Chapter 26

1. Chapter 26 The Tree of Life: An Introduction to Biological Diversity By: Cruz, Antonio

2. Overview:Changing Life on a Changing Earth • Life is a continuum extending from the earliest organisms to the great variety of species that exist today. • Throughout this unit, we will see examples of the connection between biological history and geological history. • Geologic events that alter environments change the course of biological evolution. • If one lake splits in two the fish in one part of the lake may evolve differently than the fish in the other lake. • The chapters in this unit also emphasize key junctures in evolution that have punctuated the history of biological diversity. Geologic history and biological history have been episodic, marked by what were in essence revolutions that opened many new ways of life.

3. Overview: Cont. • Historical study of any sort is an inexact discipline that depends on the preservation, reliability, and interpretation of past records. • The fossil record of past life is generally less and less complete the farther into the past we delve. • However, each organism alive today carries traces of its evolutionary history in its molecules, metabolism, and anatomy. • Such traces are clues to the past that augment the fossil record. • Still, the evolutionary episodes of greatest antiquity are generally the most obscure.

4. Overview: Cont. • We will begin this chapter by discussing the origin of life. That discussion is the most speculative in the entire unit, for no fossil evidence of that seminal episode exists. We will then turn to the fossil record and the connection between biological events and the physical history of Earth. • Next, we will present an overview of major milestones in the 3.8-billion-year story of life on Earth. • Finally, we will consider how biologists now understand the tree of life, a prelude to the survey of biological diversity.

5. Lets get started:)

6. 26.1: Conditions on early Earth made the origin of life possible • Scientific evidence is accumulating that chemical and physical processes on early Earth, aided by the emerging force of selection, produced very simple cells through a sequence of four main stages. • 1. The abiotic (nonliving) synthesis of small organic molecules, such as amino acids and nucleotides. • 2. The joining of these small molecules (monomers) into polymers, including proteins and nucleic acids. • 3. The packaging of these molecules into “protobionts,” droplets with membranes that maintained an internal chemistry different from that of their surroundings. • 4. The origin of self-replicating molecules that eventually made inheritance possible.

7. 26.1: Synthesis of Organic Compounds on Early Earth • Earth and the other planets of the solar system formed about 4.6 billion years ago, condensing from a vast cloud of dust and rocks that surrounded the young sun. • It is unlikely that life could have originated or survived on Earth for the first few hundred million years because the planet was still being bombarded by huge chunks of rock and ice left over from the formation of the solar system. • The collisions generated enough heat to vaporize all the available water and prevent seas from forming. • This phase likely ended about 3.9 billion years ago. • The oldest rocks on Earth’s surface, located at a site called Issua in Greenland, are 3.8 billion years old.

8. 26.1: Synthesis of Organic Compounds on Early Earth Cont. • There is evidence that life could have been around at that time but no fossils have been found to prove that. • As the bombardment of early Earth slowed, conditions on the planet were extremely different from those of today. • The first atmosphere was probably thick with water vapor, along with various compounds released by volcanic eruptions, including nitrogen and its oxides, carbon dioxide, methane, ammonia, hydrogen, and hydrogen sulfide. • As Earth cooled, the water vapor condensed into oceans, and much of the hydrogen quickly escaped into space.

9. 26.1: Synthesis of Organic Compounds on Early Earth Cont. • In the 1920s, ussian chemist A. I. Oparin and British scientist J. B. S. Haldane independently postulated that Earth’s early atmosphere had been a reducing (electron-adding) environment, in which organic compounds could have formed from simple molecules. • The energy for this organic synthesis could have come from lightning and intense UV radiation. • Haldane suggested that the early oceans were a solution of organic molecules, a “primitive soup” from which life arose. • In 1953, Stanley Miller and Harold Urey, of the University of Chicago, tested the Oparin-Haldane hypothesis by creating laboratory conditions comparable to those that scientists at the time thought only existed on Earth.

10. 26.1: Synthesis of Organic Compounds on Early Earth Cont. • Their apparatus yielded a variety of amino acids found in organisms today, along with other organic compounds. • Many laboratories have since repeated the experiment using different recipes for the atmosphere. • Organic compounds were also produced in some of these modified models. • However, it is unclear whether young Earth’s atmosphere contained enough methane and ammonia to be reducing. • Growing evidence suggests that the early atmosphere was made up primarily of nitrogen and carbon dioxide and was neither reducing nor oxidizing (electron removing). • Miller-Urey-type experiments using such atmospheres have not produced organic molecules.

11. 26.1: Synthesis of Organic Compounds on Early Earth Cont. • Still, it is likely that small “pockets” of the early atmosphere-perhaps near volcanic openings-were reducing. • Instead of forming in the atmosphere, the first organic compounds on Earth may have been synthesized near submerged volcanoes and deep-sea vents-weak points in Earth’s crust where hot water and minerals gush into the ocean. • These regions are also rich in inorganic sulfur and iron compounds, which are important in ATP synthesis by present-day organisms.

12. This would be the experiment that Miller and Urey conducted to see if organic molecules can form in a reducing atmosphere.

13. 26.1: Extraterrestrial Sources of Organic Compounds • Some of the organic compounds from which the first life on Earth arose may have come from space. Among the meteorites that land on Earth are carbonaceous chondrites, rocks that are 1-2% carbon compounds by mass. • Fragments of a 4.5-billion-year-old chondrite collected in southern Australia in 1969 contain more than 80 amino acids, some in large amounts. • Remarkably, the proportions of these amino acids are similar to those produced in the Miller-Urey experiment. • The chondrite amino acids cannot be contaminants from Earth because they consist of an equal mix of D and L isomers, with a few rare exceptions.

14. This is the submarine Alvin that used a robotic arm to get samples of water around a hydrothermal vent in the Sea of Cortes.

15. FUN FACT Mars is a good place to test hypotheses about the chemistry on Earth before life existed (pre-biotic chemistry). The surface of Mars is now a cold, dry, and apparently lifeless desert, but evidence is growing that billions of years ago it was relatively warm for a brief period, with liquid water and a carbon dioxide-rich atmosphere. During that period, pre-biotic chemistry similar to that on early Earth may have occurred on Mars. Did life evolve there and then die out, or was pre-biotic chemistry terminated by dropping temperatures and a thinning atmosphere before any life forms developed? Robot explorers are collecting data that may answer these questions in the next decade!

16. 26.1: Abiotic Synthesis of Polymers • Every cell has a vast assortment of macromolecules, including proteins and the nucleic acids that are essential for self replication, and it is difficult to imagine the emergence of life in an environment that did not contain similar macromolecules. • Researchers have produced amino acid polymers by dripping solutions of amino acids onto hot sand, clay, or rock. The polymers formed spontaneously, without help of enzymes or ribosomes. • Each polymer is complex and completely different. • Nevertheless, such macromolecules may have acted as weak catalysts for a variety of reactions on early Earth.

17. 26.1: Protobionts • Life is defined partly by two properties: accurate replication and metabolism. They can not exist without each other. • DNA molecules carry genetic info, including the instructions needed to replicate themselves accurately. But the replication of DNA requires an elaborate enzymatic machinery, along with a copious supply of nucleotide building blocks that must be provided by the cell’s metabolism. • The necessary conditions may have been met by protobionts, aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure. • Lab experiments demonstrate that protobionts could have formed spontaneously from abiotically produced organic compounds.

18. FUN FACT The first genetic material was probably RNA, not DNA!

19. This liposome is “giving birth” to smaller liposomes (LM).

20. 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.

21. 26.1: The “RNA World” and the Dawn of Natural Selection • Thomas Cech, of the University of Colorado, and Sidney Altman, of Yale University, found that RNA, which plays a central role in protein synthesis, can also carry out a number of enzyme-like catalytic functions. • Cech called these RNA catalysts ribosomes. • Some ribosomes can make complementary copies of short pieces of RNA, provided that they are supplied with nucleotide building blocks.

22. This RNA molecule can make a complementary copy of another piece of RNA (a template) containing up to 14 nucleotides.

23. 26.1: The “RNA World” and the Dawn of Natural Selection Cont. • Others can remove segments of themselves, or can act on different molecules, such as transfer RNA, excising pieces of these molecules and making them fully functional. • Natural selection on the molecular level has been observed operating on RNA populations in the lab. • In a particular environment, RNA molecules with certain base sequences are more stable and replicate faster with fewer errors than other sequences. • Physicist Freeman Dyson, of Princeton University, has suggested that the first RNA molecules may have been short, virus-like sequences and that these sequences were aided in their replication by random amino acid polymers that had rudimentary catalytic capabilities.

24. 26.2: The fossil record chronicles life on Earth • Questions about the earliest stages in the origin of life on Earth may never be fully answered because, as far as we know, there is no record of these ancient events. • Many later events, however, are well documented in the fossil record. • Careful study of fossils opens a window into the lives of organisms that existed long ago and provides info about the evolution of life over billions of years.

25. FUN FACT • Most fossils are found in sedimentary rock. Dead organisms are frozen in sediments. Scientists have found a way to date when an organism was around from its fossil by using radiometric dating, which is based on the decay of radioactive isotopes. Each radioactive isotope has a fixed rate of decay. An isotope’s half-life, the number of years it takes for 50% of the original sample to decay, is unaffected by temperature, pressure, and other environmental variables. • Fossils contain isotopes of elements that accumulated in the organisms when they were alive. • Paleontologists can often determine the age of fossils sand-whiched between layers of volcanic rocks by measuring the amount of the radioactive isotope potassium-40 in those layers.

26. Shelled animals called brachiopods were extremely abundant in the ancient seas. Their fossils are useful indicators of the relative ages of rock strata in different locations.

27. 26.2: The Geologic Record • Geologists have established a geologic record of Earth’s history, which is divided into three eons. • The first 2 eons were Archaean and the Proterozoic which lasted about 4 billion years. • The Phanerozoic eon lasted the last half billion years and is separated into 3 eras: the Paleozoic, Mesozoic, and Cenozoic. • Each era represents a distinct age in in the history of Earth and its life.

28. The Geologic Record

29. 26.2: Mass Extinctions A species may become extinct for many reasons • Habitat destroyed • Environment changed in an unfavorable direction for the species • Ocean temperatures fall by even a few degrees • Biological factors may change

30. 26.2: Mass Extinctions Cont. • The fossil record chronicles a number of occasions when global environmental changes were so rapid and disruptive that a majority of the species were swept away. • There are 2 main mass extinctions and those would be the Permian and the Cretaceous. • The Permian defines the boundary between the Paleozoic and Mesozoic eras. • The Cretaceous defines the boundary between the Mesozoic and Cenozoic eras.

31. 26.3: As prokaryotes evolved, they exploited and changed young Earth • The oldest known fossils, dating from 3.5 billion years ago, are fossils of stromatolites, which are rocklike structures composed of many layers of bacteria and sediment. • If bacterial communities were around 3.5 billion years ago it is reasonable to believe that life could have originated as early as 3.9 billion years ago.

32. Clock analogy for some key events in Earth’s history. The clock ticks down from the origin of Earth 4.6 billion years ago to the present.

33. Some bacterial mats form rocklike structures called stromatolites, such as these.

34. 26.3: The First Prokaryotes • The early protobionts that had both self-replicating and metabolic capabilities must have used molecules for their growth and replication that were already present in the primitive soup. • Eventually, these protobionts were replaced by organisms that could produce all their needed compounds from molecules in their environment. • These protobionts diversified into a rich variety of autotrophs, some of which could use light energy. Autotrophs most likely assisted in the making of heterotrophs. • These autotrophs and heterotrophs were the first prokaryotes, and they were Earth’s sole inhabitants from at least 3.5 to about 2 billion years ago. As we will see, these organisms transformed the biosphere of our planet.

35. 26.3: Electron Transport Systems • The chemiosmotic mechanism of ATP synthesis, in which a complex set of membrane-bound proteins pass electrons to reducible electron acceptors with the generation of ATP from AD, is common to all three domains of life-Bacteria, Archaea, and Eukarya. • The earliest of these electron transport systems likely evolved before there was any free oxygen in the environment and before the appearance of photosynthesis; the organisms that used it would have required a plentiful supply of energy-rich compounds such as molecular hydrogen, methane, and hydrogen sulfide.

36. 26.3: Photosynthesis and the Oxygen Revolution • Photosynthesis probably evolved very early in prokaryotic history, but in metabolic versions that did not split water and liberate oxygen. • The only living Photosynthetic prokaryotes that generate O2 are the cyanobacteria. • Most atmospheric O2 is of biological origin, from the water splitting step of photosynthesis. When this oxygenic photosynthesis first evolved, the free O2 it produced probably dissolved in the surrounding water until the seas and lakes became saturated with O2. • Additional O2 the reacted with dissolved iron and precipitated as iron oxide, which accumulated as sediments. • These sediments were compressed into banded iron formations, red layers of rock containing iron oxide that are a source of iron ore today.

37. The reddish streaks in this sedimentary rock are bands or iron oxide.

38. FUN FACT Once all the dissolved iron had precipitated, additional O2 finally began to “gas out” of the seas and lakes and enter the atmosphere. This change lefts its mark in the rusting of iron-rich terrestrial rocks, a process that began about 2.7 billion years ago! This chronology implies that cyanobacteria may have originated as early as 3.5 billion years ago, when the microbial mats that left fossilized stromatolites began forming.

39. 26.4: Eukaryotic cells arose from symbiosis and genetic exchanges between prokaryotes • Eukaryotic cells differ in many respects from the generally smaller cells of bacteria and archaea. • Even the smallest single-celled eukaryote is far more complex in structure than any prokaryote. • Among the most fundamental questions in biology is how these complex eukaryotic cells evolved from much simpler prokaryotic cells.

40. 26.4: The First Eukaryotes • The oldest fossils that most researchers agree are eukaryotic are about 2.1 billion years old. • Some researchers postulate a much earlier eukaryotic origin based on traces of molecules similar to cholesterol found in rocks dating back 2.7 billion years. • Such molecules are made only by eukaryotic cells that can respire aerobically. • If confirmed, these findings could mean that eukaryotes evolved when the oxygen revolution was beginning to transform Earth’s environments dramatically.

41. 26.4: Endosymbiotic Origin of Mitochondria and Plastids Prokaryotes lack many internal structures, such as: • the nuclear envelope • endoplasmic reticulum • Golgi apparatus These are characteristics of eukaryotic cells.

42. 26.4: Endosymbiotic Origin of Mitochondria and Plastids Cont. • Prokaryotes can not change the shape of their cells. • Eukaryotes can change shape enabling them to engulf other cells. • First eukaryotes may have been predators of other cells. • Internal organs can be shifted. • Closely related mechanism of meiosis became an essential part of sexual recombination of genes in eukaryotes.

43. 26.4: Endosymbiotic Origin of Mitochondria and Plastids Cont. • A process called endosymbiotic probably led to mitochondria and plastids. • Theory of endosymbiotic proposes that mitochondria and plastids were formerly smaller prokaryotes living within larger cells. • Endosymbiont refers to when a cell lives in another cell which is called the host cell. • The prokaryotic ancestors of mitochondria and plastids probably gained entry to the host cell as undigested prey or internal parasites. • It is not hard to imagine the symbiosis eventually becoming beneficial. • A heterotrophic host could use nutrients released from photosynthetic endosymbionts.

44. 26.4: Endosymbiotic Origin of Mitochondria and Plastids Cont. • Not all eukaryotes have plastids. • The hypothesis of serial endosymbiosis supposes that mitochondria evolved before plasmids.

45. A model of the origin of eukaryotes through serial endosymbiosis.

46. 26.4: Eukaryotic Cells as Genetic Chimeras • Greek mythology says that a chimera was a monster that was part goat, part lion, and part serpent. • The eukaryotic cell is a chimera of prokaryotic parts, its mitochondria derived from one type of bacteria, its plastids from another, and its nuclear genome from parts of these endosymbionts’ genomes and from at least one other cell, the cell that hosted the endosymbionts. • The genome of eukaryotic cells may be the product of genetic annealing, in which horizontal gene transfers occurred between many different bacterial and archaean lineages. • The Golgi apparatus and the endoplasmic reticulum may have originated from infoldings of the plasma membrane.

48. 26.5: Multicellularity evolved several times in eukaryotes • After the first eukaryotes appeared, a great range of unicellular forms evolved, giving rise to the diversity of single-celled eukaryotes that continue to flourish today. • Multicellular forms also evolved. • Their descendants include a variety of algae, plants, fungi, and animals.

49. 26.5: The Earliest Multicellular Eukaryotes • Molecular clocks date the common ancestor of multicellular eukaryotes to 1.5 billion years ago. Although the oldest multicellular fossil was a small algae that was about 1.2 billion years old. • Larger organisms did not appear in fossil record until several hundred million years later.

50. FUN FACT • Chinese paleontologists recently described a particularly rich site that contains 570-million-year-old fossils of a diversity of algae and animals, including beautifully preserved structures that are probably animal embryos.