History of Life On Earth

History of Life On Earth
2/20/2018 History of Life On Earth

Today’s OUTLINE: 1) Geological Time Scale
2/20/2018 Today’s OUTLINE: 1) Geological Time Scale 2) Major Episodes in History of Life 3) Extinctions and Radiations

Geology plays an Important role in Evolutionary Thinking
2/20/2018 Geology plays an Important role in Evolutionary Thinking Patterns of extinctions and evolutionary change in the fossil record were among the main influences on Darwin’s thinking

Imagine... That all of Earth History is compressed
2/20/2018 Imagine... That all of Earth History is compressed into a single year...

When did life first arise? And in what form?
2/20/2018 When did life first arise? And in what form? When did Eukaryotes arise? What about multicellular organisms (metazoans)? The invasion of land from the sea? Mammals? Humans?

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The point of this exercise
2/20/2018 The point of this exercise Life evolved under anaerobic conditions Much of the history of Life has been in the forms of prokaryotes and single cell eukaryotes (single cells) Multicellular organisms are relatively recent Humans have inhabited this planet for a very very short time

The first life on earth was in the form of prokaryotes
The Oxygen Revolution was a pivotal event that transformed life on Earth Humans have inhabited this planet for a very very short time

Key Events in Evolution of Life on Earth
1.2 bya: First multicellular eukaryotes 535–525 mya: Cambrian explosion (great increase in diversity of animal forms) 500 mya: Colonization of land by fungi, plants and animals 2.1 bya: First eukaryotes (single-celled) 3.5 billion years ago (bya): First prokaryotes (single-celled) 500 4,000 3,500 3,000 2,500 2,000 1,500 1,000 Present Millions of years ago (mya)

Carol Lee, Animal Evolution David Baum, Plant Evolution
1.2 bya: First multicellular eukaryotes 535–525 mya: Cambrian explosion (great increase in diversity of animal forms) This Lecture 500 mya: Colonization of land by fungi, plants and animals 2.1 bya: First eukaryotes (single-celled) Jeremy Glasner, Microbial Evolution 3.5 billion years ago (bya): First prokaryotes (single-celled) 500 4,000 3,500 3,000 2,500 2,000 1,500 1,000 Present Millions of years ago (mya)

The 3 Domains of Life Eukarya
Phylogenetic relationships based on 18S rRNA sequences, showing clade separation of bacteria, archaea, and eukaryotes.

Another way to look at the Geological Time Scale
Meso- zoic Cenozoic Humans Paleozoic Colonization of land Animals Origin of solar system and Earth 1 4 Proterozoic Archaean Prokaryotes Figure 25.7 Clock analogy for some key events in Earth’s history Billions of years ago 2 3 Multicellular eukaryotes Single-celled eukaryotes Atmospheric oxygen

Formation of Sedimentary rock
2/20/2018 Formation of Sedimentary rock

Fossils (1) Hard parts mineralized (chemical reactions)
2/20/2018 Fossils (1) Hard parts mineralized (chemical reactions) (2) Or the bone disintegrates mold filled with dissolved minerals (3) Total preservation: amber, ice, bogs

Can tell how old something is by how much radioisotope has disappeared
2/20/2018 Radiometric Dating Can tell how old something is by how much radioisotope has disappeared Each isotope has a known half-life, the time required for half the parent isotope to decay

Molecular Clock Mutations On average, mutations occur at a given rate
2/20/2018 Molecular Clock Mutations On average, mutations occur at a given rate Example: Mitochondria: ~2.2%/million years.

Molecular Clock Faster if Mutation rate is faster if:
2/20/2018 Molecular Clock Faster if Mutation rate is faster if: Shorter generation time (more meiosis or mitosis per time) Sloppy polymerase (e.g. HIV) Inefficient mismatch repair, etc.

Roughly so, but gaps in the fossil record
2/20/2018 Is the fossil record roughly congruent with timing of events based on the molecular clock? Roughly so, but gaps in the fossil record And molecular clock varies among genes and species

Table 25.1

2/20/2018 Cenozoic Mesozoic Paleozoic Precambrian

Origin of solar system and Earth
Cenozoic Mesozoic Paleozoic Origin of solar system and Earth 1 4 Proterozoic Archaean Billions of years ago 2 3

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Boundaries between Eras
2/20/2018 Boundaries between Eras Marked by Explosive Adaptive Radiations And Mass Extinctions

Mass Extinction Events
20 800 700 15 600 500 (families per million years): Total extinction rate 10 400 Number of families: 300 5 200 100 Figure Mass extinction and the diversity of life Era Period Paleozoic Mesozoic Cenozoic E O S D C P Tr J C P N 542 488 444 416 359 299 251 200 145 65.5 Time (millions of years ago)

2/20/2018 Adaptive Radiations Divergence of a phylogenetic group into forms adapted to various ecological niches. Happens over short geological time (~5 million years) Change in environment (Global Climate Change) Open Niches due to Extinction Or exploitation of new Niche (due to novel trait) Examples: Response to climate change, Colonization of Land, Air (flight), Cold, High Altitude, colonization of islands

On the islands of Hawaii
2/20/2018 Adaptive Radiations On the islands of Hawaii Hawaiian honeycreepers Hawaiian silverswords

Adaptive radiation often results in a star phylogeny
2/20/2018 Adaptive radiation often results in a star phylogeny Rapid speciation: Can’t tell which taxa diverged first

230 mya: Permian Extinction
2/20/2018 65 mya: Cretaceous Extinction (dinosaurs go extinct) 230 mya: Permian Extinction 570 mya: Cambrian Explosion

Cenozoic: Age of Mammals
2/20/2018 Cenozoic: Age of Mammals Mesozoic: Age of Reptiles Paleozoic: Age of Invertebrates Precambrian: Age of Single Cell

“Age of the Single Cell”
2/20/2018 ERA: Precambrian “Age of the Single Cell” 90% Earth History Origin of Life Prokaryotes Oxygen Eukaryotes First animals

Origins of Life (Herron & Freeman, Chapter 17)
2/20/2018 The Earth was formed ~4.6 billion years ago Earth’s early atmosphere likely contained water vapor and chemicals released by volcanic eruptions (nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen, hydrogen sulfide)

What were the earliest life forms?
Prokaryotes are the earliest life forms we know of, but what might have preceded them?

Protobionts 20 µm Fig. 25-3 Glucose-phosphate Glucose-phosphate Phosphatase Starch Amylase Phosphate Maltose Figure 25.3 Laboratory versions of protobionts (a) Simple reproduction by liposomes Maltose (b) Simple metabolism Protobionts are aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure Protobionts exhibit simple reproduction and metabolism and maintain an internal chemical environment

Protobionts Replication and metabolism are key properties of life
Experiments demonstrate that protobionts could have formed spontaneously from abiotically produced organic compounds For example, small membrane-bounded droplets called liposomes can form when lipids or other organic molecules are added to water

Self-Replicating RNA and the Dawn of Natural Selection
The early genetic material might have formed an “RNA world” The first genetic material was probably RNA, not DNA Early life forms might have consisted of protobionts with RNA as the genetic code Early protobionts with self-replicating, catalytic RNA would have been more effective at using resources and would have increased in number through natural selection

RNA World RNA can both serve as the genetic code (hereditary material) and also perform enzymatic functions (ribozymes) RNA molecules called ribozymes have been found to catalyze many different reactions For example, ribozymes can make complementary copies of short stretches of their own sequence or other short pieces of RNA Natural selection in the laboratory has produced ribozymes capable of self-replication (Herron& Freeman written prior to this discovery)

Self-Replicating RNA and the Dawn of Natural Selection
Ribozymes (= RNA enzyme or catalytic RNA) RNA that can catalyze chemical reactions. Many natural ribozymes catalyze either the breaking or synthesis of phosphoester bonds in DNA or RNA. Such capacity would enable the capacity to self replicate and propagate life. The functional part of the ribosome, the molecular machine that translates RNA into proteins, is fundamentally a ribozyme

The First Single-Celled Organisms
Prokaryotes Billions of years ago 4 3 2 1 The First Single-Celled Organisms The oldest known fossils are stromatolites, rock-like structures composed of many layers of bacteria and sediment Stromatolites date back 3.5 billion years ago Prokaryotes were Earth’s sole inhabitants from 3.5 to about 2.1 billion years ago

Stromatolites The oldest known fossils are of cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old

2/20/2018 ERA: Precambrian “Age of the Single Cell” 90% Earth History Origin of Life Prokaryotes Oxygen in Atmosphere Eukaryotes First animals

Oxygen Revolution “Oxygen revolution” from 2.7 to 2.2 billion yrs ago
Atmospheric oxygen Billions of years ago 4 3 2 1 Oxygen Revolution By about 2.7 billion years ago, O2 began accumulating in the atmosphere and rusting iron-rich terrestrial rocks “Oxygen revolution” from 2.7 to 2.2 billion yrs ago O2 in the atmosphere was generated by photosynthetic activity of cyanobacteria (next lecture) Posed a challenge for life (O2 toxicity) Provided opportunity to gain energy from light Allowed organisms to exploit new ecosystems

Oxygen Revolution “Oxygen revolution” from 2.7 to 2.2 billion yrs ago
Atmospheric oxygen Billions of years ago 4 3 2 1 Oxygen Revolution “Oxygen revolution” from 2.7 to 2.2 billion yrs ago O2 in the atmosphere was generated by photosynthetic activity of cyanobacteria Cyanobacteria were the first organisms to use H2O (instead of H2S or other compounds) as a source of electrons and hydrogen for fixing CO2 Photosynthesis: 6 CO2 + 6 H2O + photons → C6H12O6 + 6 O2

Oxygen Revolution O2 allows the production of more energy and more efficient metabolism C6H12O O2 → 6 CO H2O, ΔG = kJ per mole of C6H12O6 Aerobic metabolism: 36 ATP molecules per glucose Anaerobic metabolism: 2 ATP molecules per glucose Aerobic and anaerobic metabolism share the initial pathway of glycolysis but aerobic metabolism continues with the Krebs cycle and oxidative phosphorylation. However, Oxygen is also Toxic Oxygen is highly toxic to many species Electrons that escape from the electron transport chain can bind to oxygen and produce reactive oxygen species Reactive oxygen species (H2O2, O2−) can damage DNA and other molecules

Evolutionary History dictates type of Metabolism
The fact that much of prokaryotic life evolved BEFORE the oxygen revolution is reflected in the diverse forms of anaerobic metabolism Most bacteria do not require oxygen, and for many it is toxic Most bacteria use other molecules as the terminal electron acceptor when making ATP The fact eukaryotic life evolved AFTER the oxygen revolution is reflected in the fact that all eukaryotes use aerobic metabolism They use oxygen as the terminal electron acceptor in energy production

The oldest fossils of eukaryotic cells date back 2.1 billion years
Single-celled eukaryotes Billions of years ago 4 3 2 1 The First Eukaryotes The oldest fossils of eukaryotic cells date back 2.1 billion years The hypothesis of endosymbiosis proposes that mitochondria and plastids (chloroplasts and related organelles) were formerly small prokaryotes living within larger host cells (talk about this in Next Lecture) An endosymbiont is a cell that lives within a host cell

Lynn Margulis Endosymbiotic Theory Wrote the seminal paper “The Origin of Mitosing Eukaryotic Cells” 1966 Certain organelles originated as free-living bacteria that were taken inside another cell as endosymbionts. Mitochondria developed from proteobacteria (in particular, Rickettsiales or close relatives) and chloroplasts from cyanobacteria Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular in shape, its size, and DNA composition)

Covered in Chapter 15, Freeman and Herron
Figure 25.9 A model of the origin of eukaryotes through serial endosymbiosis Probably Archaea The organelles (mitochondria and chloroplasts) greatly aid in energy production in eukaryotes.

Given the evolutionary history of endosymbiosis (or endosymbiogenesis) leading to eukaryotes, eukaryotes will inevitably share traits with both archaea and bacteria Table 27.2

The Origin of Multicellularity
eukaryotes Billions of years ago 4 3 2 1 The Origin of Multicellularity Comparisons of DNA sequences date the common ancestor of multicellular eukaryotes to 1.5 billion years ago Oldest known fossils of multicellular eukaryotes are of small algae that lived about 1.2 billion years ago First major diversification of multicellular eukaryotes corresponds to a time of the thawing of the planet (starting 565 million years ago) Another major diversification happened 30 million years later (Cambrian Explosion)

2/20/2018 What is an Animal?

What is an Animal? Multicellular (metazoan)
2/20/2018 What is an Animal? Multicellular (metazoan) Heterotrophic (eat, not photo or chemosynthetic) Eukaryote No Cell Walls, have collagen Nervous tissue, muscle tissue Particular Life History-developmental patterns (Next lecture)

Origins of Multicellularity
2/20/2018 Origins of Multicellularity It is thought that metazoans arose from Colonial flagellate protists Oxygen Revolution: allow higher metabolic rate larger body size powered motion

Cells of sponges are similar to flagellate protists
2/20/2018 Cells of sponges are similar to flagellate protists

Cambrian Explosion (1) Precambrian-Paleozoic Boundary (~570 MYA)
2/20/2018 (1) Precambrian-Paleozoic Boundary (~570 MYA) Fossil Deposits: Doushanto fossils Ediacaran fossils Burgess Shale Cambrian Explosion

(Cambrian Explosion (570 MYA)
2/20/2018 (Cambrian Explosion (570 MYA) Burgess Shale

Radiations: Extinctions???? Cambrian Explosion
2/20/2018 (1) Precambrian-Paleozoic Boundary (~570 MYA) Cambrian Explosion Radiations: Evolution of hard body parts Diversification of body forms Radiation of Invertebrates Extinctions???? Hard to tell, Precambrian species were single cell, soft Calymeme celebra

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2/20/2018 When?

The Cambrian Explosion
The Cambrian explosion originally referred to the sudden appearance of fossils resembling modern phyla in the Cambrian period (~543 to 525 million years ago)—mostly based on the Burgess Shale fossils Phylogenetic analysis suggest that many animal phyla diverged before the Cambrian explosion recorded in the fossil record, perhaps as early as 700 million to 1 billion years ago

2/20/2018 Are Genetic Distances and fossil record roughly congruent?

Was the Cambrian Explosion an Explosion?
2/20/2018 Was the Cambrian Explosion an Explosion? Geology: YES Sudden Appearance of Animal Fossils Genetics: NO DNA Divergences Predate Cambrian

Precambrian Annelida Arthropoda Mollusca Agnatha Gnathostomata
2/20/2018 Annelida Mollusca Million Years Ago Arthropoda Agnatha Echinodermata Gnathostomata 200 Cambrian “Cambrian Explosion” 600 Based on phylogeny of animals based on DNA sequence data, the radiation of animals predates the geological record of the Cambrian Explosion 800 1000 Precambrian 1200 Wray et al. 1996 1400

Fossil Record vs Molecular Clock
2/20/2018 Fossil Record vs Molecular Clock Molecular clock and fossil record are not always congruent Fossil record is incomplete, and soft bodied species are usually not preserved Mutation rates can vary among species (depending on generation time, replication error, mismatch repair) But they provide complementary information Fossil record contains extinct species, while molecular data is based on extant taxa Major events in fossil record could be used to calibrate the molecular clock

Fossil Record vs Molecular Clock
2/20/2018 Fossil Record vs Molecular Clock So it’s highly likely that the divergence of animal lineages (phyla) was more gradual than the fossil record would suggest and that the time of divergence happened earlier

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The Cambrian Explosion: Major Fossil Formations
2/20/2018 The Cambrian Explosion: Major Fossil Formations Doushantuo Formation (Southern China): 570 million years ago Ediacaran Fauna (Australia): million years ago The Burgess Shale (British Columbia, Canada): million yrs ago

Doushantuo formation Southern China
2/20/2018 Doushantuo formation Southern China 570 million years ago Clusters of cells (embryos?) Sponges Fossilized metazoan embryo at the 256 cell stage

The Cambrian Explosion
The Doushantuo fossils in China provide evidence of modern animal phyla tens of millions of years before the Cambrian explosion recorded in the Burgess Shale (~570 million years ago) The Chinese fossils, along with DNA data, suggest that the Cambrian explosion occurred over a more extended period of time than previously thought (a) Two-cell stage 150 µm 200 µm (b) Later stage

Ediacaran Hills, Australia
2/20/2018 Ediacaran Fauna Dickinsonia Ediacaran Hills, Australia Tribrachidium heraldicum

Ediacaran Fauna 565-544 million years ago
2/20/2018 million years ago Soft-body animals, sponges, jellyfish, ctenophores No evidence of locomotion

2/20/2018 Burgess Shale Fauna

2/20/2018 Burgess Shale Fossils Marrella Aysheaia Canadia Hallucigenea

2/20/2018 The Paleozoic Sea

Burgess Shale http://www.burgess-shale.bc.ca/
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Burgess Shale Fauna Marrella British Columbia, Canada
2/20/2018 Burgess Shale Fauna British Columbia, Canada million yrs ago All animal phylum found Marrella Most common Fossil in the Burgess Shale

2/20/2018 WHY?

(higher energy, larger animals possible)
2/20/2018 Ecological arms race? Increase in oxygen? (higher energy, larger animals possible)

2/20/2018 What?

Evolution of Animal Body Plans
2/20/2018 Evolution of Animal Body Plans True Tissues Tissue Layers (Diplo vs Triploblasts) Body Symmetry Evolution of body cavity (Coelom) Evolution of Development

2/20/2018 Cambrian Explosion

Of course, evolution continued after the Cambrian Explosion
2/20/2018 Of course, evolution continued after the Cambrian Explosion But major body plans evolved within a short period of time

How could this happen? (genetic mechanism?) NEXT LECTURE:
2/20/2018 How could this happen? (genetic mechanism?) NEXT LECTURE:

Cambrian Explosion --> Origins of Animals: I will discuss the genetic mechanisms of this Adaptive Radiation in the lecture on Animal Diversity 2/20/2018

2/20/2018 ERA: Paleozoic “Age of Invertebrates”

The Colonization of Land
Billions of years ago 4 3 2 1 The Colonization of Land Fungi, plants, and animals began to colonize land about 500 million years ago Plants and fungi likely colonized land together by 420 million years ago Arthropods (insects) and tetrapods are the most widespread and diverse land animals Tetrapods evolved from lobe-finned fishes around 365 million years ago

Permian Extinction (2) Paleozoic-Mesozoic Boundary (230 MYA)
2/20/2018 (2) Paleozoic-Mesozoic Boundary (230 MYA) Permian Extinction Radiations: Reptiles (dinosaurs) Mammals, Birds (which are dinosaurs) appear Extinctions: ~96% of species (esp. marine) All trilobites

2/20/2018 ERA: Mesozoic “Age of Reptiles”

Figure 18.5b The Phanerozoic eon
(b) The Mesozoic, sometimes nicknamed the age of reptiles, begins after the end-Permian extinction event and ends with the extinction of the dinosaurs and other groups at the Cretaceous-Tertiary boundary. Each hash mark on the time bar represents about 7.5 million years.

(3) Mesozoic-Cenozoic (KT) Boundary (65 MYA)
2/20/2018 (3) Mesozoic-Cenozoic (KT) Boundary (65 MYA) Cretaceous Extinction

Cretaceous Extinction (KT Boundary, 65 million years ago)
Caused by asteroid impact, with dust, ash, soot blocking sun, causing rapid global cooling 60-80% of species living at the time went extinct: dinosaurs (except for birds), pterosaurs, marine reptiles Mammals, crocodilians, amphibians, turtles unharmed NORTH AMERICA Chicxulub crater Yucatán Peninsula Figure Trauma for Earth and its Cretaceous life For the Discovery Video Mass Extinctions, go to Animation and Video Files.

End of Mesozoic Radiations: Mammals, Birds Extinctions:
2/20/2018 End of Mesozoic Radiations: Mammals, Birds Flowering plants appear pollinating insects Extinctions: End of Dinosaurs (except for birds) < 50% Marine species

2/20/2018 ERA: Cenozoic Age of Mammals

Figure 18.5c The Phanerozoic eon
(c) The Cenozoic is divided into the Tertiary and Quaternary periods. The Tertiary includes the Paleocene, Eocene, Oligocene, Miocene, and Pliocene epochs. The Quaternary includes the Pleistocene and Holocene epochs. The Cenozoic is sometimes nicknamed the age of mammals. Each hash mark on the time bar represents about 2.8 million years.

Extinctions and Radiations
2/20/2018 Extinctions and Radiations

Causes of Extinctions? Environmental change Global Warming or Cooling:
2/20/2018 Causes of Extinctions? Environmental change Global Warming or Cooling: Examples: Permian Extinction: global warming Cretaceous Extinction: global cooling

The “Big Five” Extinctions
2/20/2018 The “Big Five” Extinctions End Ordovician (~ 440 mya) Late Devonian (~365 mya) End Permian (~ 250 mya) End Triassic (~215 mya) End Cretaceous (~ 65 MYA) Did extinctions also accompany the Cambrian Explosion? Don’t know, prior species were soft and did not preserve

The “Big Five” Extinctions
2/20/2018 The “Big Five” Extinctions Palaeontologists characterize mass extinctions as times when the Earth loses more than 3/4 of its species in a geologically short interval (~2 million years or less). This has happened five times in the past ~540 million years. End Ordovician (~ 440 mya) Late Devonian (~365 mya) End Permian (~ 250 mya) End Triassic (~215 mya) End Cretaceous (~ 65 MYA)

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The ‘Big Five’ mass extinction events
The Ordovician event ended ~443 Myr ago; within 3.3 to 1.9 Myr 57% of genera were lost, an estimated 86% of species. Onset of alternating glacial and interglacial episodes; repeated marine transgressions and regressions. Uplift and weathering of the Appalachians affecting atmospheric and ocean chemistry. Sequestration of CO2. The Devonian event ended ~359 Myr ago; within 29 to 2 Myr 35% of genera were lost, an estimated 75% of species. Global cooling (followed by global warming), possibly tied to the diversification of land plants, with associated weathering, paedogenesis, and the drawdown of global CO2. Evidence for widespread deep-water anoxia and the spread of anoxic waters by transgressions. The Permian event ended ~251 Myr ago; within 2.8 Myr to 160 Kyr 56% of genera were lost, an estimated 96% of species. Siberian volcanism. Global warming. Spread of deep marine anoxic waters. Elevated H2S and CO2 concentrations in both marine and terrestrial realms. Ocean acidification. The Triassic event ended ~200 Myr ago; within 8.3 Myr to 600 Kyr 47% of genera were lost, an estimated 80% of species. Activity in the Central Atlantic Magmatic Province (CAMP) thought to have elevated atmospheric CO2 levels, which increased global temperatures and led to a calcification crisis in the world oceans. The Cretaceous event ended ~65 Myr ago; within 2.5 Myr to less than a year 40% of genera were lost, an estimated 76% of species. A bolide impact in the Yucatán is thought to have led to a global cataclysm and caused rapid cooling. Preceding the impact, biota may have been declining owing to a variety of causes: Deccan volcanism contemporaneous with global warming; tectonic uplift altering biogeography and accelerating erosion, potentially contributing to ocean eutrophication and anoxic episodes. CO2 spike just before extinction, drop during extinction.

Background vs Mass Extinction
2/20/2018 Background vs Mass Extinction Mass Extinctions: Only 4% Mass Extinctions kill off a very large % of the species on the planet at a given time, but because they are short in duration, they comprise a small % of animals that ever lived on the planet Background Extinctions: 96% Extinctions are always happening in the background, and over a long long period of time, these extinctions add up to a lot of species extinctions 99% of species that have lived are extinct

Background vs Mass Extinction
2/20/2018 Background vs Mass Extinction Mass Extinctions: Only 4% Even though Mass Extinctions are eliminating ~75+% species at a given time, the total # of species killed off by Mass Extinctions are small (only 4%) because background extinctions add up to a lot of species over a long period of time Mass Extinctions are nevertheless massively disruptive to an ecosystem, given the large number of species that are removed suddenly

2/20/2018 Sixth Mass Extinction Current Extinction Rate: x background rate 1/3 US plants, animals endangered (many have already gone extinct)

6th Mass Extinction Current extinctions:
2/20/2018 6th Mass Extinction Current extinctions: Overly successful fitness of human populations (outcompeting all other species) Habitat destruction (agriculture, construction, etc) Invasive species Spreading of pathogens Killing species directly Global Climate Change

Human Population Explosion
2/20/2018 Human Population Explosion WATCH Human Population Growth: The advent of Agriculture ~10,000 yrs ago led to human population explosion

2/20/2018 Global Warming

6th Mass Extinction? So, is a Mass Extinction currently underway?
If so, how does it compare to previous Mass Extinctions?

Estimating rate and magnitude of current extinctions
Rate: number of extinctions divided by the time over which the extinctions occurred. One can also derive from this a proportional rate—the fraction of species that have gone extinct per unit time. Magnitude: percentage of species that have gone extinct. Mass Extinction: when extinction rates accelerate relative to origination rates such that over 75% of species disappear within a geologically short interval—typically less than 2 million years, in some cases much less.

Assessing Mass Extinction
To document where the current extinction episode lies on the mass extinction scale requires us to know both: (1) Whether current extinction rates are above background rates (and if so, how far above) (2) How closely historic and projected biodiversity losses approach 75% of the Earth’s species.

Assessing Mass Extinction
Rates of current species extinctions are compared to background extinction rates estimated from the fossil record

Problems with assessment:
Many existing clades are undersampled or unevenly sampled Species for which we have fossil data (marine gastropods, etc) tend to differ from those for which we have best modern data (terrestrial animals)

Data on the Current Mass Extinction
Studies estimated current rates of extinction to be orders of magnitude higher than the background rate Barnosky et al. 2011http://

Extinction rate past present
2/20/2018 Extinction rate past present Each small grey datum point represents the E/MSY (extinction per million species-years) calculated from taxon durations recorded in the Paleobiology Database30 (million-year-or-more time bins) or from lists of extant, recently extinct, and Pleistocene species compiled from the literature (100,000-year-and-less time bins)6, 32, 33, 89, 90, 91, 92, 93, 94, 95, 96, 97. More than 4,600 data points are plotted and cluster on top of each other. Yellow shading encompasses the ‘normal’ (non-anthropogenic) range of variance in extinction rate that would be expected given different measurement intervals; for more than 100,000 years, it is the same as the 95% confidence interval, but the fading to the right indicates that the upper boundary of ‘normal’ variance becomes uncertain at short time intervals. The short horizontal lines indicate the empirically determined mean E/MSY for each time bin. Large coloured dots represent the calculated extinction rates since Red, the end-Pleistocene extinction event. Orange, documented historical extinctions averaged (from right to left) over the last 1, 30, 50, 70, 100, 500, 1,000 and 5,000 years. Blue, attempts to enhance comparability of modern with fossil data by adjusting for extinctions of species with very low fossilization potential (such as those with very small geographic ranges and bats). For these calculations, ‘extinct’ and ‘extinct in the wild’ species that had geographic ranges less than 500 km2 as recorded by the IUCN6, all species restricted to islands of less than 105 km2, and bats were excluded from the counts (under-representation of bats as fossils is indicated by their composing only about 2.5% of the fossil species count, versus around 20% of the modern species count30). Brown triangles represent the projections of rates that would result if ‘threatened’ mammals go extinct within 100, 500 or 1,000 years. The lowest triangle (of each vertical set) indicates the rate if only ‘critically endangered’ species were to go extinct (CR), the middle triangle indicates the rate if ‘critically endangered’ + ‘endangered’ species were to go extinct (EN), and the highest triangle indicates the rate if ‘critically endangered’ + ‘endangered’ + ‘vulnerable’ species were to go extinct (VU). To produce Fig. 1 we first determined the last-occurrence records of Cenozoic mammals from the Paleobiology Database30, and the last occurrences of Pleistocene and Holocene mammals from refs 6, 32, 33 and 89–97. We then used R-scripts (written by N.M.) to compute total diversity, number of extinctions, proportional extinction, and E/MSY (and its mean) for time-bins of varying duration. Cenozoic time bins ranged from 25 million to a million years. Pleistocene time bins ranged from 100,000 to 5,000 years, and Holocene time bins from 5,000 years to a year. For Cenozoic data, the mean E/MSY was computed using the average within-bin standing diversity, which was calculated by counting all taxa that cross each 100,000-year boundary within a million-year bin, then averaging those boundary-crossing counts to compute standing diversity for the entire million-year-and-over bin. For modern data, the mean was computed using the total standing diversity in each bin (extinct plus surviving taxa). This method may overestimate the fossil mean extinction rate and underestimate the modern means, so it is a conservative comparison in terms of assessing whether modern means are higher. The Cenozoic data are for North America and the Pleistocene and Holocene data are for global extinction; adequate global Cenozoic data are unavailable. There is no apparent reason to suspect that the North American average would differ from the global average at the million-year timescale. Based on data for mammals: The maximum observed rates of extinction since a thousand years ago (E/MSY ≈ 24 in 1,000-year bins to E/MSY ≈ 693 in 1-year bins) are clearly far above the average fossil rate (about E/MSY ≈ 1.8)

2/20/2018 Extinction Rates Current extinction rates for mammals, amphibians, birds, and reptiles (light yellow dots on the left), if calculated over the last 500 years (a conservatively slow rate) Vertical lines on the right illustrate the range of mass extinction rates (E/MSY) that would produce the Big Five extinction magnitudes, as bracketed by the best available data from the geological record. The correspondingly coloured dots indicate what the extinction rate would have been if the extinctions had happened (hypothetically) over only 500 years. On the left, dots connected by lines indicate the rate as computed for the past 500 years for vertebrates: light yellow, species already extinct; dark yellow, hypothetical extinction of ‘critically endangered’ species; orange, hypothetical extinction of all ‘threatened’ species. TH: if all ‘threatened’ species became extinct in 100 years, and that rate of extinction remained constant, the time to 75% species loss—that is, the sixth mass extinction—would be ~240 to 540 years for those vertebrates shown here that have been fully assessed (all but reptiles). CR: similarly, if all ‘critically endangered’ species became extinct in 100 years, the time to 75% species loss would be ~890 to 2,270 years for these fully assessed terrestrial vertebrates. ….are faster than (birds, mammals, amphibians) or as fast as (reptiles) all rates that would have produced the Big Five extinctions over hundreds of thousands or millions of years

The current extinction has just started
The current extinction has just started. So, how many more years it would take for current extinction rates to produce species losses equivalent to Big Five magnitudes? If all ‘threatened’ species became extinct within a century, and that rate then continued unabated, terrestrial amphibian, bird and mammal extinction would reach Big Five magnitudes in ~240 to 540 years (241.7 years for amphibians, 536.6 years for birds, 334.4 years for mammals). If extinction were limited to ‘critically endangered’ species over the next century and those extinction rates continued, the time until 75% of species were lost per group would be 890 years for amphibians, 2,265 years for birds and 1,519 years for mammals. For scenarios that project extinction of ‘threatened’ or ‘critically endangered’ species over 500 years instead of a century, mass extinction magnitudes would be reached in about 1,200 to 2,690 years for the ‘threatened’ scenario (1,209 years for amphibians, 2,683 years for birds and 1,672 years for mammals) or ~4,450 to 11,330 years for the ‘critically endangered’ scenario (4,452 years for amphibians, 11,326 years for birds and 7,593 years for mammals). This emphasizes that current extinction rates are higher than those that caused Big Five extinctions in geological time; they could be severe enough to carry extinction magnitudes to the Big Five benchmark in as little as three centuries.

Are modern extinctions different from those in the past?
2/20/2018 Are modern extinctions different from those in the past?

Past vs Modern Extinctions
2/20/2018 Past vs Modern Extinctions Past extinctions: Over millions of years (though KT meteor impact was quick) Lead to adaptation radiation of new species Current extinctions: Over decades/centuries (much faster than the Big Five) No radiation of larger-bodied species Habitat is occupied by humans rather than by new species Species recover and radiate when the extinction dissipates: currently no end of extinction in sight Article by Paleontologist Niles Eldredge

Modern Extinction Adaptive Radiations of : Disease organisms (HIV)
2/20/2018 Modern Extinction Adaptive Radiations of : Disease organisms (HIV) Human commensals (lice) Invasive Species (adapted to unstable environments) Genetically-Modified Organisms?

Synthetic Life Humans can now create synthetic life, by constructing a genome on the computer, synthesizing the DNA and injecting the genetic code into a cell

Summary (1) Geological Time Scale
2/20/2018 Summary (1) Geological Time Scale (2) Major Episodes in the History of Life (3) Extinctions and Radiations

Concepts Geological Time Scale Four Eras Paleontology Fossil
2/20/2018 Concepts Geological Time Scale Four Eras Paleontology Fossil Sedimentary Rock Radiometric Dating Molecular Clock Cambrian Explosion Extinction Adaptive Radiation

Study Question: Put the following Key Events in order:
2/20/2018 Study Question: Put the following Key Events in order: (1) The Appearance of Dinosaurs (2) The Oxygenation of the Atmosphere (3) The Appearance of Bacteria (4) The Appearance of Plants (5) The Invasion of Land from the Sea (6) The Appearance of Eurkaryotes (you don’t need to memorize the nitty gritty details on the history of life, but I want you to develop a general sense of time scale of the major events in evolutionary history- in Table 25.1 and in this lecture)

(A) Not much, some tiny round objects (B) Lots of plant species
2/20/2018 1. You are a geologist, and while digging through a rock formation, you have come across a layer of fossils characterized by animals with lots of hard parts, segments, and diverse body shapes. There are a lot of trilobites, and also some very strange-looking animals (alien-like, with multiple eyes, spines, claws, jaws, etc.). As you keep on digging below this layer, what are you likely to find? (A) Not much, some tiny round objects (B) Lots of plant species (C) Dinosaurs, birds, early mammals (D) More and more complex and specialized species

2. Choose the correct sequence of events in the History of Life.
2/20/2018 2. Choose the correct sequence of events in the History of Life. (A) Origin of Life, oxygen in atmosphere, bacteria, eukarya, origin of animals, dinosaurs, mammals. (B) Origin of Life, oxygen in atmosphere, eukarya, origin of invertebrates, origin of vertebrates, dinosaurs, mammals (C) Origin of Life, eukarya, oxygen in atmosphere, origin of invertebrates, origin of vertebrates, dinosaurs, mammals (D) Origin of Life, oxygen in atmosphere, eukarya, origin of vertebrates, dinosaurs, Cambrian Explosion, mammals

2/20/2018 3. Which of the following is FALSE regarding extinctions and radiations? (A) The major eras in the geological time scale is marked by extinctions and radiations (B) Extinctions are of a major concern today because species extinctions are not being accompanied by major radiations, as the habitats where extinctions have occurred have been removed or are occupied by humans (C) Genetic drift and inbreeding can increase the chances that a population will go extinct (D) Adaptive Radiations often occur after extinctions because of available niches, or when a group colonizes a novel niche (habitat). (E) The Big Five Mass Extinctions are responsible for more than 90% of all species extinctions.

4. Choose the CORRECT sequence of events in the History of Life, based on the fossil record. (a) Origin of life, oxygen in atmosphere, origin of eukaryotes, appearance of stromatolites, origin of animals, origin of dinosaurs, origin of mammals, appearance of Australopithecines, Cretaceous extinction (b) Oxygen in the atmosphere, origin of bacteria, origin of eukarya, multicellularity, origin of animals, the invasion of land, Cretaceous extinction, origin of mammals (c) Origin of life, oxygen in the atmosphere, origin of eukaryotes, origin of animals, the invasion of land, origin of reptiles, appearance of mammals, extinction of dinosaurs (except for birds) (d) Origin of bacteria, oxygen in atmosphere, origin of eukaryotes, the invasion of land, evolution of hox genes and radiation of animal body plans, origin of dinosaurs, origin of mammals, appearance of Australopithecines (e) Oxygen in the atmosphere, origin of eukaryotes, evolution of multicellularity, origin of dinosaurs, Permian extinction, origin of mammals, Cretaceous extinction, origin of birds

2/20/2018 5. Which of the following is TRUE regarding events of the Cambrian Explosion? (a) According to genetic data, radically new animal body plans appeared suddenly and within a short time span (within 50 million years), in contrast to fossil data, which suggest a longer radiation (b) There is clear fossil evidence that a mass extinction of soft bodied organisms preceding the Cambrian Explosion (c) Only a few animal phyla appeared at this time, such as the arthropods (trilobites) and molluscs (d) The Cambrian Explosion is characterized by the radiation of radically different animal body plans that we classify into different animal phyla (e) At this time, there was sudden warming of the planet and extinction of 60-80% of species, allowing the adaptive radiation of diverse animal phyla

2/20/2018 6. Which of the following is most TRUE regarding the current 6th Mass Extinction? (a) The 6th mass extinction is likely to be followed by adaptive radiations of large bodied organisms and many predators (b) Studies estimate that current rates of extinction are orders of magnitude higher than the background rate of extinctions (c) The current 6th mass extinction will result in a much greater number of species going extinct than the total number of species that have gone extinct from background extinctions throughout earth history (d) Based on fossil data of vertebrates from the previous Big Five mass extinctions, the current rate of extinction is occurring much more slowly than previous mass extinctions (e) The current mass extinction is unique, as previous extinctions did not coincide with global climate change

Answers 1A 2B 3E 4C 5D 6B

Questions What are some of the key biological revolutions that occurred during the history of life on earth, and how did they come about? Why is it hypothesized that early life on earth was in the form of RNA? How did the Oxygen Revolution come about? What are the implications of a high oxygen atmosphere for organismal physiology? How were Eukaryotes created? What are animals? About when did animals evolve? Is there congruence between fossil estimates versus molecular clock estimates of the timing? How did animals diversify (Cambrian Explosion)? Where did life evolve (land, sea)? About when did organisms begin to live on land? What are some challenges of living on land (relative to the sea)?

Which of the following is MOST likely to be true regarding evolutionary relationships among the major domains of life? (A) Bacteria and Archaea are both grouped into the category of “Prokaryotes” because they are more closely related to each other than to Eukaryotes (B) Archaea are ancestral to all other forms of Life (C) The Oxygen Revolution defines the emergence of life on Earth (D) Eukaryotes arose from a symbiotic relationship among prokaryotes (E) Eukaryotes evolved from Prokaryotes through Horizontal Gene Transfer

2. Which of the following is Least likely to be true regarding Prokaryotic Metabolism and the Oxygen Revolution? The oxygen revolution led to the proliferation of diverse types of prokaryotic metabolism (B) The oxygen revolution enabled the preponderance of more efficient metabolism that could produce more ATP per unit glucose (C) The oxygen revolution altered the atmosphere of the Earth (D) The oxygen revolution created an inhospitable habitat for many classes of prokaryotes that use molecules other than oxygen as their terminal electronic acceptor for energy production (E) The oxygen revolution was caused as a byproduct of photosynthetic activity of cyanobacteria

3. Which of the following does NOT make RNA a good candidate for early life on earth? (a) RNA could act as an enzyme (b) RNA could serve as the genetic code (c) RNA is much more stable than DNA in our current atmosphere (d) RNA can catalyze chemical reactions that break or synthesize phosphodiester bonds in RNA or DNA (e) Recent studies suggest that RNA is capable of self replication

4. Which is the following is NOT a consequence of the Oxygen Revolution? (a) The ability of organisms to metabolically produce more ATP by using oxygen as the terminal electron acceptor during respiration (b) Eukaryotes, which evolved after the Oxygen Revolution, all use aerobic metabolism (c) The transformation of the earth's atmosphere ~2.5 billion years ago from one that was chemically reducing to one that is oxidizing (d) The heightened risk of DNA and cellular damage in organisms through oxygen free radicals (e) The proliferation of bacteria that use oxygen as the terminal electron acceptor during respiration, such that nearly all bacterial species are aerobic

Answers 1D 2A 3C 4E

RNA World RNA can both serve as the genetic code and also perform enzymatic functions (ribozymes) But, can RNA self replicate? If so, it would have all components to be considered “life” Laboratory experiments indicate that RNA can self replication

Figure 17.2a The ribozyme from Tetrahymena thermophila
(a) The primary nucleotide sequence, which is the genotype of this catalytic RNA. This RNA is an intron (an intervening sequence between two genes) that separates two regions of the Tetrahymena genome that code for ribosomal RNA (rRNA) genes. Tom Cech and colleagues found that this sequence has the catalytic capability to splice itself out from between the two adjacent rRNAs after they have been transcribed (Kruger et al. 1982). The sequence shown here is a 413-nucleotide version, shortened from the naturally occurring form by the use of a restriction enzyme. A secondary structure of this molecule is formed when nucleotides base pair with each other as the molecule folds back upon itself during transcription from DNA. Note that in RNA, uridine (U) replaces thymidine (T), and that three types of base pairs are common: A-U, G-U, and G-C. The secondary structure shown here is drawn such that no RNA strands cross each other and, as such, does not accurately reflect how the molecule folds further into a tertiary (three-dimensional) structure.

Figure 17.2b The ribozyme from Tetrahymena thermophila
(b) A cartoon of the catalysis performed by the Tetrahymena ribozyme in vitro, which is its phenotype. A short oligonucleotide substrate (orange) binds to the 5' end of the ribozyme (red) through complementary base pairing (green ticks). In the presence of a divalent cation, such as Mg2+, the ribozyme catalyzes the breakage of a phosphoester bond in the substrate and the ligation of the 3' fragment to its own 3' end. This "pick-up-the-tail" event can be used to discriminate catalytically active mutant sequences from less active or inactive mutants during in vitro evolution experiments (see Figure 17.4).

Figure 17.6 Test-tube selection scheme for identifying ribozymes that can synthesize RNA
See text for explanation. After Bartel and Szostak (1993).

Figure 17.8a A ribozyme that can catalyze template-based RNA synthesis.
(a) Shows a schematic diagram of a ribozyme evolved in the lab by Wendy Johnston and colleagues (2001). The RNA of which the ribozyme is made is represented by green, black, magenta, and blue lines. The RNA sequence shown in red is the template that the researchers challenged their ribozyme to copy. The sequence in orange is a primer, complementary to the beginning of the template, which gives the ribozyme a place to start. The primer is also radioactively labeled (asterisk), which allowed the researchers to detect it, and any longer strands built from it, in an electrophoresis gel. (b) Shows the full sequence of the template. The nucleotides that extend beyond the primer are numbered. (c) Shows an electrophoresis gel revealing the products that the ribozyme had made after various lengths of time. By the end of 24 hours, the ribozyme had made complete copies of the template, 14 base pairs longer than the primer. From Johnston et al. (2001).

Figure 18.5a The Phanerozoic eon
The diagrams show a selection of events from the three eras that make up the Phanerozoic. The labels indicate the first appearances of life forms discussed in this and other chapters, the names of periods or epochs within the era, absolute ages assigned by radioactive dating, notes on prominent plant communities, and the climate and important geological events. The maps show the estimated positions of major landmasses. (a) The Paleozoic begins with the radiation of animals and ends with a mass extinction at the end of the Permian. Each hash mark on the time bar represents about 12 million years.

History of Life On Earth

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