Welcome to Introductory Biology II Organismic and Evolutionary Biology (BIOL 202)

1. Welcome to Introductory Biology II Organismic and Evolutionary Biology (BIOL 202) Comparative Genomics helps elucidate ancestor/descendent relationships among major lineages of mammals, from the primordial mammal, with an early divergence of montremes, then marsupials, then placentals, including primates and their close relatives the bats.

3. Lecture Topics in Unit I: Evolutionary Processes • History, Science and Life • How populations evolve • What species are and how they arise • Macroevolution; patterns and process • How to determine evolutionary relationships • How molecules and genomes evolve Fossils of the large (15-30 cm) soft-bodied organisms Pteridinum simplex are locally abundant in sandstone beds of the terminal Proterozoic (~550 my old) Nama group in Namibia. New insights from paleontology, geochemistry and molecular genetics are collectively illuminating the pattern, developmental basis, and environmental context of early animal evolution • Today’s Topics: • Descent with modification; development of evolutionary thinking • History of Life on Earth • Classification • Scientific Inquiry

4. Lecture 1:History, Life and Science

5. What Darwin and Wallace Figured Out • Evolution happens; species’ characters (traits) change over time and indeed such evolutionary change may result in origin of new species from existing ones • Natural selectiondrives evolution; evolution is a consequence • Diversity of life on earth is the consequence of evolution, and all organisms, ultimately, share a common ancestry A young Charles Darwin, and a reproduction of the HMS Beagle

6. Prevailing Ideas about Life, Change and Evolution arose in Ancient Greece • Scientific inquiry arose with the Ancient Materialists of Greece and Her Colonies (5th, 6th century BC) • Methodically applied observation and logic to problem solving • (eg, Anaximander, Empedocles)

7. Classical Traditionalists of Greece and her Colonies (4th and 3rd century BC) departed from the “scientific approach” of their predecessors. • Culminated in writings of Plato and Arisotle • Plato’s Theory of Forms (Eidos) • Aristotle • Father of Modern Biology • Applied Plato’s theory of forms to living things • Developed important, unifying, enduring biological concept; Scala naturae • Aristotle’s non-evolutionary concepts, including immutability of species and “Scala Naturae” that were incorporated in Christian Theology and remained the principal model of biological thought for 2000 years – until the 18th century

8. Emergence of Scientific Thinking Arose with the Breakdown of Classical Tradition -- in the1500’s • Contributing factors to that breakdown • Renaissance • Global Exploration • Protestant Reformation • Important contributors to “new” approaches to Knowledge • Gutenberg • Copernicus • Thomas Aquinas • Francis Bacon • Redi World exploration, the renaissance, the protestant reformation…all contributed to a new intellectual atmosphere that led to the advance of scientific empiricism and rationalistic thinking

9. Intellectual Climate of Darwin’s Era (late 1700’s-Origin) • William Paley and others develop and promote Natural Theology, which pervades European and American Science • Carolus Linnaeus establishes huge intellectual model; Systema naturae • Inception of modern systematics, built on Aristotelian Scala naturae; non-evolutionary • New Sciences of Geology and Paleontology are strong intellectual influences • Catastrophism and progressionism prevailed in many early cultures and were incorporated in Geology – toppled by theories of gradualism and uniformitarianism of Hutton and Lyell • Growing knowledge of geological processes leads to questions regarding age of earth

10. 19th Century England: The Intellectual Context in which Darwin Developed His Ideas • Important concepts, publications that strongly influenced early 19th century scientific thinking • -Botanist Carolus Linneaus Systema Naturae-Reverend William Paley Natural Theology-Ettiene George St. HillaireEnvironmentalism-Cuvier Catastrophism • Radical 19th century geological concepts about the nature and pace of geological processes –age of earth- that influenced Darwin’s thinking during the voyage • -Geologist Hutton Gradualism -Geologist Lyell Uniformitarianism • Concept that influenced Darwin’s thinking after the voyage • -Thomas Malthus An Essay on Population

12. The Voyage of the Beagle

13. Course of the HMS Beagle’s World Journey Continental comparisons of floras and faunas Taxa showed continental affinities --even to the point that plants and animals from temperate South America showed a stronger affinity to those of tropical South America than those of temperate Europe

14. Within-continent comparisons of fossil and living taxa • Found fossils of extinct taxa that appeared to be ancestral to living taxa found there – i.e., distinct resemblances to living South American taxa

15. Unique “species groups” with curious distributions on the Galapagos Islands Found that most species were “endemic”, yet bore resemblance to South American taxa with unique distribution on the archipelago

16. From the Beagle to “Origin” • Darwin turned his “post-Beagle” attention to: • Artificial Selection • Population Theory of Thomas Malthus • Published “Origins” some 20 years after his voyage • Central Thesis of Origins: Descent with modification results in a branching tree of species, in which related species share common ancestry The mathematical model on which Thomas Malthus based his hypothesis; food production is arithmetic, population growth is geometric (An Essay on the Principal of Population, 1778) Darwin studied domestic pigeons, which were subjected to artificial selection by pigeon fanciers to such an extent that the various races produced showed levels of differentiation that one might expect among species

17. Darwin’s Line of Reasoning in Support of Descent with Modification (Evolution through Natural Selection) Observation 1. All species have potential fertility for exponential population growth Observation 2. Populations tend to remain stable in size Observation 3. Environmental resources are limited Inference 1: More individuals are produced than can survive; struggle for existence leads to survival of a fraction of offspring each generation; differential survival Observation 4: Individuals within a population vary extensively in their characteristics Observation 5. Much variation is heritable Inference 2.Survival is not random; depends in part on hereditary makeup; individuals with inherited traits best fit to the environment are likely to have more offspring than others; differential reproduction Inference 3.Unequal survival and reproduction will lead to gradual change in a population, with favorable characteristics accumulating over generations

18. Darwin developed his idea of Evolution, of descent with modification, on five ideas that are each now regarded as theories (well-supported ideas with broad explanatory power) • Perpetual Change. Life is very old and life forms undergo perpetual inter-generational change in form and diversity • Common Descent. All life forms share a common ancestry. • Multiplication of Species. New species arise from pre-existing species • Gradualism. Large differences in form among species is due to incremental accumulation of many small differences over long periods of time • Natural Selection. Organisms in a population experience differential survival and reproduction as a consequence of variability in heritable traits.

19. History of Life on Earth • Earth is more than 5 billion years old • Life originated some 3.5 billion years ago • Diversification of life has ensued only in the last 10% of Earth’s existence • That 600 million years includes the Paleozoic, Mesozoic and Cenozoic Eras Continental Drift. Earth’s crust consists of moving plates some 40 km thick, suspend on a molten, fluid mantle

20. Much of our knowledge on the history of life on Earth is based on interpretation of fossils -- the Fossil Record

21. 1000 2000 3000 4000 5000 History of Earth and Life Oldest Eukaryotic fossils Accum. of atmospheric. O2 and evolution of aerobic respiration ~ 2 billion years of a strictly prokaryotic world!! RNA sequence data shows Bacteria and Archaea diverged early, about 3 billion years ago Millions of Years Ago (mya) Photosynthesis evolves Oldest prokaryotic fossils Origin of life - anaerobic Earth Cools Earth forms 5+ billion years ago

23. 1000 2000 3000 4000 5000 History of Earth and Life Beginning of Paleozoic Era Oldest Eukaryotic fossils Symbiotic theory of origin of Eukaryotes Substantial atmospheric O2 Millions of Years Ago (mya) Photosynthesis evolves Oldest prokaryotic fossils Origin of life Earth Cools Earth forms

24. Cenozoic Era ~65 mya Laurasia Mesozoic Era Gondwana Pangea ~250 mya Paleozoic Era Eras are bounded by major faunal turnovers that are thought to be related to cataclysmic phenomena of global dimensions

25. A thin band rich in iridium marks the boundary between rocks deposited in the Cretaceous and the Tertiary Periods

26. Cenozoic Era H C Periods of cold climates and glaciations have punctuated Earth’s history Mesozoic Era Paleozoic Era

27. Today Paleozoic Mesozoic Cenozoic ~600 mya ~250 mya ~65 mya Phanerozoic Eon (Time of “visible” life) Paleozoic Era (Time of “Old Animals”) Mesozoic Era (Time of “Middle Animals”) Cenozoic Era (Time of “New Animals”)

28. Paleozoic Era Precambrian Cambrian ~600 mya ~500 mya ~250 mya • The Cambrian Period is the oldest geological period from which fossils of relatively complex organisms are represented • Most of the extant (currently living) phyla are represented in the Cambrian, but not before.

29. Evolutionary tree of vertebrate animals and close relatives Width of the track indicates relative species abundance of each group through geological time PreCambrian Paleozoic Mesozoic Cenozoic

30. Mass Extinctions and the Geological Time Scale • A Mass Extinction is the widespread extinction of many taxa, globally, that occurs in a relatively brief period of geologic time. • Many of the periods between periods, and between eras, are demarcated by mass extinctions • Two important mass extinctions to be aware of, now, are the: • Permian Extinctions (“ended” the Paleozoic Era) • K/T Extinctions (“ended the Mesozoic Era)

31. Changes in numbers of families of marine invertebrate and vertebrate animals; five major extinctions since the Cambrian Explosion

32. Along the coast of Tethys, an ancient warm ocean that stretched from Spain to Indonesia, an undulating Basilosaurus catches fish with its four-foot long jaws and battery of sharp teeth (Valkenburgh. Natural History. April 1994)

33. Evolutionary patterns in the rocks; Ambulocetus natans is an important find and a useful case study

34. Fossil formation in sedimentary deposits

35. Edinburgh Scotland

37. Dating Fossils • Relative Dating

40. Absolute Dating of Fossils and Rocks: Radiometric Dating Radiometric Dating; Using decay rates of radioisotopes to accurately estimate age of a fossils and rocks

41. Radioactive isotopes can be detected and their amounts measured by the radiation they emit as they decompose to more stable atoms. • Paleontologists use the clocklike decay of radioactive isotopes to date fossils and rocks

43. Emergence of Scientific Thinking Arose with the Breakdown of Classical Tradition -- in the1500’s • Renaissance • Global Exploration • Protestant Reformation

44. Intellectual Climate of Darwins Era (late 1700’s-Origin) Natural Theology, ala William Paley, pervades European and American Science Carolus Linnaeus establishes huge intellectual model; ________ _____________

45. Intellectual Climate of Darwins Era (late 1700’s-Origin) • William Paley and others develop and promote Natural Theology, which pervades European and American Science • Carolus Linnaeus establishes huge intellectual model; Systema naturae • Inception of modern systematics, built on Aristotelian Scala naturae; non-evolutionary

46. New Sciences of Geology and Paleontology are strong intellectual influences… • Catastrophism of Georges Cuvier • Gradualism of Hutton • Uniformitarianism of Lyell • Environmental Determinism

47. Charles Darwin (1809-1882) and Darwinism • Charles Darwin • …Rich kid; natural-born naturalist and observationist; graduated Cambridge having studied religion and medicine • ...Credited with figuring out that “natural selection” imposes character changes (adaptations) on populatons over time, one outcome being “speciation”, such that “diversity” is the consequence of a “species branching process” • ...collected and synthesized a compelling body of information to back it up -- voyage of the Beagle (1831-1836) • published it -- Origin of Species 1859

48. Voyage of the Beagle • Cape Verde Island • Brazil to Tierra del Fuego • The Galapagos Islands

49. From the Beagle to Origin • Artificial Selection • Population Theory of Thomas Malthus • Central Thesis of Origins: Descent with modification results in a branching tree of species, in which related species share common ancestry

50. Ernst Mayr’s formalization of Darwin’s Theory (stated as inferences based on observations)