Bios 101 PM Biology of Populations and Communities

1. Bios 101 PMBiology of Populations and Communities • Dr. Alan Molumby • molumby@uic.edu • 6-2994 • 3084 SEL • Office Hours MF 9, W at 11, or by appointment

2. What is Out There? Reading: Freeman Chps. 1, 50 and 55

3. Biology is the study of life, but what is life?

4. processes that define a living thing • Organization and Information • Need for an Energy Source • Reproduction and Evolution

5. Organization and Information • Living things are born and living things die. Although true by definition, this underlies an essential property-they are organized. • So long as an organism maintains a given level of organization, it is alive. When this organization breaks down, it dies. • Living things impose organization on nonliving matter by growth, development, and reproduction. • In death and decomposition, this organization breaks down.

6. Homeostasis • A critical aspect of life's organization is a constant internal environment, called homeostasis, which makes the complex biochemical machinery of life possible.

7. Information • Living things use a template to impose order on nonliving things and to maintain order within their own bodies. • In all present-day living things, this template is DNA (many viruses use RNA, but are they living?.) • This template makes proteins, which are responsible for our structure, function, and metabolism-it is copied every time living things reproduce.

8. DNA • DNA is the prime substance of life itself (on this planet, at least), it is as close to the basis of life as we can get. • DNA is the information template for life on earth. Without DNA, living organisms could not reproduce or function.

9. Need for and Energy Source • All living things require constant input of energy to survive. • This is because life exists in a state of dynamic equilibrium. • A dynamic equilibrium is an organized system that requires a constant input of energy to maintain itself. • Without input of energy, the organization breaks down and death is imminent.

10. Humans are Heterotrophs • Humans, like other animals, are heterotrophs. We process energy that was originally captured by other living things. • Unlike plants, we cannot fix energy from sunlight, nor can we fix energy by reducing hydrogen sulfide these organisms are autotrophs and chemoautotrophs respectively.) • All of the energy we use to survive, and most of the nutrients, were taken from another organism.

11. Reproduction and Evolution • All living things are able to make copies of themselves. • It is in this area that the ambiguous nature of viruses becomes apparent. A virus alone is inert. It does not use energy and cannot reproduce. In the presence of the right living cells, however, viruses can direct the production of million copies of themselves.

12. On Earth, types of living things fall into (more or less) discrete categories called “species” • The definition of a species, and our reasons for defining it that way, will come up several times during this course. • Basically, species are groups of organisms that • 1-can interbreed and produce fertile offspring and/or • 2-share a set of traits in common that distinguishes them from other such groups and • 3-is an evolutionary lineage that persists, ancestor to descendant, over time

13. Question: Which of the following are inherent properties of living things? • Information B) Sexual Reproduction C) Need for an Energy Source D) Respiration E) A and C

14. How Many Species are Out There?

15. There are approximately 2 million described species on Earth, estimates of the true number range from 5 to 30 million, with the number ranging as high as 100 million if prokaryote “species” are recognized. • So, most of what is out there remains undescribed. • The process of describing a species is time-consuming, and demands special skills which are in short supply. • There is no central database of species, though several projects are underway to change this. • There is also an attempt to create a central database of phylogenetic information. • There are difficulties with the species concept; cryptic species, species named more than once, and polymorphic species • As a result, only a small fraction of species are named and described, some existing species have been named several times.

16. Some taxa are known much better than others. • For example, birds, mammals, flowering plants, and butterflies are well known,. • Most species in these groups have been described and named. • Most insect groups, such as the chalcidoids and beetles, are less well-known, but becoming much better-understood. • Only a fraction of the insects have a name and a description. • For some groups, including most microorganisms, we are only beginning to comprehend their true diversity. Above is a chalcidoid, named and described, Below are microbes from a Greenland glacier, no formal description yet

17. This is what we have described so far, note the large number of insects • Group No. of described species • Prokaryotes 4,760 • Fungi 46,983 • Algae 26,900 • Bryophytes 17,000 • Gymnosperms 750 • Angiosperms 250,000 • Protozoans 30,800 • Sponges 5,000 • Corals and jellyfish 9,000 • Roundworms and earthworms 24,000 • Crustaceans 38,000 • Insects 751,000 • Other arthropods and minor invertebrates 132,461 • Mollusks 50,000 • Echinoderms 6,100 • Fishes (teleosts) 19,056 • Amphibians 4,184 • Reptiles 6,300 • Birds 9,198 • Mammals 4,170 • Total species 1,435,662

18. From E.O Wilson’s Biodiversity This figure is fairly old, the numbers of described species In each group have increased, but the proportions have remained fairly similar.

19. Clicker Question: Which of the following taxonomic groups has the LARGEST proportion of UNDESCRIBED species? • Birds B) Butterflies C) Mice D) Beetles E) Bats

20. The Old Classification This “five kingdom” scheme of classification replaced the old animal kingdom vs. plant kingdom scheme in the 1970’s. It is an excellent grouping of organisms based on their characteristics, but it does not reflect evolution very well.

21. The “Tree Within a Tree” Phenomenon • Very often, groups of organisms appear to be similar because they share a great many “primitive” characteristics. • This similarity is superficial, however, because very different organisms often possess the ancestral state for many characteristics, despite a great deal of evolution in different directions. • Best way to define groups is based upon synapomorphies, new traits that arise in the common ancestor of a lineage and are inherited by the members • When organisms are classified this way, it becomes apparent that most of the organisms that seem familiar to us are a cluster of branches within a much larger tree. • An important adaptation has enabled diversification • This pattern is repeated many times in evolution.

22. From paleos.com New ideas on the tree of life Modern methods of sequencing DNA, and a modern approach to systematics allows a greater understanding of the true “tree of life” The tree on the left, based upon ribosomal RNA, which is very evolutionarily conservative endicates that there are three major “domains” of living things. The prokaryote archaea are closer To eukaryotes than the bacteria.

23. From wikipedia.com • This is a reasonably current universal phylogeny of living things. • As we know more, the picture changes. • To surf the tree of life, go to http://www.tolweb.org

24. Some Highlights in the Tree of Life http://www.ucmp.berkeley.edu/archaea/archaea.html

25. Prokaryotes • “Prokaryotes” are the most ancient, most abundant, and most metabolically diverse organisms. • This term describes a state of organization (no nucleus) rather than a taxonomic group. • Prokaryotes include the: • Bacteria • Archaea

26. Bacteria • Proteobacteria • Cyanobacteria • Gram-Positive Bacteria • Chlamydias • Spirochetes

27. Proteobacteria • The proteobacteria are a large and diverse group that includes photoautotrophs, chemoautotrophs, and heterotrophs. • There is no taxonomic divide between “good” bacteria, those that are essential to the functioning of the biosphere, and “bad” bacteria, those that can kill us. • Pathogenic bacteria occur within many different groups. • On the basis of 16s RNA, they can be broken down into five basic groups • Alpha Beta Gamma Delta Epsilon

28. www.biology.ed.ac.uk/.../microbes/myxococc.htm Among the delta proteobacteria are the myxobacteria, interesting gliding bacteria that produce “fruiting bodies” under conditions of starvation. Myxobacteria live in the soil, and “glide” along solid surfaces via a polysaccharide slime.

29. Among the alpha proteobacteria are the ancestors of mitochondria. • Also included are Rhizobium species that live in the roots of plants, • and the rickettsias, tiny pathogens that live within the cells of animals bioinfo.bact.wisc.edu/.../Effects.html

30. Spirochetes • These are among the most distinctive bacteria • they move by a spiraling corkscrew motion. • They can be free living or parasitic. • Syphilis and Lyme’s disease are caused by spirochetes

31. Archaea Although we know very little about them, the archaea are some of the most abundant, and important, organisms on the planet. The group is very ancient-some bear a striking resemblance to fossils dated at more than two billion years old and many exploit ecological niches that were probably more important billions of years ago. Though the majority live in ordinary habitats, the group includes many exptremophiles. These include; methanogens-live in anerobic conditions and break down methane extreme thermophiles-live in incredibly hot environments extreme halophiles-live in extremely salty environments

33. Eukaryotes • Eukaryotes are much more diverse than was previously thought. • Modern studies of eukaryote taxonomy indicate there are probably between 11 and 20 eukaryote kingdoms, rather than simply plants, animals, fungi, and protists. These kingdoms include many groups formerly classed simply as “protists”, such as Diplomonads and Parabasalids.

34. From Baldauf, SL Science, 2003, Jun 13 1703-6

35. Some Kingdoms of Eukarya • Euglenoids • Alveolates • Discicristates • “Ameboid” protists • Ophistokonts • This includes us, by the way

36. “Protists” • “Protists” are simply eukaryotes that are unicellular for most of their life cycle. • There are many groups of distantly related protists, which are now thought of as “kingdoms” in their own right. • Several groups have independently acquired photosynthesis, and become “algae”, others have evolved multicellularity. • One group of multicellular protists evolved into animals. • Another lineage evolved into fungi. • There are several multicellular lineages, such as slime molds, that neither plant nor animal nor fungi.

37. Fungi • Fungi are a kingdom of organisms that includes decomposers, parasites, and mutualisms. • There are four major groups; • Chrytridomycots • Zygomycots • Ascomycots • Basidiomycots

38. EO Wilson’s Biodiversity again

39. Viridiplantae • This group includes the green plants and the basal “bush” from which they originated. They have chlorophyls a and b, as well as certain other distinguishing characteristics. • Green Algae-Chlorophytes • Charophytes • Plants

40. True Plants • These include several groups of multicellular, terrestrial photosynthesizers, including • Bryophytes-mosses, etc. • Pteridophytes-ferns. • Gymnosperms • Angiosperms-flowering plants

41. Animals • Animals are a true lineage of multicellular organisms evolved from one line of protists (probably resembling a group called the choanocytes). • They have evolved many different body plans, each of which represents a phylum. • There are about 30 present-day animal phyla, there were probably more in the distant past.

42. Organisms Create Habitats for Other Organisms. Many individuals of a single species are called a biological population Populations of organisms tend to assemble into biological communities

43. Biodiversity • Genetic Diversity within Populations • Diversity of Populations Within Species • Number of Species • in a given habitat (alpha diversity) • accounting for the diversity of habitats, and the change in species from one habitat to the next (beta) • total number of species (gamma) • Communities and Ecosystems

44. Question: Which of the following organisms is NOT a eukaryote? • A spirochete (Treponema sp.) • Euglena sp. • A frog (Hyla sp.) • A dandelion (Taxacum sp.) • All of the above are eukaryotes.

45. Ecology and Evolution • The sciences of ecology and evolutionary biology are often taught together, and at many universities, the two sciences are part of a single academic department. • This is because the mechanisms that drive evolution are fundamentally ecological, and the participants in ecological interactions are products of evolution. • The two subject areas interrelate so extensively that some areas of research, such as life history evolution, biogeography, coevolution, and macroevolution, are inextricably entwined in both sciences. • They provide an answer to the question of why there are so many species are out there, as well as an answer to the question of why they take the forms they do.

46. Example: Pollination Syndromes in Flowers • Naturalists have long observed that flowering plants, in a wide variety of taxa convergently evolve characteristics which match one of several “pollination syndromes.” • The same pollination syndromes evolve in widely disparate types of plants. Likewise, widely disparate types of pollinators will evolve to exploit these syndromes. • These “syndromes” are discrete sets of floral, nectar, and pollen characteristics that match the sensory abilities, metabolism, and biology of their pollinators, and act to ensure efficient pollination by manipulating the behavior of the pollinator. • Pollinators evolve in response to these floral characteristics, the result being a coevolutionary interaction that intensifies the relationship. • Example; A flower evolves a long corolla to ensure that hawkmoth visitors must reach deeply into a flower in order to reach the nectar “reward” provided by the flower, thus placing their faces in the appropriate location to receive pollen. • The hawkmoths respond by evolving longer tongues, to enable them to more easily reach the nectaries of the flowers. • This, in turn, places selective pressure on the flowers, and intensifies the relationship. The longer nectary, in turn, makes it nearly impossible for long-tongued bees to visit the flowers, and drives the system toward an obligate mutualism, rather than a looser, facultative mutualism.

47. Charles Darwin was fascinated by pollinators. • Upon examination of a Madagascar Star orchid, (Angraecum sesquipedale), which has a nectar tube over ten inches long, he famously predicted that there must be a hawkmoth with a tongue ten inches long to pollinate it. • At the time, only the orchid had been discovered. • 40 years later, the moth was discovered, Xanthophan morgani praedicta, now called Darwin’s hawkmoth. • In this particular scenario, part of the selective pressure driving the system is that the moths are safer from predatory spiders, but less effective as pollinators, if they never get too close to the flowers as they feed.

48. In addition to the evolutionary consequences of these syndromes, they have ecological aspects as well. • Under some circumstances, flowers effectively “compete” for pollinators. Flowers that are more conspicuous, and offer greater rewards, get more pollinators, but since these syndromes restrict the types of pollinators that can visit flowers, they restrict the scope of competition. • Pollinators very often compete for nectar, and for pollen. Specialist pollinators that visit only one type of flower are sometimes protected from interspecific competition (sometimes not, pollinator specialization does not imply that the flower can only receive one type of visitor), but at the cost of extreme ecological specialization. • This specialization causes the pollinator to evolve behavior and life history to match the appearance of the flowers they pollinate. • Other pollinators are “generalists”, able to visit a wide variety of flowers within their own pollination syndrome.

49. For instance, the squash bee, Peponapis pruinosa feeds on the nectar and pollen of squash, exclusively. Though other bees visit squash, it is the most effective pollinator. Males hide in squash flowers day and night, waiting for females to mate with in the early mornings as they forage for pollen.The abundance of this pollinator makes squash and pumpkins easy to cultivate, even though most gardeners do not know the squash bee exists. Squash bees time their emergence to late summer.

50. The most common pollination syndromes: • Flies and generalists-open flowers, easy to reach pollen, accessible nectaries. Large amounts of pollen because most of the visitors are after pollen. Usually early spring. • Long-tongued bees-moderately long corollas, flowers are white, blue, yellow, infrared, small amounts of sucrose-concentrated nectar, sometimes a “landing pad” for bees, and sometimes petals that must be pushed apart for the bee to reach the nectar. Scented flowers, open in daytime. Sticky pollen that bees can easily collect and transport, nectar guides. • Short-tongued bees-white, yellow, infrared flowers, short corollas with easily available pollen, no special tricks with petals, but usually asymmetric. Scented flowers open in daytime. Sticky pollen. Sucrose-dominated nectar in variable amounts. • Bumblebees, Amigillia bees-as with long-tongued bee flowers, but bee must hang upside and buzz to release pollen. • Hawkmoths-very long corollas that effectively force the moth to push its face into the stamens in order to reach reward (moths are not after pollen, so they must be tricked into transporting it), white flowers that are heavily scented and open at night, small amounts of concentrated nectar. • Butterflies-as above, but flowers run more to the pink or lavender and have a landing platform. • Hummingbirds-red flowers (only vertebrates see that color well) with very long corollas and large amounts of dilute nectar, flowers open in daytime, and bird is forced to push face into stamens in order to feed. No scent. • Bats-large amounts of dusty pollen that will stick to mammal hairs, very big flowers that bats can reach into with their faces, open at night, • Beetles-flowers smell like carrion and offer large amounts of pollen