The exam is closed book; you have 3 hours to complete it (9 &endash;12). There are 25 multiple choice questions for which you can score 2 points each (50 points total). There are 6 essay questions to which you should give short answers (take no more than about half a page in the blue book) at 5 points each (30 points total). There are 2 essay questions to which you should give longer answers (about 3-4 pages in the blue book if your handwriting is average) at 10 points each (20 points total).

MULTIPLE CHOICE QUESTIONS:

1. During the Phanerozoic:

• Ecological niches changed, but we can distinguish no long-term pattern
• Less energy-intensive life forms became more common
• More energy-intensive life forms became more common (as discussed in Mesozoic Marine revolution lecture)
• Ecological niches were pretty much the same between the Cambrian revolution and the Present.

2. Eukaryotic cells probably evolved from:

• Colonies of various prokaryotes
• Symbiosis of various prokaryotes (as discussed when we talked about mitochondria)
• Degeneration of multicellular organisms
• Colonies of various viruses

3. Development of infaunal tiering in the Paleozoic marine community led to:

• increased burial of organic matter in marine sediments
• decreased burial of organic matter in marine sediments (increased burrowing means reuse of organic matter and return to the biosphere)
• no difference in burial of organic matter in marine sediments
• we can not predict the burial efficiency of organic matter in marine sediments from knowledge of infaunal behavior

4. The Out of Africa hypothesis is different from other hypotheses on the evolution of humans because it states that:

• hominid genera evolved in Africa only
• the genus Homo evolved in Africa only
• the species Homo sapiens evolved in Africa and replaced more ancient Homo species elsewhere
• the species Homo sapiens evolved in Africa first, and in other regions only later

5. The evolution of large forests on Earth and the subsequent formation of coal deposits led to:

• an increase of oxygen levels in the atmosphere
• a decrease of oxygen levels in the atmosphere
• an increase in carbon dioxide in the atmosphere
• had no effect on atmospheric composition

6. According to Darwin, variability in characters of specimens of the same species:

• Confuses the issues, and we should try to recognize what a ‘typical organism’ looks like
• Is an integral part of, and an important factor in, evolutionary theory
• Is interesting in itself but not relevant to evolutionary theory
• May teach us about the ontogeny of a species

7. Animal phyla are subdivided using information on:

• Presence of DNA within the chromosomes in the nucleus
• Embryological development (protostome-deuterostome etcetera).
• Structures within the cells and in the cell walls
• Presence/absence of HOX genes

8. Zoophycos is a common trace fossil:

• In sandy sediments
• Together with the feeding traces of trilobites
• In sediments from shallow waters
• In sediments from low oxygen environments (see textbook as well as web notes)

9. Cladistics is a powerful method because:

• It is more objective and quantitative than other methods
• It uses genetic information rather than unreliable morphological observations
• It uses morphological information rather than unreliable genetic observations
• It forces the investigator make clear her/his assumptions and observations

10. In an isolated valley on a remote Pacific island valley a snail is discovered which is a ‘living fossil’, and very closely resembles a Jurassic snail. According to the ‘Arms Race’ hypothesis:

• The Jurassic-type survivor would easily out-compete a modern snail
• The Jurassic-type survivor would be easily out-competed by a modern snail
• We can not make any prediction regarding ‘superiority’ of modern or Jurassic type snail, because this depends on environmental factors
• Both probably have the same fitness, since both are living today

11. If we classify vertebrates cladistically:

• Birds are most closely related to mammals because both groups are endothermic
• Birds are most closely related to crocodiles because they have very similar limb structures
• 'Birds' is a scientifically invalid name because 'birds' is a polyphyletic group
• Birds are dinosaurs

12. Most fossil species:

• Grade imperceptibly from their ancestors and into their descendants in morphology
• Show rapid and major morphological changes over their species life
• Show gradual changes in morphology over their 'species life '
• Show little to no change in morphology over their 'species life' (hence punctuated equilibrium)

13. The Cambrian Explosion was:

• A geologically short period in which life on Earth first showed up in the fossil record and then rapidly diversified
• A geologically short period during which multi-cellular animals first showed up in the fossil record and then rapidly diversified
• A geologically short period during which bilaterally symmetrical animals with skeletons first showed up in the fossil record and then rapidly diversified
• A geologically short period of major extinction in which many complex, bilaterally symmetrical organisms became extinct

14. The different types of mollusc shell:

• Can be all derived from rather simple developmental variations on one basic building plan: hypothetical ancestral mollusc.
• Show major differences in design that can be used to reconstruct cladograms of the detailed Molluscan Phylogeny
• Are analogs, not homologs from each other and thus can not be used to construct cladograms
• Are strongly influenced by the external environment during development and can not be used in phylogenetic reconstructions

15. Hox genes:

• Are typical for chordates only and control such factors as limb development
• Are typical for arthropods only and control such factors as segmentation
• Are typical for all animals (not all life on earth, but even non bilaterally symmterical animals have such genes even though not many)
• Are typical for all life on earth

16. The ‘Snowball Earth’ hypothesis describes how during some periods in Earth history the oceanic productivity drops off sharply because the world’s oceans are covered with ice. Limestones formed during these periods of very low biotic productivity in shallow waters of the ocean have a carbon isotopic composition that is:

• Unusually light because light carbon not/little used in photosynthesis at such times
• Unusually heavy
• About the same as today
• Impossible to say

17. The word 'allometry' describes:

• A change in gene composition during growth
• A change in morphology during ontogeny due to changes in the environment
• A net change in shape during ontogeny
• A change in developmental timing during metamorphosis

18. When oxygenic photosynthesis evolved:

• Free O₂ did not directly accumulate in the atmosphere because it was used in breathing by many organisms present
• Free O₂ did not directly accumulate in the atmosphere because it was blown away by the impact of a Mars-sized object that later formed the Moon
• Free O₂ did not directly accumulate in the atmosphere because elements in reduced state (Fe²⁺, S) in the oceans and earth’s crust (and even into the mantle) were oxidized first; it COULD not accumulate directly, what with a whole non-oxidized world sitting there
• Free O₂ directly accumulated in the atmosphere

19. An adult neotenous individual:

• Looks like a juvenile life stage of its ancestor
• Looks like an ancient life stage of its ancestor
• Has added stages to its life unknown to its ancestor
• Is larger than its ancestor

20. From all individuals of living organisms that have a shell that becomes fossilized easily, such as mussels or snails:

• Only a few percent become fossils
• 10-15 % become fossils
• Roughly half become fossils
• Almost all individuals fossilize because they have a shell

21. At the major mass extinctions at the end of the Paleozoic and the Mesozoic:

• Land plants as well as terrestrial and marine animals suffered a major loss of species followed by slow evolution, taking about 5-10 millions of years before recovering diversity
• Land plants as well as terrestrial and marine animals suffered a major, short term ecosystem disturbance but recovered diversity within a few thousand years
• Land plants suffered a major, short term ecosystem disturbance but recovered diversity within a few thousand years, whereas terrestrial and marine animals suffered a major loss of species followed by slow evolution, taking about 5-10 millions of years before recovering diversity
• Land plants suffered a major loss of species followed by slow evolution, taking about 5-10 millions of years before recovering diversity, whereas terrestrial and marine animals underwent major, short term ecosystem disturbance but recovered diversity within a few thousand years

22. On soft muddy ocean bottoms in the present oceans, in general:

• Articulate brachiopods are generally at a disadvantage compared to bivalves; both groups filter feed, but mollusca are active filter feeders. In addition, molluscs can burrow themselves out when they are covered with sediment during a storm.
• Articulate brachiopods are generally at an advantage compared to bivalves
• Articulate brachiopods and bivalves do not compete for food sources and the question is therefore irrelevant
• Articulate brachiopods or bivalves win this competition depending upon the local circumstances

23. Coral reefs:

• Can grow in the dark because the coral organism is an animal and thus heterotroph
• Can not grow in the dark because the coral organism is a plant and needs sunlight for photosynthesis
• Can not grow in the dark because the coral organism is an animal which relies on photosynthesizing symbionts for a large part of its energy
• Can grow in the dark because the coral organism is an animal which relies on chemosynthesizing symbionts

24. During periods of coal formation:

• Climate cools because much carbon dioxide from the atmosphere is stored in organic matter in the rock record
• Climate warms because all the plants that are preserved as coal produce much carbon dioxide during their life
• Climate warms because all the plants that are preserved as coal produce so much oxygen during their life
• Climate remains the same because there is no influence of coal formation (in the rock record) on the atmospheric composition

25. The word 'disparity' describes:

• The number of species present on Earth
• The number of species combined with a mathematical expression describing the distribution of specimens over species
• The variability in basic building plans of organisms
• The total morphological variability in organisms

1. How does a trilobite grow from larva to adult (growth processes)? How large do you think the largest trilobite could have been, and what would have limited its growth?
   1. By addition of elements (segments) to an initial single head-shield, as well as by growth of segments later in life. Trilobites, like modern crustaceans, molt, and are limited in size because the soft-bodied form during molting must be able to survive (Attenborough movie); largest where about a soup-plate size (reading; length about 1 foot). See answers to practice questions for midterm; Trilobite reading, trilobite lab handout, also chapter 2 text book on growth, p. 20.
2. What is the main point of punctuated equilibrium theory, and how is it related to the theory of allopatric speciation?
   1. See lecture 6 notes; pages 74-76 text book. Punctuated equilibrium: in the evolution of species long periods of time in which nothing happens to the morphology of a species (stasis) alternate with relatively short periods of rapid morphological change (punctuations). Of importance is mentioning the fact that what is static is the morphology of a species. We would expect this if allopatric speciation is common and most species originate by allopatric speciation: species originate in marginal areas of the species where few specimens are present, then migrate widely if they become reproductively isolated from their parent-species. It is only the widespread species which are commonly found; we thus see fossil species showing up in the fossil record apparently suddenly. See also answers to practice questions for midterm.
3. Darwin first published ‘The Origin of Species’ in 1859. Present-day ideas about evolution contain concepts described by Darwin, as well as concepts added later. Describe Darwin’s theory of evolution, additions that make up the so-called ‘Modern Synthesis’, and additions made after the formulation of the ‘Modern Synthesis’.
   1. Components of Darwinism as Darwin knew it: 1).Evolution occurred; 2) Common descent: all life on Earth has a single ancestor; 3)Multiplication of species: number of species increased during earth history; 4) Gradualism: evolution occurs gradually; 5. Natural selection is main cause. Natural selection:
      • All individuals of a species are slightly different
      • These differences are heritable
      • Not all young of a species survive into adulthood and reproduce
      • The individuals who are best adapted to their environment leave most offspring
      • Individuals who leave most offspring transfer their heritable characteristics into the next generation

      Neodarwinism: 'The Modern Synthesis' combines Darwin's concepts with the concepts of Mendelian inheritance (1865 -1900), as well as with these of population genetics (Fisher, Haldane, Sewall Wright), genetics: (Dobzhansky), population field studies: (Mayr ), and paleontology (Simpson), with later added the information on the structure of genetic material (DNA-RNA) 1953 (Watson & Crick); one could possibly mention later discussions on rate of evolution such as these on punctuated equilibrium. See also answers to practice questions for midterm; see notes lecture 6 ; textbook chapter 5.

4. What were the major steps in human evolution? About when did they occur?
   • Evolution of Primates from other mammals (large eyes, grasping hand, few slowly developing young, large brain for body size), 55 Ma in fossil record, much earlier in molecular records.
   • Evolution of bipedal primates from tree-dwelling primates; oldest possibly bipedal forms 6-7 Ma, Africa; various bipedal forms (e.g., robust and gracile Australopithecus) in East Africa by 4-3 Ma).
   • Evolution of genus Homo (species H. erectus) in Africa (~2.0-1.8 Ma), first to migrate over Old World (Asia, Europe).
   • Evolution of consciousness in 'modern' Homo sapiens. Anatomically modern H. sapiens by ~160-170 kyr. No agreement whether H. sapiens evolved in Africa from earlier Homo species, then replaced H. erectus in rest of world (Out of Africa theory), or whether H. erectus evolved into H. sapiens all over the Old World (multiregionalism theory). Genetic evidence strongly favors 'Out of Africa', which is in line with allopatric speciation in other organisms.
   • Homo sapiens migrated over Old and later New Worlds, Homo neanderthalensis evolved in Europe - middle East, was replaced by H. sapiens.
   • Development of modern, 'thinking' humans: maybe by 70,000 years ago (evidence from beads, suggesting symbolic thought), definitely by about 40,000 years ago (cave art). See lecture 22.
   • Human characters: bipedal locomotion, large brain, large size, small teeth, jaws an arc rather than u-shaped, prominent nose, small chin did not all evolve at same time: bipedalism before larger brain.
5. What are Vendobionta, in what type of ecosystem did they live, and when did they live?
   1. What are included in 'Vendobionta' are various organisms. Jellyfish or sea anemones, frond-like organisms, possibly related to modern soft corals and worms. There are also trace fossil (shallow burrows) maybe made by worms. Then there are unusual forms (quilted mattress structure, no mouth, gut or anus). All were either suspension feeders (taking particles from water), detritus feeders (picking up bacteria from sea floor), or lived on bacterial symbionts. There were no predators (no jaws), no burrowing up old organic matter ('Graden of Ediacara'). They lived from before the Cambrian revolution (starting at 650 Ma or so) into the Cambrian. See lecture 10; See also answers to practice questions for midterm.
6. Ammonites became extinct during the mass  extinction at the end of the Cretaceous. Their relative Nautilus survived, living in the Indo-Pacific Ocean, usually at depth between 100-500 m, along reefs, in regions where fairly low oxygen conditions occur at least seasonally. Nautilus lays large eggs, and the young hatch when they have formed several chambers and are about 2.5-3.0 cm in diameter. Ammonites occurred in a large profusion of shapes, in many habitats of the world’s oceans. Forms of which larvae are known as fossils had much smaller free-swimming juveniles than Nautilus (a few mm at most). Speculate on why Nautilus survived the end Cretaceous mass extinction while ammonites did not.
   1. I wanted you to use knowledge of what happens environmentally when asteroids strike; there really is no clear link between asteroid impact and anoxia in the oceans (maybe if the asteroid blows up gas hydrates....). Main effect: short period of dark and cold, ending photosynthesis of the short-lived oceanic phytoplankton, base of food chain. I did not give ANY information on whether ammonites could survive low oxygen conditions, where they were living depth-wise, or anything else; they may very well have been able to do so. There were very many different ammonites, so they may have been more specialistic than Nautilus, a generalistic scavenger, and generalists may be less vulneable to extinction than generalists. But in the event of a total kill off of all adults in both Nautilus and the ammonites, the juvenile Nautilus (who develop until larger in the egg, and thus almost certainly take much longer to hatch) could have survived the period of dark and cold and no phytoplankton to live on while living comfortably on the yolk of their eggs (for a month or so). This was the information given for both groups that you should have used, in addition to a short description of possible environmental problems during this extinction.

      You needed information on environmental aspects of extinction at end Cretaceous.

1. Describe the major steps in the evolution of Mammals from chordate ancestors. Discuss Stephen J. Gould’s ideas on the contingency of evolution, and compare to the ‘Red Queen’ hypothesis. Does the evolution of mammals as you described it conform more to patterns as expected from one of these hypotheses or not?
   1. I was expecting a discussion of the patterns of evolution of chordates/vertebrates, which is characterized by increasing complexity, as well as adding more and more features, going from Chordates to Vertebrates to Mammals. Chordates show Deuterostome properties (embryonic development) plus dorsal nerve chord (notochord), segmental muscles, ventral gut. Then a brain and skull develop (Craniates), and jaws develop from gill arches (Gnathostomates). Vertebrates have in addition a head (plus skull, cranium), an at least 2-chambered heart, bone (vertebrae) around dorsal nerve chord, red blood cells. Mammals have Vertebrate properties, plus paired appendages back and front (4 legs), with digits which number not more than 5 in living forams (fingers, toes) (Tetrapod properties), plus synapsid skull fenestration 4-chambered heart, hair, warm-blooded, jaw-joint simple (1 in part lower jaw), complex inner ear bones (hearing in air), heterodont dentition.

      This pattern thus seems to show evidence for the Red Queen hypothesis: more and more complexity, increasing evolution of an engineering-wise 'better functioning' organism (remember discussion on locomotion and feeding efficiency in Tetrapods). But mammals only became the dominant group of terrestrial and marine vertebrates after extinction of the dinosaurs, which argues for influence from contingency of earth history.

2. Describe the main factors in which the global ecology during the time period that you described in your term paper differed from that in the present world.