The Tree of Life: An Introduction to Biological Diversity

1. Chapter 26 The Tree of LifeAn Introduction to Biological Diversity http://genomed.dlearn.kmu.edu.tw 生物醫學暨環境生物學系 張學偉 助理教授 changhw@kmu.edu.tw

2. Lecture Outline-1: The Origin of Life  1.Describe the four stages of the hypothesis for the origin of life on Earth by chemical evolution.  2.Describe the contributions that A. I. Oparin, J.B.S. Haldane, and Stanley Miller made toward developing a model for the abiotic synthesis of organic molecules.  3.Describe the evidence that suggests that RNA was the first genetic material. Explain the significance of the discovery of ribozymes.  4.Describe how natural selection may have favored the proliferation of stable protobionts with self-replicating, catalytic RNA.

3. Lecture Outline-2:Introduction to the History of Life  5. Explain how the histories of Earth and life are inseparable.  6. Explain how index fossils can be used to determine the relative age of fossil-bearing rock strata.  7. Describe the major events in Earth’s history from its origin until 2 billion years ago. Describe when Earth first formed, when life first evolved, and what forms of life existed in each eon.  8. Describe the mass extinctions of the Permian and Cretaceous periods. Discuss a hypothesis that accounts for each of these mass extinctions.

4. Lecture Outline -3: The Major Lineages of Life 9.Describe how chemiosmotic ATP production may have arisen. 10.Describe the timing and significance of the evolution of oxygenic photosynthesis. 11.Explain the endosymbiotic theory for the evolution of the eukaryotic cell. Describe the evidence that supports this theory. 12.Explain how genetic annealing may have led to modern eukaryotic genomes. 13.Describe the timing of key events in the evolution of the first eukaryotes and later multicellular eukaryotes. 14.Explain how the snowball-Earth hypothesis. Explains why multicellular eukaryotes were so limited in size, diversity, and distribution until the late Proterozoic. 15.Describe the key evolutionary adaptations that arose as life colonized land. 16.Explain why R. H. Whittaker’s five-kingdom system has been replaced by a new system with three domains.

5. Overview: Changing Life on a Changing Earth • Geological events  alter environments  change biological evolution Figure 26.1 • Conversely, life changes the planet that it inhabits

6. Concept 26.1: Conditions on early Earth made the origin of life possible • credible hypothesis by most biologists now • That chemical and physical processes on early Earth produced very simple cells through a sequence of stages

7. Four stages can be tested in the laboratory: • (1) the abiotic synthesis of small organic molecules. • (2) joining these small molecules into polymers. • (3) packaging of these molecules into “protobionts.” • (4) origin of self-replicating molecules.

8. (1) Synthesis of Organic Compounds on Early Earth • Earth formed about 4.6 billion years ago In the 1920’s, A.I. Oparin and J.B.S. Haldane independently postulated  that conditions on the early Earth favored the synthesis of organic compounds from inorganic precursors. • Earth’s early atmosphere •  contained water vapor and many chemicals released by volcanic eruptions.

9. Laboratory experiments • simulating an early Earth atmosphere • Have produced organic molecules from inorganic precursors • but the existence of such an atmosphere on early Earth is unlikely EXPERIMENT Miller and Urey set up a closed system in their laboratory to simulate conditions thought to have existed on early Earth. A warmed flask of water simulated the primeval sea. The strongly reducing “atmosphere” in the system consisted of H2, methane (CH4), ammonia (NH3), and water vapor. Sparks were discharged in the synthetic atmosphere to mimic lightning. A condenser cooled the atmosphere, raining water and any dissolved compounds into the miniature sea. CH4 Electrode Water vapor H2 NH3 Condenser Cold water RESULTS As material circulated through the apparatus, Miller and Urey periodically collected samples for analysis. They identified a variety of organic molecules, including amino acids such as alanine and glutamic acid that are common in the proteins of organisms. They also found many other amino acids and complex,oily hydrocarbons. Cooled water containing organic molecules CONCLUSION H2O Organic molecules, a first step in the origin of life, can form in a strongly reducing atmosphere. Sample for chemical analysis Figure 26.2

10. Instead of forming in the atmosphere • The first organic compounds on Earth may have been synthesized near submerged volcanoes and deep-sea vents Figure 26.3

11. 26.3 Hydro Thermal Vent

12. Extraterrestrial Sources of Organic Compounds • May have come from space. • Carbon compounds • found in some of the meteorites landed on Earth Looking Outside Earth for Clues About the Origin of Life • The possibilitythat life is not restricted to Earth • Is becoming more accessible to scientific testing

13. (2) Abiotic Synthesis of Polymers • Small organic molecules • Polymerize when they are concentrated on hot sand, clay, or rock (3) Protobionts Are aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure

14. Glucose-phosphate 20 m Glucose-phosphate Phosphorylase Starch Amylase Phosphate Maltose Maltose (a) Simple reproduction. This lipo-some is “giving birth” to smallerliposomes (LM). (b) Simple metabolism. If enzymes—in this case, phosphorylase and amylase—are included in the solution from which the droplets self-assemble, some liposomes can carry out simple metabolic reactions and export the products. • Laboratory experiments demonstrate that • protobionts could have formed spontaneously from abiotically produced organic compounds Figure 26.4a, b

15. The “RNA World” and the Dawn of Natural Selection • The first genetic material • Was probably RNA, not DNA

16. Ribozyme (RNA molecule) 3 Template Nucleotides Figure 26.5 5 5 Complementary RNA copy • RNA molecules called ribozymes have been found to catalyze many different reactions, including • Self-splicing • Making complementary copies(self-replication) of short stretches of their own sequence or other short pieces of RNA

17. (4) Early protobionts with self-replicating, e.g., catalytic RNA. • becoming more effective at using resources and through natural selection.

18. Concept 26.2: The fossil record chronicles life on Earth • Careful study of fossils • Opens a window into the lives of organisms about the evolution of life. How Rocks and Fossils Are Dated • Sedimentary strata • Reveal the relative ages of fossils

19. 26.6 Grand Canyon

20. Index fossils • Are similar fossils found in the same strata in different locations • Allow strata at one location to be correlated with strata at another location Figure 26.6

21. Accumulating “daughter” isotope 1 2 Ratio of parent isotope to daughter isotope 1 4 Remaining “parent” isotope 1 8 1 16 1 2 3 4 Time (half-lives) isotope • The absolute ages of fossils • Can be determined by radiometric dating Figure 26.7

22. The magnetism of rocks • also provide dating information

23. The Geologic Record • The geologic record is divided into • Three eons: the Archaean, the Proterozoic, and the Phanerozoic • Many eras and periods • By studying rocks and fossils at many different sites  established a geologic record of Earth’s history.

24. http://tw.knowledge.yahoo.com/question/?qid=1205081201537 顯生元 (Phanerozoic Eon) 顯生元是生命大量出現的意思，包含了自5億7千萬年前以來的這一段時間。由於生命在5億5千萬年前時迅速地展開 (稱寒武紀大爆發)，所以形成了現今留存在岩石中的許多化石與地殼變動的現象，成為研究較詳細的部份。因此，本文將顯生元再細分為古生代、中生代及新生代予以說明。 1.古生代 (Paleozoic Era.) 古生代意思是古代生物生活的時期，時間自5億7千萬年前至2億4千5百萬年前，由寒武紀、奧陶紀、志留紀、泥盆紀、石炭紀及二疊紀等六個紀組成。古生代早期 (包括寒武紀、奧陶紀和志留紀)，古生代晚期則為泥盆紀、石炭紀和二疊紀。 (1) 寒武紀 (Cambrian Period) 是指古生代中最老的一個紀，涵蓋的時間自5億7千萬年至5億5百萬年前的這一段時間。Cambrian由Cambria演變而來，而Cambria是羅馬文中威爾斯(Wales)的意思。在這一段時間內重要的事件為生物的「寒武紀大爆發」，而且單細胞生物繁多，三葉蟲普遍存在。 (2) 奧陶紀 (Ordovician Period) 是古生代的第二個紀，為5億5百萬年前到4億3千8百萬年前的這一段時間。Ordovician名稱是由生活在愛爾蘭、威爾斯及蘇格蘭高地的Celt 族的一支稱為Ordovices所演變而來的。在奧陶紀約6千萬年的時間裡，地球大部分為溫和的氣候，在海中大多數還覆蓋了生物建造之沈積物，珊瑚礁、藻礁、海綿及貝類豐富。 (3) 志留紀 (Silurian Period) 志留紀介於奧陶紀與泥盆紀之間，為早古生代的末期，是指4億3千8百萬年前至4億8百萬年前的這一段時間。Silurian亦是由生活在愛爾蘭、威爾斯及蘇格蘭高地的Celt 族的一支稱為Silures所演變而來的。在志留紀時魚類出現了，成為第一個脊椎動物，陸生植物亦出現。另外，加里東造山運動發生在志留紀末期，這個重大的造山運動形成自蘇格蘭一直延伸至斯堪地半島的山脈。 (4) 泥盆紀 (Devonian Period) 泥盆紀為晚古生代的第一個紀，介於志留紀與石炭紀之間，涵蓋的時間範圍為4億8百萬年前到3億6千萬年前，約有5千萬年的時距。Devonian (泥盆紀)是由英格蘭西南部Devonshire州演變而來的，因為這一時代的岩層最早是在此開始進行研究的。泥盆紀為古生代中造山運動的顛峰期，同時因為魚類繁衍，故泥盆紀又稱為魚的時代。不僅如此，第一個陸地脊椎動物兩生類，在泥盆紀進化形成了。 (5) 石炭紀 (Carboniferous Period) 石炭紀為3億6千萬年至2億8千6百萬年前的這段時間，因為在這段時間裡所形成的岩層中含有豐富的煤炭，因此石炭紀又可稱為煤炭的時代，目前全世界所使用的煤炭，大部份是形成於這個時代。在北美洲習慣上將石炭紀分為老的密西西比(Mississippian)及年輕的賓夕法尼亞(Pennsylvanian)二個期。石炭紀時氣候相當溫合，北美和歐洲富含森林、沼澤和三角洲，形成大煤田。昆蟲繁茂，第一個爬蟲類出現。 (6) 二疊紀 (Permian Period) 二疊紀為古生代最後一個紀，時距為2億8千6百萬年至2億4千5百萬年前。Permian 是由首先研究前蘇聯Perm地區這一時代的岩層演變而來的。二疊紀時形成了超級的大陸塊，稱為盤古大陸 (Pangaea)。二疊紀時造山運動劇烈，海西寧 (Hercynian)造山運動帶來了岩漿活動、褶皺和斷層。形成了德國的哈次山 (Harz)、中國的天山、崑崙山和阿爾泰山。此外，美國東部的阿帕拉契山脈和俄羅斯的烏拉山脈都在這一個時期造成。對於台灣而言，目前所知道且有化石證據的最古老岩層-大南澳雜岩帶中的大理岩即是在二疊紀晚期堆積形成的。二疊紀時兩棲類生物大量繁衍，因此二疊紀亦稱為兩棲類的時代。二疊紀末期地球發生了重大的變化，目前推側是類似6千五百萬年前白堊紀末期發生的隕星或慧星撞地球的事件，造成了約90%生物滅絕。 2.中生代 (Mesozoic Era.) 中生代指的是2億4千5百萬年前至6千6百50萬年前的這一段時間。在這一段時間內，恐龍出現並大量繁衍，成為主宰地球的脊椎動物。因此，中生代又稱為恐龍的時代。在這一時代的末期，哺乳動物首度出現，並經歷過6千5百萬年前的大浩劫而留存下來，進而稱霸於自6千5百萬年前至今的新生代。 (1) 三疊紀 (Triassic Period) 在經過二疊紀末其生物的大量滅絕之後，三疊紀成為中生代的第一個紀，是指距今2億4千5百萬年至2億8百萬年前，為一段約3千7百萬年時間。三疊紀名稱的由來，是在研究位於德國此一時代的地層時，發現岩層互相疊置呈三層狀，所以稱三疊紀。中生代初期三疊紀時，全球各地大多乾旱，與古生代的濕潤狀況不同。在三疊紀時，全球原來祇有一片原始大陸 (盤古大陸)(Pangaea)。第一個恐龍和巨大的海上爬蟲普遍出現，同時小型原始哺乳動物進化出現。 (2) 侏儸紀 (Jurassic Period) 侏儸紀的名稱是由首次研究位於法國與瑞士間的侏儸山(Jura Mtns.)演變而來，為距離現在2億8百萬年到1億4千4百萬年這一段約6千4百萬年的時間。侏儸紀時恐龍廣泛分布，飛行的爬蟲類與原始鳥類征服天空。同時自侏羅紀開始，大陸開始分裂，由於美洲和歐洲分開，造成大西洋。而侏羅紀末至白堊紀，全球的造山運動更趨激烈，形成了美國西部的內華達 (Sierra Nevada)山脈及東側的落磯山脈。 (3) 白堊紀 (Cretaceous Period) 白堊紀為中生代最末一個紀，代表1億4千4百萬年至6千6百50萬年前的這一段時間。Creta拉丁文中為白堊(chalk)的意思，英國南部及法國有許多這一時期、這一種岩類的地層，而由比利時地質學家Omalius d’Halloy依據巴黎盆地含有化石的白堊地層命名為Cretaceous。中國在白堊紀中期至末期，發生燕山造山運動，在沿海各省有火山活動，台灣亦因為太平洋板塊與歐亞大陸的隱沒作用，形成中央山脈的雛型。白堊紀末期發生了隕星或慧星撞地球的毀滅性事件，導致大部份的生物死亡，同時結束了恐龍統治地球的時代。 3.新生代 (Cenozoic Era.) 新生代包括中生代末期直到現在的這段時間。較老的部分稱為第三紀 (自6千6百50萬年前開始到160萬年前)，年輕的部分稱為第四紀 (自160萬年前開始至今)。新生代雖然時間短，但是它在地球歷史上是一個非常獨特的時期。造山運動達到最高峰，如喜馬拉雅山、台灣島都是在這個時期形成的。 (1) 第三紀 (Tertiary Period) 第三紀由古新世 (Paleocene)、始新世 (Eocene)、漸新世 (Oligocene)、中新世 (Miocene)和上新世 (Pliocene)等五個世所組成，名稱均由希臘文演變而成，用來描述地球歷史上最近的這一段時期。古新世是指6千6百50萬年前到5千7百80萬年前的這一段時間；始新世為5千7百80萬年到3千6百60萬年前的這一段時間；漸新世是3千6百60萬年到2千3百70萬年前的這一段時間；中新世為2千3百70萬年到5百30萬年前的這一段時間；而上新世則是5百30萬年前到160萬年前的這一段時間。在第三紀初期，當時的臺灣、喜馬拉雅山和阿爾卑斯山都是接受沉積物的沉積環境，均為海水所掩蓋。到了第三紀末期，受到造山運動的影響，形成阿爾卑斯山脈、喜馬拉雅山脈和台灣的中央山脈。 此外，在經歷了白堊紀末期大量生物死亡、滅絕後，哺乳動物爆炸性成長，開花植物普遍出現，而且氣候涼冷，所以草地出現。同時大致上已經隆起的中央山脈，成為現今為雪山山脈與麓山帶沉積盆地來源，形成大量的堆積。(2) 第四紀 (Quaternary Period) 第四紀是由更新世 (Pleistocene)和全新世 (Holocene)二個世所組成。更新世約自160萬年前開始，全新世則由10,000年開始至今的這一段時間，全新世亦稱現代 (Recent)，是地質時代中最晚的時期。在這個時代裏，哺乳動物增長和適應，現生動物興起，而人類進化並成為地球上優勢的族群。

25. The geologic record Table 26.1

26. Millions of years ago 600 400 300 200 500 100 0 2,500 100 Number of taxonomic families 80 2,000 Permian mass extinction Extinction rate 60 1,500 Number of families ( ) Extinction rate ( ) 40 1,000 Cretaceous mass extinction 500 20 0 0 Carboniferous Neogene Cretaceous Ordovician Paleogene Cambrian Devonian Jurassic Permian Triassic Proterozoic eon Silurian Ceno- zoic Paleozoic Mesozoic Mass Extinctions • The fossil record occasions.  global environmental changes rapid and disruptive a majority of species. • Two major mass extinctions: the Permian and the Cretaceous Figure 26.8

27. The Permian extinction • Claimed about 96% of marine animal species and 8 out of 27 orders of insects • Is thought to have been caused by enormous volcanic eruptions

28. 26.19 Volcanic Eruption

29. NORTH AMERICA Chicxulub crater Yucatán Peninsula • The Cretaceous extinction • Doomed many marine and terrestrial organisms, most notably the dinosaurs • Is thought to have been caused by the impact of a large meteor Figure 26.9

30. Ceno-zoic Meso-zoic Paleozoic Humans Land plants Origin of solar system and Earth Animals 4 1 Proterozoic Eon Archaean Eon Billions of years ago 2 3 Multicellular eukaryotes Single-celled eukaryotes Prokaryotes Figure 26.10 Atmospheric oxygen • The analogy of a clock • for major events in the Earth’s history in the geological record

31. Concept 26.3: As prokaryotes evolved, they exploited and changed young Earth • The oldest known fossils are stromatolites. • Rocklike structures composed of many layers of bacteria and sediment • Which date back 3.5 billion years ago.

32. The First Prokaryotes • Prokaryotes were Earth’s sole inhabitants • From 3.5 to about 2 billion years ago Electron Transport Systems • Electron transport systems of a variety of types • Were essential to early life (detail in chapter 27) Photosynthesis and the Oxygen Revolution • The earliest types of photosynthesis • Did not produce oxygen

33. Oxygenic photosynthesis • Probably evolved about 3.5 billion years ago incyanobacteria Figure 26.12

34. When oxygen began to accumulate in the atmosphere about 2.7 billion years ago • It posed a challenge for life • It provided an opportunity to gain abundant energy from light • It provided organisms an opportunity to exploit new ecosystems

35. Concept 26.4: Eukaryotic cells arose from symbioses and genetic exchanges between prokaryotes The First Eukaryotes • The oldest fossils of eukaryotic cells • Date back 2.1 billion years

36. Endosymbiotic Origin of Mitochondria and Plastids • The theory of endosymbiosis • Proposes that mitochondria and plastids were formerly small prokaryotes living within larger host cells. • The evidence • Similarities in inner membrane structures and functions. (2 membr.) • Both have their own circular DNA

37. Cytoplasm DNA Plasma membrane Ancestral prokaryote Infolding of plasma membrane Nucleus Endoplasmic reticulum Nuclear envelope Engulfing of aerobic heterotrophic prokaryote Cell with nucleus and endomembrane system Mitochondrion Mitochondrion Engulfing of photosynthetic prokaryote in some cells Ancestral heterotrophic eukaryote Plastid Ancestral Photosynthetic eukaryote Figure 26.13 • The prokaryotic ancestors of mitochondria and plastids Probably gained entry to the host cell as undigested prey or internal parasites.

38. Eukaryotic Cells as Genetic Chimeras • Additional endosymbiotic events and horizontal gene transfers • May have contributed to the large genomes and complex cellular structures of eukaryotic cells 探討基因從細菌平行轉移到人類基因體中的可能性? http://tw.knowledge.yahoo.com/question/?qid=1005031701918

39. 50 m • eukaryotic flagella and cilia • Evolved from symbiotic bacteria, based on symbiotic relationships between some bacteria and protozoans. Chimera Figure 26.14

40. Concept 26.5: Multicellularity evolved several times in eukaryotes The Earliest Multicellular Eukaryotes • Molecular clocks 分子時鐘 http://tw.knowledge.yahoo.com/question/?qid=1005040506915 • Date the common ancestor of multicellular eukaryotes to 1.5 billion years • The oldest known fossils of eukaryotes • Are of relatively small algae that lived about 1.2 billion years ago

41. Figure 26.15a, b (a) Two-cell stage (b) Later stage 150 m 200 m • Larger organisms do not appear in the fossil record-- Until several hundred million years later • Chinese paleontologists recently described 570-million-year-old fossils • That are probably animal embryos

42. snowball Earth hypothesis  ice age (750 to 570 million years ago) may be responsible for the limited diversity and distribution of multicellular eukaryotes until the very late Precambrian.  The first major diversification at the time of thawing of snowball Earth.

43. 10 m The Colonial Connection • The first multicellular organisms were colonies • Collections of autonomously replicating cells 盤星藻(Pediastrum) Figure 26.16

44. The “Cambrian Explosion” = Cambrian radiation • Most of the major phyla of animals • Appear suddenly in the fossil record that was laid down during the first 20 million years of the Cambrian period.

45. Bar from fossil record; however, sometimes the molecular evidence suggested that it has originated eariler. 500 Annelids Sponges Molluscs Chordates Cnidarians Arthropods Brachiopods Echinoderms Early Paleozoic era (Cambrian period) Millions of years ago 542 Late Proterozoic eon Figure 26.17

46. Colonization of Land by Plants, Fungi, and Animals • Plants, fungi, and animals • Colonized land about 500 million years ago • Symbiotic relationships between plants and fungi.  Are common today

47. Eurasian Plate North American Plate Juan de Fuca Plate Caribbean Plate Philippine Plate Arabian Plate Indian Plate Cocos Plate South American Plate Pacific Plate Nazca Plate African Plate Australian Plate Scotia Plate Antarctic Plate Continental Drift • Earth’s continents are not fixed Pulling apart or pushing against each plate Figure 26.18

48. 26.19 Lava Flow

49. Volcanoes and volcanic islands Oceanic ridge Trench Subduction zone Oceanic crust Seafloor spreading Figure 26.19 • Many important geological processes • Occur at plate boundaries or at weak points in the plates themselves

50. India collided with Eurasia just 10 million years ago, forming the Himalayas, the tallest and youngest of Earth’s major mountain ranges. The continents continue to drift. 0 Cenozoic North America Eurasia By the end of the Mesozoic, Laurasia and Gondwana separated into the present-day continents. 65.5 Africa India South America Madagascar Australia Antarctica By the mid-Mesozoic, Pangaea split into northern (Laurasia) and southern (Gondwana) landmasses. Laurasia Millions of years ago 135 Gondwana Mesozoic At the end of the Paleozoic, all of Earth’s landmasses were joined in the supercontinent Pangaea. 251 Pangaea Paleozoic Figure 26.20 • The formation of the supercontinent Pangaea during the late Paleozoic era • And its breakup during the Mesozoic era explain many biogeographic puzzles Continental drift