bacteria - earliest living cells </li></ul></ul><ul><ul><li>no nucleus or membrane enclosed organelles, rigid cell wall </li></ul></ul><ul><ul><li>no mitosis </li></ul></ul><ul><li>Eukaryotes </li></ul><ul><ul><li>usually larger </li></ul></ul><ul><ul><li>have a nucleus and other membrane enclosed organelles </li></ul></ul><ul><ul><li>DNA organized in chromosomes </li></ul></ul><ul><ul><li>cell division includes mitosis </li></ul></ul>
  14. 14. The Five Kingdom System <ul><li>The first modern classification system recognized 5 kingdoms </li></ul><ul><li>All prokaryotes were kingdom Prokaryotae (or Monera ) </li></ul><ul><li>Eukaryotes were divided into 4 kingdoms: </li></ul><ul><li>Plantae , Animalia , Fungi , Protista </li></ul>
  15. 15. The Six Kingdom System <ul><li>Further study of bacteria (kingdom Prokaryotae ) show there are really two distinct groups </li></ul><ul><li>So we now use a 6 kingdom system </li></ul><ul><ul><li>An updated version of the 5 kingdom system </li></ul></ul><ul><li>Divides prokaryotes into 2 kingdoms: </li></ul><ul><ul><li>Archebacteria : ancient bacteria </li></ul></ul><ul><ul><li>Eubacteria : true bacteria </li></ul></ul>
  16. 16. The Prokaryote Debate <ul><li>More recent analysis of prokaryotes has shown that these two groups of bacteria are very different: </li></ul><ul><li>The Eubacteria </li></ul><ul><ul><li>Include five clades: proteobacteria, chlamydia, spirochetes, gram-positive bacteria, cyanobacteria </li></ul></ul><ul><li>The Archebacteria </li></ul><ul><ul><li>Include euryarchaeota, crenarchaeota </li></ul></ul><ul><ul><li>Confined to extreme environments </li></ul></ul><ul><ul><li>Similar to early earth </li></ul></ul><ul><ul><li>More closely related to eukaryotes than to modern bacteria </li></ul></ul><ul><li>Led to addition of a taxonomic level broader than the kingdom: the domain </li></ul><ul><ul><li>Three domains: bacteria, archaea, eukarya </li></ul></ul>
  17. 17. The Last Common Ancestor <ul><li>Last universal common ancestor represents ancient divisions </li></ul><ul><li>Archbacteria are more closely related to eukaryotes than to other prokaryotes </li></ul>
  18. 18. The Three Domain System <ul><li>An alternative to the six kingdom system </li></ul><ul><li>Based on comparing sequences of ribosomal RNA </li></ul><ul><li>Groups living things in 3 broad categories called domains </li></ul>
  19. 19. The Eubacteria <ul><li>formerly Prokaryotae </li></ul><ul><ul><li>Included blue-green algae, bacteria and other micro-organisms that lack nuclei </li></ul></ul><ul><ul><li>A very diverse group </li></ul></ul>
  20. 20. The Plants <ul><li>Plantae </li></ul><ul><ul><li>Autotrophic organisms that produce food through photosynthesis </li></ul></ul><ul><ul><li>Multicellular </li></ul></ul><ul><ul><li>Develop from an embryo that lacks a blastula </li></ul></ul>
  21. 21. Divisions of the Plant Kingdom
  22. 22. The Fungi <ul><li>Fungi </li></ul><ul><ul><li>Develop directly from spores </li></ul></ul><ul><ul><li>Reproduce either sexually or asexually </li></ul></ul><ul><ul><li>Includes yeasts, molds, bracket fungi, mushrooms </li></ul></ul>
  23. 23. The Animals <ul><li>Animalia </li></ul><ul><ul><li>All organisms we think of as animals </li></ul></ul><ul><ul><li>All organisms developing from an embryo that has a blastula stage </li></ul></ul><ul><ul><li>Includes vertebrates and invertebrates – insects, worms, mollusks, fish, birds, reptiles, etc. </li></ul></ul>
  24. 24. The Protists <ul><li>Protista </li></ul><ul><ul><li>Remaining eukaryotes </li></ul></ul><ul><ul><li>Most are single celled </li></ul></ul><ul><ul><li>Includes algae, protozoa, slime molds, etc. </li></ul></ul><ul><ul><li>Have characteristics that are both plant and animal like </li></ul></ul>
  25. 25. Cladistic Analysis <ul><li>Attempts to build trees expressing phylogenetic relationships </li></ul><ul><li>This type of tree = cladogram </li></ul><ul><ul><li>A tree constructed from a series of dichotomies (choices) </li></ul></ul><ul><ul><li>2-way branching points </li></ul></ul><ul><ul><li>Each branch point represents the divergence of 2 species from a common ancestor </li></ul></ul><ul><ul><li>Sequence of branching symbolizes chronology </li></ul></ul><ul><li>Each evolutionary line in cladogram = clade </li></ul><ul><ul><li>A monophyletic group </li></ul></ul><ul><ul><li>Consists of an ancestral species and all its descendants </li></ul></ul>
  26. 26. Connecting Classification & Phylogeny
  27. 27. Cladograms ~ Phylogenetic Trees <ul><li>A family tree that shows the evolutionary relationships among groups of organisms </li></ul><ul><li>Can diagram divurgence of two species </li></ul><ul><li>Can also diagram divurgence of taxa more inclusive than species (family, order, etc.) </li></ul><ul><li>Phylogenetic trees are hypotheses </li></ul>
  28. 28. Cladistic Taxonomy
  29. 29. Basis of Classification <ul><li>Classification is based on homologies </li></ul><ul><ul><li>similarities that indicate related ancestry </li></ul></ul><ul><li>Structural homologies </li></ul><ul><ul><li>similarities of structure </li></ul></ul><ul><ul><li>example: limb pattern of reptiles, birds, mammals. </li></ul></ul><ul><ul><li>Fossil record </li></ul></ul><ul><ul><li>Modern organisms </li></ul></ul><ul><li>Biochemical homologies </li></ul><ul><ul><li>similarities of body substances (e.g. blood) or molecules (e.g. DNA). </li></ul></ul><ul><ul><li>These are recent tools and have helped clarify some classification problems </li></ul></ul><ul><li>Taxonomic classification is not permanent </li></ul><ul><ul><li>with new evidence, can change </li></ul></ul>
  30. 30. Analogies vs. Homologies <ul><li>Not all structural similarities are homologies </li></ul><ul><li>Not all similarities reflect common ancestry </li></ul><ul><li>Convergent evolution produces similarities in unrelated species </li></ul><ul><li>These are referred to as analogies </li></ul><ul><li>Can confuse conventional classification </li></ul>
  31. 31. Shared Derived Characteristics <ul><li>Study of common characteristics can be used to create a cladogram </li></ul><ul><li>Shared derived characteristics establish evolutionary relationships </li></ul><ul><li>Derived character: </li></ul><ul><ul><li>a feature that evolved only within the group under consideration </li></ul></ul>
  32. 32. Characteristics Shape Cladograms
  33. 33. Molecular Data <ul><li>Can infer phylogeny from molecular data </li></ul><ul><li>The more recently two species branched from a common ancestor, the more similar the DNA </li></ul><ul><li>Rates of change of DNA over evolutionary time vary from one part of the genome to another </li></ul><ul><li>Different sequences are studied in determining closer relationships than those used for more distant relationships. </li></ul>
  34. 34. The Principle of Parsimony <ul><li>The simplest explanation that accounts for all of the available data is the best answer </li></ul><ul><li>Occam’s razor </li></ul><ul><li>Construct phylogentic trees that represent the smallest number of evolutionary changes </li></ul>
  35. 35. Phylogenetic Trees are Hypotheses <ul><li>Competing evidence or ideas can yield different results </li></ul><ul><li>Tree “A” places the bird & mammal on a clade that excludes the lizard </li></ul><ul><ul><li>Tree “A” interprets the 4 chambered hearts of birds and mammals as homologous </li></ul></ul><ul><ul><li>This is the most parsimonious hypothesis </li></ul></ul><ul><li>Tree “B” places the bird & lizard in a clade </li></ul><ul><ul><li>The 4 chambered hearts of birds and mammals are analogous </li></ul></ul><ul><li>Evidence actually supports “B” </li></ul><ul><ul><li>Birds & lizards are closer than birds & mammals </li></ul></ul>
  36. 36. Analogy or Homology?
  37. 37. Taxonomy is Subject to Change <ul><li>Systematics and molecular evidence are changing classification </li></ul><ul><li>In traditional vertebrate taxonomy, crocodiles snakes, lizards, and other reptiles are grouped together in the class Reptilia </li></ul><ul><li>Birds are placed in a separate class, Aves </li></ul><ul><li>Newer methodologies show that crocodiles are more closely related to birds than to lizards or snakes </li></ul><ul><li>Class Reptillia in its traditional form is paraphyletic, not monophyletic </li></ul>
  38. 38. Changing Views