Chapter 10

1. Chapter 10 Prospecting for Biological Gold Biodiversity and Classification 0

2. Biological Classification- How Many Species Exist? Biodiversity is the variety within and among living species. Number of species known to science is between 1.4 and 1.8 million Uncertainty due to differences in methods of storing and describing specimens Total number of species – estimates range from 3 – 100 million Average estimate is ~10 million species on Earth This number is likely to increase with newer discovery technologies

3. Biological Classification - How Many Species Exist? Systematists are scientists who specialize in describing and categorizing organisms. They work in the field of biological classification. Biological collections such as natural history museums and herbaria store samples of the different species. Systematists evaluate these collections to determine overlap in identifying of species.

4. Biological Classification - Kingdoms and Domains Modern species are divided into three large groups, or domains. Bacteria, Archaea, and Eukarya Within Eukarya, three kingdoms are uniformly recognized Plantae Animalia Fungi Protista (a catch-all of 20 additional kingdoms)

5. The tree of life. Eukarya Protista Bacteria Archaea Plants Fungi Animals Presenttime More recentdivergence Time Divergence earlyin life’s history 4 billionyears ago

6. Biological Classification - Kingdoms and Domains [INSERT TABLE 13.2 ON THIS SLIDE]

7. Biological Classification - A Closer Look: Kingdoms and Domains Recently, some scientists have begun to suggest that organisms should be classified based on evolutionary relationships. Major groups under this system correspond to divergences early in life’s history. Determining evolutionary relationships requires comparing DNA (What was combination of genetics and evolution called again?). DNA of closely related organisms should be more similar than DNA of distantly related organisms.

8. Biological Classification - A Closer Look: Kingdoms and Domains rRNA is used to determine relationships among distantly related organisms

9. The Diversity of Life - Bacteria and Archaea Life on earth arose at least 3.6 billion years ago, according to the fossil record. Most ancient fossilized cells are very similar to modern bacteria and archaea Prokaryotes like bacteria and archaea don’t have a nucleus, lack mitochondria and chloroplasts, and most are unicellular Incredibly numerous and diverse Found on every square centimeter of the earth’s surface, even inside deep sea vents, far underground, in clouds, and on glaciers Prokaryotes are called microbes and are studied by microbiologists.

10. Domain Bacteria Domain Bacteria Most bacteria are harmless to humans. We are most familiar with the ones that cause disease We cared about ourselves before we cared about the Earth Many known bacteria obtain nutrients by decomposing dead organisms Competition between bacteria has produced compounds that humans make use of. Antibiotics – ~50% of antibiotics are derived from bacterial sources Restriction enzymes – proteins that chop DNA at specific sequences; useful in biotechnology Metabolic enzymes can be useful in bioremediation – recycling of garbage to make useful biomaterials

11. Domain Archaea Superficially similar to bacteria Differ in structure of cell membranes and ribosomes Archaeans typically found in extreme environments (high temperature, high pressure, high salt concentration) Taq polymerase comes from an archaean, Thermophilus aquaticus Archaeans are likely to be source of other interesting biomolecules (those that work at high salt or high temperature)

12. The Diversity of Life – Domain Eukarya Evolution of the Eukaryotes Protists are the simplest of the eukaryotes Oldest eukaryotic fossils are ~2 billion years old, 1.5 billion years later than the first prokaryotic cells (3.5 billion years old) Endosymbiotic theory explains the evolution of eukaryotes and their specialized structures. Many chromosomes needed to be organized together – nucleus Internalized food needs to be chewed up – lysosomes Mitochondria burn sugars and chloroplasts create sugars

13. The Diversity of Life – Evolution of Eukaryotes [INSERT FIGURE 13.8 ON THIS SLIDE] Endosymbiotic Theory

14. The Diversity of Life – Protista Modern protists contain members that resemble animals, plants, and fungi. Most members of the kingdoms are not known Protists are eukaryotes that don’t belong in Kingdom Fungi, Kingdom Plantae or Kingdom Animalia All have nuclei, but some lack basic organelles Chloroplasts A few contain chloroplasts (euglena, algae) Mitochondria Some lack mitochondria Some have vesicle-like organelles that burn energy like mitochondria do

15. The Diversity of Life – Protista • The Diversity of Protists: • Ciliates, flagellates, amoebas, diatoms, algae, slime molds

16. The Diversity of Life – Protista Bioprospectors have examined the plant-like protists most closely for useful compounds. Evolution occurs most rapidly in these organisms (similar to fungi) Natural selection (they are food for animals) has driven the evolution of defensive compounds in these organisms. Extracts from red algae might be used in anti-viral medication. Carageenan, a stabilizer and thickener present in toothpastes, also comes from protists.

17. (a) Animal-like protist (b) Fungus-like protist Mattesiaoryzaephiliis a parasite that infests and killsbeetles in stored grain. M. oryzaephili may be useful in controlling these pests. Lagenidium giganteum, sprayed on ponds to controlmosquito populations (c) Plant-like protist (d) Plant-like protist Gonyaulax polyedra, a luminescent alga used to measurelevels of toxic materials in ocean sediments Chondrus crispus, a red alga that is the source ofcarageenan

18. The Diversity of Life – Kingdom Animalia Kingdom animals comprise a wide range of organisms, but all share a common set of characteristics. No cell wall Multicellular Heterotrophic (must eat to get energy) Mobile during at least one stage of life By 530 million years ago, all modern animal groups were present, including chordates. Most appeared quickly in fossil record Multicellular organisms quickly proliferated Known as Cambrian explosion

19. The Diversity of Life – Animalia A sampling of animal diversity

20. 13.2 The Diversity of Life – Animalia A sampling of animal diversity

21. The Diversity of Life – Animalia Most bioprospecting work focuses on invertebrates. Vertebrates only account for ~4% of animals Vertebrates are relative new comers to the earth (450-500 Million years) Think about how many insects there are compared to us; think about how many worms there are compared to us Invertebrates are far more numerous and diverse Many invertebrates produce compounds found nowhere else in nature Corals produce large numbers of highly toxic biomolecules – used in cancer research, antibiotics

22. The Diversity of Life – Animalia

23. The Diversity of Life – Fungi Kingdom Fungi characteristics Immobile Many reproduce by releasing spores Heterotrophic Feed by means of hyphae The hyphae of fungi can extend over a very large area DNA analysis by mycologists indicates fungi is more closely related to animals than to plants They also evolve very rapidly, and their enzymes and antibiotics are of use to biotechnologists

24. The Diversity of Life – Fungi Fungi are grouped on the basis of spore formation

25. The Diversity of Life – Fungi Commercially important fungal forms Yeast is a single celled type of fungi that is used in bread, wine, mead, kefir, kambucha, and beer making. Mold is quickly reproducing and fast growing to produce flavorful cheeses and protect aged steaks and cured meats (pepperoni, sopresseta, salami) Fungi produce a number of important drugs Antibiotics Cyclosporin Statins

26. The Diversity of Life – Plantae Characteristics of Kingdom Plantae Multicellular Eukaryotic Autotrophic (manufacture own food from carbon dioxide form the air, or carbonates from the soil and water) via photosynthesis

27. The Diversity of Life – Plantae Plants have been present on land for ~400 million years. First plants were low to ground, lacked vascular tissue Evolution of vascular tissue for water and nutrient transport Allowed growth to tree size Allowed growth in drier areas Most modern plants in group only ~140 million years old Flowering plants and conifers

29. Diversity of flowering plants. Bewildering variety of leaf and flower structures! (a) Foxglove (Digitalispurpurea) (b) Aloe (Aloe barbadensis) (c) Willow (Salix alba) Source of heart drug digitalis Source of aloe vera, used to treat burns and dry skin Source of aspirin

30. The Diversity of Life – Plantae Over 90% of modern plants are flowering plants and many specializations Rapid increase of flower plant species is called adaptive radiation. Flowering plants employ double fertilization method or reproduction (one zygote makes the embryonic plant; another zygote makes seed food called endosperm) Also often involve animals in reproductive process (pollination) – lots of coevolution has happened with flowering plants and animals that eat them Also synthesize many secondary compounds that deter predators (e.g., cannabis “confuses” flies)

31. 2 The Diversity of Life – Plantae Double fertilization

32. The Diversity of Life – Plantae Kingdom Plantae is the source of many drugs and compounds. Source of most naturally derived drugs Aspirin, Digitalis, Morphine, and Caffeine Pharmaceutical manufacturers (legal and illegal) reproduce hundreds of compounds first found in plants

33. The Diversity of Life - Viruses • A virus consists of a strand of DNA or RNA • Viruses hijack transcription machinery of cells to reproduce • Once hijacked, a cell cannot perform own functions • HIV, smallpox, polio, influenza, zikaare all caused by viruses • Adaptive immunity evolved to slow viral infections Figure 12.18

34. Learning About Species - Fishing For Useful Species • The National Cancer Institute has employed a brute-force approach to looking for anti-cancer compounds • Receive specimens from around the world, extract materials and screen against cancer cell lines • One major compound, Taxol, has been identified using this technique • Isolated from Pacific yew tree, a mitotic inhibitor used as cancer medication http://en.wikipedia.org/wiki/Taxus_brevifolia

35. Learning About Species – Understanding Ecology Understanding an organism’s ecology—how it lives in its environment—can be helpful in evaluating potentially beneficial compounds. Survival in extreme environments High levels of competition with bacteria and fungi Susceptibility to predation Ability to live on or in other organisms Survival in high population densities

36. Learning About Species – Reconstructing Evolutionary History A classification system reflecting evolutionary relationships is more useful to scientists. An organism’s chemical traits will probably be similar to those of its closest relative If looking for new compounds (especially variants of already successful or promising but failed compounds), one could begin by screening close relatives of organisms already known to produce the promising compounds

37. Learning About Species – Reconstructing Evolutionary History The challenge in making an evolutionary classification is that organisms do not always resemble their closest living relatives. Which two are most closely related???

38. Learning About Species – Developing Evolutionary Classifications An evolutionary classification of sparrows

39. Learning About Species – Developing Evolutionary Classifications Reconstructing evolutionary history not always as easy as the sparrow example. Can be confounded by loss of traits, and convergence (both bats and birds evolved wings; whales, manatees, and seals all evolved flippers) DNA provides a means of testing evolutionary hypotheses

40. Learning About Species – Testing Evolutionary Classifications Scientists can test evolutionary hypotheses with data from fossils and from living organisms. Fossils provide information about the genealogy of different living groups Comparison of DNA from living organisms can also validate or refute proposed classifications DNA supports vulture classification, but does not support sparrow classification DNA can give clues to near relatives, but lab process can take time

41. Learning About Species – Learning From the Shamans Often local people in biologically diverse areas make extensive use of naturally occurring products. “hillbillies” created recipes for poke salad to avoid poisons; Japanese chefs harvest food from blowfish Shamans often have much knowledge of locally useful compounds. Biopiracy is when local knowledge is used without benefiting local people. UN Convention on Biodiversity is supposed to address this (politics and “more important situations” ruin this). Our biodiversity represents an enormous potential, but only if we recognize its value.

42. Overview of Classification • Domain Bacteria – prokaryotic • Bacteria we are familiar with • Domain Archaea – prokaryotic • Includes extremophile bacteria • Domain Eukarya – eukaryotic • Includes protists, fungi, plants, animals

43. Which of the following is a kingdom? Animalia Eukarya Bacteria Archaea

44. Which of the following is a kingdom? Animalia Eukarya Bacteria Archaea

45. How many species have currently been discovered? 14,000-18,000 140,000-180,000 1.4-1.8 million 1.4-1.8 billion

46. How many species have currently been discovered? 14,000-18,000 140,000-180,000 1.4-1.8 million 1.4-1.8 billion

47. Which statement correctly describes the domain Archaea? Archaeans are not alive. Archaeans are typically found in extreme environments. Archaeans are the simplest known eukaryotes. Archaeans reproduce using spores.

48. Which statement correctly describes the domain Archaea? Archaeans are not alive. Archaeans are typically found in extreme environments. Archaeans are the simplest known eukaryotes. Archaeans reproduce using spores.

49. The kingdom Protista is made up of the simplest known _______. An example from this kingdom includes _______. Prokaryotes; algae Prokaryotes; fungi Eukaryotes; algae Eukaryotes; fungi

50. The kingdom Protista is made up of the simplest known _______. An example from this kingdom includes _______. Prokaryotes; algae Prokaryotes; fungi Eukaryotes; algae Eukaryotes; fungi