Tree of Life

1. Tree of Life • Planet Earth is about 4.6 billion years old. • Oldest known rocks are about 3.8 billion years old. • Oldest fossils (prokaryotes) are about 3.5 billion years old.

2. Tree of Life • All living organisms on this planet share a common ancestor. • The tree of life reflects the branching pattern of speciation (phylogenetic history of life) that has occurred since the origin of life.

3. Tree of Life • There is an excellent Tree of Life website in which you can trace the branching pattern of the history of life and explore classification. • http://tolweb.org/tree/

4. Tree of Life • There is a hierarchichal classification of life in which organisms are progressively nested within larger and larger categories as more distant relatives are included in the classification (we will explore classification shortly). • The highest level of classification is the Domain of which there are three.

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8. “Bacterial” Domains • Domain Bacteria • Domain Archaea • The domains Bacteria and Archaea are both prokaryotes (they have no nucleus and the DNA is not arranged in chromosomes). Prokaryote derived from the Greek Pro meaning before and karyon meaning a kernel [i.e. a nucleus]

9. Domain Bacteria • Includes most of the bacteria people are familiar with including disease-causing species (Salmonella; Vibriocholerae which causes cholera), nitrogen-fixing (Nitrosomonas) and parasites (Borreliaburgdorferi which causes Lyme disease).

11. Domain Bacteria • Bacteria play a major role in decomposition and many live symbiotically with other organisms including humans helping to break down or synthesize foods needed by the host.

12. Domain Archaea • The Archaea include many extremophiles, organisms that live in extreme environments. • Includes thermophiles which tolerate extreme heat (e.g. live in geysers and hot springs where temps may reach 90 degrees celsius) and halophiles (salt lovers, which live in very saline environments (e.g. Great Salt Lake, Dead Sea)

13. Archaea in hot springs

14. Bacteria and Archaea • Bacteria and Archaea are both prokaryotes and their DNA is arranged in circular structures called plasmids. • However, they have substantial differences in their biochemistry, cell wall structure and other molecular details.

15. Domain Eukarya • Domain Eukarya contains the eukaryotic organisms (from Greek eu true and karyon akernal) which have a true nucleus and DNA arranged in chromosomes. • Eukaryotic cells are much larger and complex than prokaryotic cells and contain organelles such as mitochondria, chloroplasts, and lysosomes.

16. Domain Eukarya • Domain Eukarya includes three kingdoms the Plantae, Fungi and Animalia. • There are also a number of unicellular eukaryotes that may form as many as five other kingdoms. These were formerly grouped in the paraphyletic group the Protista.

17. Domain Eukarya • Plantae, Fungi and Animalia are mostly multicellular, but plants are autotrophic (produce their own food by photosynthesis) whereas the fungi and animals are heterotrophic (consume other organisms).

18. Animalia • Zoology is the study of animals and multicellular organisms of the kingdom Animalia are the focus of this semester, although we will briefly discuss some single-celled protozoans (“Protistans” when discussing a variety of parasitic diseases).

19. Animalia • Traditionally, zoologists divide the Animalia into vertebrates and invertebrates. • Vertebrates are those that possess a vertebral column and a suite of other unique derived features. • Vertebrates are a subphylum of the phylum Chordata. • The Chordata includes all the vertebrates: fish and tetrapods (amphibians, reptiles, birds and mammals) and two non-vertebrate chordates the Urochordates (sea squirts) and the Cephalochordates (lancelets).

20. Animalia: Invertebrates • The non-chordate animals are the traditional Invertebrates and include all the other phyla in the Animalia. These are the groups we will focus on this semester. • Major phyla include the Porifera (sponges), Annelida (earthworms and relatives), Mollusca (molluscs), Arthropoda (crustaceans, insects and relatives) and Echinodermata (seastars and relatives).

21. Animalia • Animals are heterotrophic eukaryotes. Most are multicellular. • Except for sponges, all animals have tissues which are specialized collections of cells separated from other tissues by membranes. • Tissues are arranged together to produce organs and organs are organized into organ systems (e.g. digestive system).

22. Animalia • Most animals are bilaterally symmetrical and form a large clade called the Bilateria. • Bilateral animals have a left and right side, top and bottom, as well as front and rear ends. • A smaller number are radially symmetrical (e.g. jellyfish).

24. Classification • Before exploring the many groups of animals we need to review the general topic of classification or how we group organisms into a manageable framework.

25. Classification • Science of Systematics dates to Linnaeus in the 18th century who devised the basic systems of binomial nomenclature and hierarchical classification in use today. • All organisms have a unique binomial name • E.g. Humans are Homo sapiens

26. Classification • Organisms are classified into a hierarchical classification that groups closely related organisms and progressively includes more and more organisms.

28. Phylogenetic trees • Systematists aim to figure out the evolutionary relationships among species. • Branching diagrams called phylogenetic trees summarize evolutionary relationships among organisms.

30. Phylogenetic trees • In a phylogenetic tree the tips of the branches specify particular species and the branching points represent common ancestors.

32. Phylogenetic trees • Phylogenetic trees are constructed by studying features of organisms formally called characters. • Characters may be morphological or molecular. • Character similarity resulting from sharedancestry is called homology.

33. Cladistics and the construction of phylogenetic trees • Cladograms are diagrams that display patterns of shared characteristics. • If shared characteristics are due to common ancestry (are homologous) the cladogram forms the basis of a phylogenetic tree.

34. Cladograms • Within a tree a clade is defined as a group that includes an ancestral species and all of its descendants. • Cladistics is the science of how species may be grouped into clades.

35. Shared derived characters • Cladograms are largely constructed using synapomorphies or shared derived characters. • These are characteristics that are evolutionary novelties or new developments that are unique to a particular clade. • For example, for birds possession of feathers is a shared derived character and for mammals possession of hair is.

36. Shared primitive characters • Shared primitive characters are characters that are shared beyond the taxon we are interested in. Among groups of vertebrates the backbone is an example because it evolved in the ancestor of all vertebrates. • If you go back far enough in time a shared primitive character will become a shared derived character. Thus, the backbone is a shared derived character that distinguishes vertebrates from all other animals.

37. Constructing a cladogram • Outgroup comparison is used to begin building a cladogram. • An outgroup is a close relative of the members of the ingroup (the various species being studied) that provides a basis for comparison with the others.

38. Constructing a cladogram • The outgroup lets us know if a character state within the ingroup is ancestral or not. • If the outgroup and some of the ingroup possess a character state then that character state is considered ancestral.

39. Constructing a cladogram • For example, birds, mammals and reptiles are all amniotes (produce hard-shelled or amniotic eggs). Birds have no teeth, but mammals and reptiles do. • An outgroup to the amniotes, fish, possesses teeth. Therefore, the ancestral state among the amniotes is to possess teeth and birds have secondarily lost them.

40. Constructing a cladogram • Having the outgroup for comparison enables researchers to focus on those characters derived after the separation from the outgroup to figure out relationships among species in the ingroup.

41. Constructing a cladogram • Cladogram of various vertebrates: monkey, horse, lizard, bass and amphioxus. • Use amphioxus as outgroup (is a chordate, but has no backbone).

42. Cladogram

43. Constructing a cladogram • In the cladogram new characters are marked on the tree where they originate and these characters are possessed by all subsequent groups.

44. Cladograms and Phylogenetic Trees • A cladogram and a phylogenetic tree are similar, but not identical. • A phylogentic tree’s branches represent real evolutionary lineages and branch lengths represent time or amounts of evolutionary change. • Cladogram branches contain no such information. Branching order of cladogram should, however, match that of phylogenetic tree.

45. Early phylogenetic tree of amniotes based on cytochrome c gene by Fitch and Margoliash (1967). Note numbers on branches. These represent estimated numbers of mutational changes in gene.

46. Theories of taxonomy There are two current major theories of taxonomy: • Traditional Evolutionary Taxonomy • Phylogenetic Systematics (Cladistics) • Both based on evolutionary principles, but differ in the application of those principles to formulate taxonomic groups.

47. Theories of taxonomy • There are three different ways a taxon may be related to a phylogentic tree. • The taxon may be a monophyletic, paraphyletic or polyphyletic grouping

48. Monophyletic Group • A monophyletic taxon includes the most recent common ancestor of a group and all of its descendents.

50. Paraphyletic group • A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all of its descendents.